From 970a50e2052003387cac8fa4a91cb09fb4784c52 Mon Sep 17 00:00:00 2001 From: Brayan Almonte Date: Thu, 3 Oct 2024 16:39:10 -0400 Subject: [PATCH 01/27] fix(shared-data): adjust the gripper pickup parameters for the plate reader lid. (#16415) --- .../1.json | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/shared-data/labware/definitions/2/opentrons_flex_lid_absorbance_plate_reader_module/1.json b/shared-data/labware/definitions/2/opentrons_flex_lid_absorbance_plate_reader_module/1.json index 82b5a1f54d8..a477991f629 100644 --- a/shared-data/labware/definitions/2/opentrons_flex_lid_absorbance_plate_reader_module/1.json +++ b/shared-data/labware/definitions/2/opentrons_flex_lid_absorbance_plate_reader_module/1.json @@ -33,8 +33,8 @@ "version": 1, "schemaVersion": 2, "allowedRoles": ["fixture"], - "gripForce": 20.0, - "gripHeightFromLabwareBottom": 53.0, + "gripForce": 21.0, + "gripHeightFromLabwareBottom": 48.0, "cornerOffsetFromSlot": { "x": 0, "y": 0, @@ -43,12 +43,12 @@ "gripperOffsets": { "default": { "pickUpOffset": { - "x": 14, + "x": 9, "y": 0, "z": 0 }, "dropOffset": { - "x": 14, + "x": 9, "y": 0, "z": 0 } From 3b680dc9147e4b8b072c2f302ef8150765c9f35a Mon Sep 17 00:00:00 2001 From: Jamey Huffnagle Date: Thu, 3 Oct 2024 17:38:54 -0400 Subject: [PATCH 02/27] =?UTF-8?q?fix(components,=20app):=20Fix=20newly=20m?= =?UTF-8?q?igrated=20`atoms`=C2=A0to=20`components`=20on=20the=20ODD=20(#1?= =?UTF-8?q?6412)?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- app/src/molecules/OddModal/OddModalHeader.tsx | 2 +- .../ErrorRecoveryFlows/RecoverySplash.tsx | 38 +------ components/src/atoms/buttons/LargeButton.tsx | 107 ++++++++++-------- 3 files changed, 67 insertions(+), 80 deletions(-) diff --git a/app/src/molecules/OddModal/OddModalHeader.tsx b/app/src/molecules/OddModal/OddModalHeader.tsx index 5544a14ecbc..5f2a403a8af 100644 --- a/app/src/molecules/OddModal/OddModalHeader.tsx +++ b/app/src/molecules/OddModal/OddModalHeader.tsx @@ -34,7 +34,7 @@ export function OddModalHeader(props: OddModalHeaderBaseProps): JSX.Element { borderRadius={`${BORDERS.borderRadius12} ${BORDERS.borderRadius12} 0px 0px`} {...styleProps} > - + {iconName != null && iconColor != null ? ( @@ -297,30 +295,6 @@ const SHARED_BUTTON_STYLE_ODD = css` width: 29rem; height: 13.5rem; ` -const BTN_STYLE_DISABLED_ODD = css` - ${SHARED_BUTTON_STYLE_ODD} - - background-color: ${COLORS.grey35}; - color: ${COLORS.grey50}; - border: none; - box-shadow: none; - - #btn-icon: { - color: ${COLORS.grey50}; - } - - &:active, - &:focus, - &:hover { - background-color: ${COLORS.grey35}; - color: ${COLORS.grey50}; - } - &:active, - &:focus, - &:hover #btn-icon { - color: ${COLORS.grey50}; - } -` const PRIMARY_BTN_STYLES_DESKTOP = css` background-color: ${COLORS.red50}; diff --git a/components/src/atoms/buttons/LargeButton.tsx b/components/src/atoms/buttons/LargeButton.tsx index 28beb378495..28f3f555373 100644 --- a/components/src/atoms/buttons/LargeButton.tsx +++ b/components/src/atoms/buttons/LargeButton.tsx @@ -1,11 +1,10 @@ import type * as React from 'react' import { css } from 'styled-components' -import { Box, Btn } from '../../primitives' +import { Btn } from '../../primitives' import { BORDERS, COLORS } from '../../helix-design-system' import { RESPONSIVENESS, SPACING, TYPOGRAPHY } from '../../ui-style-constants' -import { LegacyStyledText } from '../../atoms/StyledText' -import { fontSizeBodyLargeSemiBold } from '../../helix-design-system/product/typography' +import { StyledText } from '../StyledText' import { ALIGN_CENTER, ALIGN_FLEX_START, @@ -49,6 +48,8 @@ export function LargeButton(props: LargeButtonProps): JSX.Element { ...buttonProps } = props + const computedDisabled = disabled || ariaDisabled + const LARGE_BUTTON_PROPS_BY_TYPE: Record< LargeButtonTypes, { @@ -155,6 +156,26 @@ export function LargeButton(props: LargeButtonProps): JSX.Element { ? `color: ${LARGE_BUTTON_PROPS_BY_TYPE[style].activeIconColor}` : '' + // In order to keep button sizes consistent and expected, all large button types need an outline. + // The outline color is always the same as the background color unless the background color is uniquely different + // from the outline. + const computedBorderStyle = (): string => { + const borderColor = (): string => { + if (computedDisabled) { + return LARGE_BUTTON_PROPS_BY_TYPE[buttonType].disabledColor + } else if (buttonType === 'alertStroke') { + return LARGE_BUTTON_PROPS_BY_TYPE[buttonType].defaultColor + } else { + return LARGE_BUTTON_PROPS_BY_TYPE[buttonType].defaultBackgroundColor + } + } + + const calculatedBorderRadius = + buttonType === 'stroke' ? BORDERS.borderRadius2 : BORDERS.borderRadius4 + + return `${calculatedBorderRadius} solid ${borderColor()}` + } + const LARGE_BUTTON_STYLE = css` color: ${LARGE_BUTTON_PROPS_BY_TYPE[buttonType].defaultColor}; background-color: ${ @@ -162,10 +183,10 @@ export function LargeButton(props: LargeButtonProps): JSX.Element { }; cursor: ${CURSOR_POINTER}; padding: ${SPACING.spacing16} ${SPACING.spacing24}; - text-align: ${TYPOGRAPHY.textAlignCenter}; + text-align: ${TYPOGRAPHY.textAlignLeft}; border-radius: ${BORDERS.borderRadiusFull}; align-items: ${ALIGN_CENTER}; - border: ${buttonType === 'stroke' ? `2px solid ${COLORS.blue50}` : 'none'}; + border: ${computedBorderStyle()}; &:active { background-color: ${ @@ -184,7 +205,9 @@ export function LargeButton(props: LargeButtonProps): JSX.Element { }; border: ${ - buttonType === 'stroke' ? `2px solid ${COLORS.blue55}` : 'none' + buttonType === 'stroke' + ? `2px solid ${COLORS.blue55}` + : `${computedBorderStyle()}` }; } @@ -215,33 +238,17 @@ export function LargeButton(props: LargeButtonProps): JSX.Element { padding: ${SPACING.spacing24}; line-height: ${TYPOGRAPHY.lineHeight20}; gap: ${SPACING.spacing60}; - outline: ${BORDERS.borderRadius4} solid - ${ - buttonType === 'alertStroke' && !disabled - ? LARGE_BUTTON_PROPS_BY_TYPE[buttonType].defaultColor - : 'none' - }; - - ${TYPOGRAPHY.pSemiBold} - - #btn-icon: { - color: ${ - disabled - ? LARGE_BUTTON_PROPS_BY_TYPE[buttonType].disabledIconColor - : LARGE_BUTTON_PROPS_BY_TYPE[buttonType].iconColor - }; - } &:active { background-color: ${ - disabled + computedDisabled ? LARGE_BUTTON_PROPS_BY_TYPE[buttonType].disabledBackgroundColor : LARGE_BUTTON_PROPS_BY_TYPE[buttonType].activeBackgroundColor }; - ${!disabled && activeColorFor(buttonType)}; + ${!computedDisabled && activeColorFor(buttonType)}; outline: ${BORDERS.borderRadius4} solid ${ - disabled + computedDisabled ? LARGE_BUTTON_PROPS_BY_TYPE[buttonType].disabledBackgroundColor : LARGE_BUTTON_PROPS_BY_TYPE[buttonType].activeBackgroundColor }; @@ -252,15 +259,15 @@ export function LargeButton(props: LargeButtonProps): JSX.Element { &:focus-visible { background-color: ${ - disabled + computedDisabled ? LARGE_BUTTON_PROPS_BY_TYPE[buttonType].disabledBackgroundColor : LARGE_BUTTON_PROPS_BY_TYPE[buttonType].focusVisibleBackgroundColor }; - ${!disabled && activeColorFor(buttonType)}; + ${!computedDisabled && activeColorFor(buttonType)}; padding: calc(${SPACING.spacing24} + ${SPACING.spacing2}); - border: ${SPACING.spacing2} solid ${COLORS.transparent}; + border: ${computedBorderStyle()}; outline: ${ - disabled + computedDisabled ? 'none' : `3px solid ${LARGE_BUTTON_PROPS_BY_TYPE[buttonType].focusVisibleOutlineColor}` @@ -276,6 +283,11 @@ export function LargeButton(props: LargeButtonProps): JSX.Element { }; } ` + + const appliedIconColor = computedDisabled + ? LARGE_BUTTON_PROPS_BY_TYPE[buttonType].disabledIconColor + : LARGE_BUTTON_PROPS_BY_TYPE[buttonType].iconColor + return ( - {buttonText} - + {iconName ? ( - - - + ) : null} ) } + +const ICON_STYLE = css` + width: 1.5rem; + height: 1.5rem; + @media ${RESPONSIVENESS.touchscreenMediaQuerySpecs} { + width: 5rem; + height: 5rem; + } +` From 66cfff9ac2173193939da288a01f9674dfb4a79b Mon Sep 17 00:00:00 2001 From: Jamey Huffnagle Date: Fri, 4 Oct 2024 09:11:25 -0400 Subject: [PATCH 03/27] feat(robot-server): Add `GET` `runs/:runId/currentState` (#16402) Works toward RSQ-161 To support partial tip during error recovery during certain flows, the server must expose details about the current pipetting tip layout for the current run. NozzleMap contains details the client is interested in, but we really shouldn't return the entirety of NozzleMap, since it is A) quite large and B) contains a lot of info irrelevant from a client perspective. To that end, we return an ActiveNozzleLayout derived from the NozzleMap for the pipette of interest. This commit returns nozzle data on a new endpoint, /runs/:runId/currentState. --- .../opentrons/protocol_engine/state/tips.py | 4 + .../protocol_runner/run_orchestrator.py | 5 + .../robot_server/runs/router/base_router.py | 84 +++++++++++++- .../robot_server/runs/run_data_manager.py | 12 +- robot-server/robot_server/runs/run_models.py | 42 ++++++- .../runs/run_orchestrator_store.py | 7 +- .../tests/runs/router/test_base_router.py | 105 +++++++++++++++++- .../tests/runs/test_run_data_manager.py | 46 +++++++- 8 files changed, 296 insertions(+), 9 deletions(-) diff --git a/api/src/opentrons/protocol_engine/state/tips.py b/api/src/opentrons/protocol_engine/state/tips.py index a2c75ba2af4..7b50b291f4d 100644 --- a/api/src/opentrons/protocol_engine/state/tips.py +++ b/api/src/opentrons/protocol_engine/state/tips.py @@ -486,6 +486,10 @@ def get_pipette_nozzle_map(self, pipette_id: str) -> NozzleMap: """Get the current nozzle map the given pipette's configuration.""" return self._state.nozzle_map_by_pipette_id[pipette_id] + def get_pipette_nozzle_maps(self) -> Dict[str, NozzleMap]: + """Get current nozzle maps keyed by pipette id.""" + return self._state.nozzle_map_by_pipette_id + def has_clean_tip(self, labware_id: str, well_name: str) -> bool: """Get whether a well in a labware has a clean tip. diff --git a/api/src/opentrons/protocol_runner/run_orchestrator.py b/api/src/opentrons/protocol_runner/run_orchestrator.py index 9bb5c330788..697e4a14e3a 100644 --- a/api/src/opentrons/protocol_runner/run_orchestrator.py +++ b/api/src/opentrons/protocol_runner/run_orchestrator.py @@ -14,6 +14,7 @@ from . import protocol_runner, RunResult, JsonRunner, PythonAndLegacyRunner from ..hardware_control import HardwareControlAPI from ..hardware_control.modules import AbstractModule as HardwareModuleAPI +from ..hardware_control.nozzle_manager import NozzleMap from ..protocol_engine import ( ProtocolEngine, CommandCreate, @@ -397,6 +398,10 @@ def get_deck_type(self) -> DeckType: """Get engine deck type.""" return self._protocol_engine.state_view.config.deck_type + def get_nozzle_maps(self) -> Dict[str, NozzleMap]: + """Get current nozzle maps keyed by pipette id.""" + return self._protocol_engine.state_view.tips.get_pipette_nozzle_maps() + def set_error_recovery_policy(self, policy: ErrorRecoveryPolicy) -> None: """Create error recovery policy for the run.""" self._protocol_engine.set_error_recovery_policy(policy) diff --git a/robot-server/robot_server/runs/router/base_router.py b/robot-server/robot_server/runs/router/base_router.py index 429097c24ab..3b0e7040e02 100644 --- a/robot-server/robot_server/runs/router/base_router.py +++ b/robot-server/robot_server/runs/router/base_router.py @@ -37,6 +37,7 @@ MultiBodyMeta, ResourceLink, PydanticResponse, + Body, ) from robot_server.protocols.dependencies import get_protocol_store @@ -46,11 +47,20 @@ ) from robot_server.protocols.router import ProtocolNotFound -from ..run_models import RunNotFoundError +from ..run_models import ( + RunNotFoundError, + ActiveNozzleLayout, + RunCurrentState, + CommandLinkNoMeta, + NozzleLayoutConfig, +) from ..run_auto_deleter import RunAutoDeleter from ..run_models import Run, BadRun, RunCreate, RunUpdate from ..run_orchestrator_store import RunConflictError -from ..run_data_manager import RunDataManager, RunNotCurrentError +from ..run_data_manager import ( + RunDataManager, + RunNotCurrentError, +) from ..dependencies import ( get_run_data_manager, get_run_auto_deleter, @@ -115,6 +125,15 @@ class AllRunsLinks(BaseModel): ) +class CurrentStateLinks(BaseModel): + """Links returned with the current state of a run.""" + + current: Optional[CommandLinkNoMeta] = Field( + None, + description="Path to the current command when current state was reported, if any.", + ) + + async def get_run_data_from_url( runId: str, run_data_manager: Annotated[RunDataManager, Depends(get_run_data_manager)], @@ -523,3 +542,64 @@ async def get_run_commands_error( ), status_code=status.HTTP_200_OK, ) + + +@PydanticResponse.wrap_route( + base_router.get, + path="/runs/{runId}/currentState", + summary="Get a run's current state.", + description=dedent( + """ + Get current state associated with a run if the run is current. + "\n\n" + Note that this endpoint is experimental and subject to change. + """ + ), + responses={ + status.HTTP_200_OK: {"model": SimpleBody[RunCurrentState]}, + status.HTTP_409_CONFLICT: {"model": ErrorBody[RunStopped]}, + }, +) +async def get_current_state( + runId: str, + run_data_manager: Annotated[RunDataManager, Depends(get_run_data_manager)], +) -> PydanticResponse[Body[RunCurrentState, CurrentStateLinks]]: + """Get current state associated with a run if the run is current. + + Arguments: + runId: Run ID pulled from URL. + run_data_manager: Run data retrieval interface. + """ + try: + active_nozzle_maps = run_data_manager.get_nozzle_maps(run_id=runId) + + nozzle_layouts = { + pipetteId: ActiveNozzleLayout.construct( + startingNozzle=nozzle_map.starting_nozzle, + activeNozzles=list(nozzle_map.map_store.keys()), + config=NozzleLayoutConfig(nozzle_map.configuration.value.lower()), + ) + for pipetteId, nozzle_map in active_nozzle_maps.items() + } + + current_command = run_data_manager.get_current_command(run_id=runId) + except RunNotCurrentError as e: + raise RunStopped(detail=str(e)).as_error(status.HTTP_409_CONFLICT) + + # TODO(jh, 03-11-24): Use `last_completed_command` instead of `current_command` to avoid concurrency gotchas. + links = CurrentStateLinks.construct( + current=CommandLinkNoMeta.construct( + id=current_command.command_id, + href=f"/runs/{runId}/commands/{current_command.command_id}", + ) + if current_command is not None + else None + ) + + return await PydanticResponse.create( + content=Body.construct( + data=RunCurrentState.construct(activeNozzleLayouts=nozzle_layouts), + links=links, + ), + status_code=status.HTTP_200_OK, + ) diff --git a/robot-server/robot_server/runs/run_data_manager.py b/robot-server/robot_server/runs/run_data_manager.py index c8d0db1b0d3..b756b185bf1 100644 --- a/robot-server/robot_server/runs/run_data_manager.py +++ b/robot-server/robot_server/runs/run_data_manager.py @@ -1,9 +1,12 @@ """Manage current and historical run data.""" from datetime import datetime -from typing import List, Optional, Callable, Union +from typing import List, Optional, Callable, Union, Dict from opentrons_shared_data.labware.labware_definition import LabwareDefinition from opentrons_shared_data.errors.exceptions import InvalidStoredData, EnumeratedError + +from opentrons.hardware_control.nozzle_manager import NozzleMap + from opentrons.protocol_engine import ( EngineStatus, LabwareOffsetCreate, @@ -473,6 +476,13 @@ def get_command_errors(self, run_id: str) -> list[ErrorOccurrence]: # TODO(tz, 8-5-2024): Change this to return the error list from the DB when we implement https://opentrons.atlassian.net/browse/EXEC-655. raise RunNotCurrentError() + def get_nozzle_maps(self, run_id: str) -> Dict[str, NozzleMap]: + """Get current nozzle maps keyed by pipette id.""" + if run_id == self._run_orchestrator_store.current_run_id: + return self._run_orchestrator_store.get_nozzle_maps() + + raise RunNotCurrentError() + def get_all_commands_as_preserialized_list( self, run_id: str, include_fixit_commands: bool ) -> List[str]: diff --git a/robot-server/robot_server/runs/run_models.py b/robot-server/robot_server/runs/run_models.py index 1860e86d3e8..962c3ab51e7 100644 --- a/robot-server/robot_server/runs/run_models.py +++ b/robot-server/robot_server/runs/run_models.py @@ -1,7 +1,9 @@ """Request and response models for run resources.""" from datetime import datetime + +from enum import Enum from pydantic import BaseModel, Field -from typing import List, Optional, Literal +from typing import List, Optional, Literal, Dict from opentrons.protocol_engine import ( CommandStatus, @@ -280,6 +282,44 @@ class LabwareDefinitionSummary(BaseModel): ) +class NozzleLayoutConfig(str, Enum): + """Possible valid nozzle configurations.""" + + COLUMN = "column" + ROW = "row" + SINGLE = "single" + FULL = "full" + SUBRECT = "subrect" + + +class ActiveNozzleLayout(BaseModel): + """Details about the active nozzle layout for a pipette used in the current run.""" + + startingNozzle: str = Field( + ..., description="The nozzle used when issuing pipette commands." + ) + activeNozzles: List[str] = Field( + ..., + description="A map of all the pipette nozzles active in the current configuration.", + ) + config: NozzleLayoutConfig = Field( + ..., description="The active nozzle configuration." + ) + + +class RunCurrentState(BaseModel): + """Current details about a run.""" + + activeNozzleLayouts: Dict[str, ActiveNozzleLayout] = Field(..., description="") + + +class CommandLinkNoMeta(BaseModel): + """A link to a command resource without a meta field.""" + + id: str = Field(..., description="The ID of the command.") + href: str = Field(..., description="The HTTP API path to the command.") + + class RunNotFoundError(GeneralError): """Error raised when a given Run ID is not found in the store.""" diff --git a/robot-server/robot_server/runs/run_orchestrator_store.py b/robot-server/robot_server/runs/run_orchestrator_store.py index 2e8d8146dd8..46a384b96ea 100644 --- a/robot-server/robot_server/runs/run_orchestrator_store.py +++ b/robot-server/robot_server/runs/run_orchestrator_store.py @@ -1,7 +1,7 @@ """In-memory storage of ProtocolEngine instances.""" import asyncio import logging -from typing import List, Optional, Callable +from typing import List, Optional, Callable, Dict from opentrons.protocol_engine.errors.exceptions import EStopActivatedError from opentrons.protocol_engine.types import ( @@ -16,6 +16,7 @@ from opentrons.config import feature_flags from opentrons.hardware_control import HardwareControlAPI +from opentrons.hardware_control.nozzle_manager import NozzleMap from opentrons.hardware_control.types import ( EstopState, HardwareEvent, @@ -324,6 +325,10 @@ def get_loaded_labware_definitions(self) -> List[LabwareDefinition]: """Get loaded labware definitions.""" return self.run_orchestrator.get_loaded_labware_definitions() + def get_nozzle_maps(self) -> Dict[str, NozzleMap]: + """Get the current nozzle map keyed by pipette id.""" + return self.run_orchestrator.get_nozzle_maps() + def get_run_time_parameters(self) -> List[RunTimeParameter]: """Parameter definitions defined by protocol, if any. Will always be empty before execution.""" return self.run_orchestrator.get_run_time_parameters() diff --git a/robot-server/tests/runs/router/test_base_router.py b/robot-server/tests/runs/router/test_base_router.py index 5f23d459e2a..37e5cd6dd3d 100644 --- a/robot-server/tests/runs/router/test_base_router.py +++ b/robot-server/tests/runs/router/test_base_router.py @@ -1,18 +1,23 @@ """Tests for base /runs routes.""" +from typing import Dict + import pytest from datetime import datetime from decoy import Decoy from pathlib import Path -from opentrons.types import DeckSlotName +from opentrons.types import DeckSlotName, Point from opentrons.protocol_engine import ( LabwareOffsetCreate, types as pe_types, errors as pe_errors, CommandErrorSlice, + CommandPointer, ) from opentrons.protocol_reader import ProtocolSource, JsonProtocolConfig +from opentrons.hardware_control.nozzle_manager import NozzleConfigurationType, NozzleMap + from robot_server.data_files.data_files_store import DataFilesStore, DataFileInfo from robot_server.errors.error_responses import ApiError @@ -34,9 +39,20 @@ from robot_server.runs.run_auto_deleter import RunAutoDeleter -from robot_server.runs.run_models import Run, RunCreate, RunUpdate +from robot_server.runs.run_models import ( + Run, + RunCreate, + RunUpdate, + RunCurrentState, + ActiveNozzleLayout, + CommandLinkNoMeta, + NozzleLayoutConfig, +) from robot_server.runs.run_orchestrator_store import RunConflictError -from robot_server.runs.run_data_manager import RunDataManager, RunNotCurrentError +from robot_server.runs.run_data_manager import ( + RunDataManager, + RunNotCurrentError, +) from robot_server.runs.run_models import RunNotFoundError from robot_server.runs.router.base_router import ( AllRunsLinks, @@ -48,6 +64,8 @@ update_run, put_error_recovery_policy, get_run_commands_error, + get_current_state, + CurrentStateLinks, ) from robot_server.deck_configuration.store import DeckConfigurationStore @@ -84,6 +102,23 @@ def labware_offset_create() -> LabwareOffsetCreate: ) +@pytest.fixture +def mock_nozzle_maps() -> Dict[str, NozzleMap]: + """Get mock NozzleMaps.""" + return { + "mock-pipette-id": NozzleMap( + configuration=NozzleConfigurationType.FULL, + columns={"1": ["A1"]}, + rows={"A": ["A1"]}, + map_store={"A1": Point(0, 0, 0)}, + starting_nozzle="A1", + valid_map_key="mock-key", + full_instrument_map_store={}, + full_instrument_rows={}, + ) + } + + async def test_create_run( decoy: Decoy, mock_run_data_manager: RunDataManager, @@ -803,3 +838,67 @@ async def test_get_run_commands_errors_defualt_cursor( cursor=expected_cursor_result, totalLength=3 ) assert result.status_code == 200 + + +async def test_get_current_state_success( + decoy: Decoy, + mock_run_data_manager: RunDataManager, + mock_nozzle_maps: Dict[str, NozzleMap], +) -> None: + """It should return the active nozzle layout for a specific pipette.""" + run_id = "test-run-id" + + decoy.when(mock_run_data_manager.get_nozzle_maps(run_id=run_id)).then_return( + mock_nozzle_maps + ) + decoy.when(mock_run_data_manager.get_current_command(run_id=run_id)).then_return( + CommandPointer( + command_id="current-command-id", + command_key="current-command-key", + created_at=datetime(year=2024, month=4, day=4), + index=101, + ) + ) + + result = await get_current_state( + runId=run_id, + run_data_manager=mock_run_data_manager, + ) + + assert result.status_code == 200 + assert result.content.data == RunCurrentState.construct( + activeNozzleLayouts={ + "mock-pipette-id": ActiveNozzleLayout( + startingNozzle="A1", + activeNozzles=["A1"], + config=NozzleLayoutConfig.FULL, + ) + } + ) + assert result.content.links == CurrentStateLinks( + current=CommandLinkNoMeta( + href="/runs/test-run-id/commands/current-command-id", + id="current-command-id", + ) + ) + + +async def test_get_current_state_run_not_current( + decoy: Decoy, + mock_run_data_manager: RunDataManager, +) -> None: + """It should raise RunStopped when the run is not current.""" + run_id = "non-current-run-id" + + decoy.when(mock_run_data_manager.get_nozzle_maps(run_id=run_id)).then_raise( + RunNotCurrentError("Run is not current") + ) + + with pytest.raises(ApiError) as exc_info: + await get_current_state( + runId=run_id, + run_data_manager=mock_run_data_manager, + ) + + assert exc_info.value.status_code == 409 + assert exc_info.value.content["errors"][0]["id"] == "RunStopped" diff --git a/robot-server/tests/runs/test_run_data_manager.py b/robot-server/tests/runs/test_run_data_manager.py index 801f09f080f..49399447597 100644 --- a/robot-server/tests/runs/test_run_data_manager.py +++ b/robot-server/tests/runs/test_run_data_manager.py @@ -1,6 +1,6 @@ """Tests for RunDataManager.""" from datetime import datetime -from typing import Optional, List +from typing import Optional, List, Dict import pytest from decoy import Decoy, matchers @@ -26,6 +26,8 @@ from opentrons.protocol_runner import RunResult from opentrons.types import DeckSlotName +from opentrons.hardware_control.nozzle_manager import NozzleMap + from opentrons_shared_data.errors.exceptions import InvalidStoredData from opentrons_shared_data.labware.labware_definition import LabwareDefinition @@ -113,6 +115,13 @@ def run_time_parameters() -> List[pe_types.RunTimeParameter]: ] +@pytest.fixture +def mock_nozzle_maps(decoy: Decoy) -> Dict[str, NozzleMap]: + """Get a mock NozzleMap.""" + mock_nozzle_map = decoy.mock(cls=NozzleMap) + return {"mock-pipette-id": mock_nozzle_map} + + @pytest.fixture def run_resource() -> RunResource: """Get a StateSummary value object.""" @@ -1146,3 +1155,38 @@ async def test_create_policies_translates_and_calls_orchestrator( decoy.when(mock_run_orchestrator_store.current_run_id).then_return("run-id") subject.set_policies(run_id="run-id", policies=input_rules) decoy.verify(mock_run_orchestrator_store.set_error_recovery_policy(expected_output)) + + +def test_get_nozzle_map_current_run( + decoy: Decoy, + mock_run_orchestrator_store: RunOrchestratorStore, + subject: RunDataManager, + mock_nozzle_maps: Dict[str, NozzleMap], +) -> None: + """It should return the nozzle map for the current run.""" + run_id = "current-run-id" + + decoy.when(mock_run_orchestrator_store.current_run_id).then_return(run_id) + decoy.when(mock_run_orchestrator_store.get_nozzle_maps()).then_return( + mock_nozzle_maps + ) + + result = subject.get_nozzle_maps(run_id=run_id) + + assert result == mock_nozzle_maps + + +def test_get_nozzle_map_not_current_run( + decoy: Decoy, + mock_run_orchestrator_store: RunOrchestratorStore, + subject: RunDataManager, +) -> None: + """It should raise RunNotCurrentError for a non-current run.""" + run_id = "non-current-run-id" + + decoy.when(mock_run_orchestrator_store.current_run_id).then_return( + "different-run-id" + ) + + with pytest.raises(RunNotCurrentError): + subject.get_nozzle_maps(run_id=run_id) From 8e1dabe4d6df05f165a5b77c64da1dc9dfdd298b Mon Sep 17 00:00:00 2001 From: koji Date: Fri, 4 Oct 2024 11:20:13 -0400 Subject: [PATCH 04/27] fix(protocol-designer): fix LiquidEditForm change detecting bug (#16419) * fix(protocol-designer): fix LiquidEditForm change detecting bug --- .../src/components/LiquidsPage/LiquidEditForm.tsx | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/protocol-designer/src/components/LiquidsPage/LiquidEditForm.tsx b/protocol-designer/src/components/LiquidsPage/LiquidEditForm.tsx index 1bf69d7ebd1..f7697dc2add 100644 --- a/protocol-designer/src/components/LiquidsPage/LiquidEditForm.tsx +++ b/protocol-designer/src/components/LiquidsPage/LiquidEditForm.tsx @@ -7,12 +7,12 @@ import * as Yup from 'yup' import { Card, DeprecatedCheckboxField, - FormGroup, - LegacyInputField, - OutlineButton, DeprecatedPrimaryButton, Flex, + FormGroup, JUSTIFY_END, + LegacyInputField, + OutlineButton, TYPOGRAPHY, } from '@opentrons/components' import { DEPRECATED_WHALE_GREY } from '@opentrons/shared-data' @@ -97,7 +97,7 @@ export function LiquidEditForm(props: LiquidEditFormProps): JSX.Element { const { handleSubmit, - formState: { errors, touchedFields }, + formState: { errors, touchedFields, isDirty }, control, watch, setValue, @@ -219,10 +219,11 @@ export function LiquidEditForm(props: LiquidEditFormProps): JSX.Element { From 1a736799feda0e5ae99890c32fca91b0db95a6fb Mon Sep 17 00:00:00 2001 From: Jamey Huffnagle Date: Fri, 4 Oct 2024 11:29:28 -0400 Subject: [PATCH 05/27] feat(api-client, react-api-client): Wire up `/runs/:runId/currentState` (#16417) Works towards RSQ-161 --- api-client/src/runs/getRunCurrentState.ts | 17 +++++++++++ api-client/src/runs/index.ts | 1 + api-client/src/runs/types.ts | 28 +++++++++++++++++++ react-api-client/src/runs/index.ts | 1 + .../src/runs/useRunCurrentState.ts | 28 +++++++++++++++++++ 5 files changed, 75 insertions(+) create mode 100644 api-client/src/runs/getRunCurrentState.ts create mode 100644 react-api-client/src/runs/useRunCurrentState.ts diff --git a/api-client/src/runs/getRunCurrentState.ts b/api-client/src/runs/getRunCurrentState.ts new file mode 100644 index 00000000000..6a64d9b9e0f --- /dev/null +++ b/api-client/src/runs/getRunCurrentState.ts @@ -0,0 +1,17 @@ +import { GET, request } from '../request' + +import type { ResponsePromise } from '../request' +import type { HostConfig } from '../types' +import type { RunCurrentState } from './types' + +export function getRunCurrentState( + config: HostConfig, + runId: string +): ResponsePromise { + return request( + GET, + `/runs/${runId}/currentState`, + null, + config + ) +} diff --git a/api-client/src/runs/index.ts b/api-client/src/runs/index.ts index 9f314f4b025..183b8f7e4d4 100644 --- a/api-client/src/runs/index.ts +++ b/api-client/src/runs/index.ts @@ -10,6 +10,7 @@ export { getCommands } from './commands/getCommands' export { getCommandsAsPreSerializedList } from './commands/getCommandsAsPreSerializedList' export { createRunAction } from './createRunAction' export { getRunCommandErrors } from './commands/getRunCommandErrors' +export { getRunCurrentState } from './getRunCurrentState' export * from './createLabwareOffset' export * from './createLabwareDefinition' export * from './constants' diff --git a/api-client/src/runs/types.ts b/api-client/src/runs/types.ts index 5998259ae50..241a3892622 100644 --- a/api-client/src/runs/types.ts +++ b/api-client/src/runs/types.ts @@ -87,10 +87,24 @@ export interface Run { data: RunData } +export interface RunCurrentState { + data: RunCurrentStateData + links: RunCommandLink +} + export interface RunsLinks { current?: ResourceLink } +export interface RunCommandLink { + current: CommandLinkNoMeta +} + +export interface CommandLinkNoMeta { + id: string + href: string +} + export interface GetRunsParams { pageLength?: number // the number of items to include } @@ -100,6 +114,10 @@ export interface Runs { links: RunsLinks } +export interface RunCurrentStateData { + activeNozzleLayouts: Record // keyed by pipetteId +} + export const RUN_ACTION_TYPE_PLAY: 'play' = 'play' export const RUN_ACTION_TYPE_PAUSE: 'pause' = 'pause' export const RUN_ACTION_TYPE_STOP: 'stop' = 'stop' @@ -173,3 +191,13 @@ export interface UpdateErrorRecoveryPolicyRequest { } export type UpdateErrorRecoveryPolicyResponse = Record + +/** + * Current Run State Data + */ +export interface NozzleLayoutValues { + startingNozzle: string + activeNozzles: string[] + config: NozzleLayoutConfig +} +export type NozzleLayoutConfig = 'column' | 'row' | 'full' | 'subrect' diff --git a/react-api-client/src/runs/index.ts b/react-api-client/src/runs/index.ts index 4b04d913487..71e3360a5f9 100644 --- a/react-api-client/src/runs/index.ts +++ b/react-api-client/src/runs/index.ts @@ -1,5 +1,6 @@ export { useAllRunsQuery } from './useAllRunsQuery' export { useRunQuery } from './useRunQuery' +export { useRunCurrentState } from './useRunCurrentState' export { useCreateRunMutation } from './useCreateRunMutation' export { useDeleteRunMutation } from './useDeleteRunMutation' export { useCreateCommandMutation } from './useCreateCommandMutation' diff --git a/react-api-client/src/runs/useRunCurrentState.ts b/react-api-client/src/runs/useRunCurrentState.ts new file mode 100644 index 00000000000..6eb46589e87 --- /dev/null +++ b/react-api-client/src/runs/useRunCurrentState.ts @@ -0,0 +1,28 @@ +import { useQuery } from 'react-query' +import type { AxiosError } from 'axios' +import type { RunCurrentState, HostConfig } from '@opentrons/api-client' +import type { UseQueryOptions, UseQueryResult } from 'react-query' +import { useHost } from '../api' +import { getRunCurrentState } from '@opentrons/api-client' + +export function useRunCurrentState( + runId: string | null, + options: UseQueryOptions = {}, + hostOverride?: HostConfig +): UseQueryResult { + const contextHost = useHost() + const host = + hostOverride != null ? { ...contextHost, ...hostOverride } : contextHost + + return useQuery( + [host, 'runs', runId, 'currentState'], + () => + getRunCurrentState(host as HostConfig, runId as string).then( + response => response.data + ), + { + enabled: host != null && runId != null && options.enabled !== false, + ...options, + } + ) +} From 12ebf2750473b05d41b4b85504ea58826af58de6 Mon Sep 17 00:00:00 2001 From: Nick Diehl <47604184+ncdiehl11@users.noreply.github.com> Date: Fri, 4 Oct 2024 13:20:05 -0400 Subject: [PATCH 06/27] feat(protocol-designer): add thermocycler form profile cycle functionality (#16418) Adds the ability to program thermocycler profile cycle steps and wires up to thermocycler step form. TODO: add tests Closes AUTH-810 --- .../src/assets/localization/en/form.json | 3 +- .../StepForm/StepFormToolbox.tsx | 8 +- .../ThermocyclerTools/ThermocyclerCycle.tsx | 548 ++++++++++++++++++ .../ThermocyclerProfileModal.tsx | 41 +- .../ThermocyclerTools/ThermocyclerStep.tsx | 49 +- .../StepTools/ThermocyclerTools/index.tsx | 7 +- 6 files changed, 626 insertions(+), 30 deletions(-) create mode 100644 protocol-designer/src/pages/Designer/ProtocolSteps/StepForm/StepTools/ThermocyclerTools/ThermocyclerCycle.tsx diff --git a/protocol-designer/src/assets/localization/en/form.json b/protocol-designer/src/assets/localization/en/form.json index 8bfad8971f2..aaa000a1668 100644 --- a/protocol-designer/src/assets/localization/en/form.json +++ b/protocol-designer/src/assets/localization/en/form.json @@ -186,8 +186,9 @@ "add_cycle_step": "Add a cycle step", "add_step": "Add step", "add_step_button": "+ Step", + "cycle": "cycle", "cycle_step": "cycle step", - "cycles": "Cycles {{repetitions}}", + "cycles": "Cycles {{repetitions}}x", "delete": "delete", "edit": "Edit Thermocycler profile steps", "lid_closed": "Closed", diff --git a/protocol-designer/src/pages/Designer/ProtocolSteps/StepForm/StepFormToolbox.tsx b/protocol-designer/src/pages/Designer/ProtocolSteps/StepForm/StepFormToolbox.tsx index 1d268ea0549..b3236eb1e0e 100644 --- a/protocol-designer/src/pages/Designer/ProtocolSteps/StepForm/StepFormToolbox.tsx +++ b/protocol-designer/src/pages/Designer/ProtocolSteps/StepForm/StepFormToolbox.tsx @@ -90,7 +90,13 @@ export function StepFormToolbox(props: StepFormToolboxProps): JSX.Element { getTimelineWarningsForSelectedStep ) const timeline = useSelector(getRobotStateTimeline) - const [toolboxStep, setToolboxStep] = useState(0) + const [toolboxStep, setToolboxStep] = useState( + // progress to step 2 if thermocycler form is populated + formData.thermocyclerFormType === 'thermocyclerProfile' || + formData.thermocyclerFormType === 'thermocyclerState' + ? 1 + : 0 + ) const icon = stepIconsByType[formData.stepType] const ToolsComponent: typeof STEP_FORM_MAP[keyof typeof STEP_FORM_MAP] = get( diff --git a/protocol-designer/src/pages/Designer/ProtocolSteps/StepForm/StepTools/ThermocyclerTools/ThermocyclerCycle.tsx b/protocol-designer/src/pages/Designer/ProtocolSteps/StepForm/StepTools/ThermocyclerTools/ThermocyclerCycle.tsx new file mode 100644 index 00000000000..4e2ac9962d2 --- /dev/null +++ b/protocol-designer/src/pages/Designer/ProtocolSteps/StepForm/StepTools/ThermocyclerTools/ThermocyclerCycle.tsx @@ -0,0 +1,548 @@ +import { css } from 'styled-components' +import { useEffect, useState } from 'react' +import { useTranslation } from 'react-i18next' + +import { + ALIGN_CENTER, + ALIGN_FLEX_END, + BORDERS, + Btn, + COLORS, + CURSOR_POINTER, + DIRECTION_COLUMN, + Flex, + Icon, + InputField, + JUSTIFY_SPACE_BETWEEN, + NO_WRAP, + PrimaryButton, + SPACING, + StyledText, + TYPOGRAPHY, +} from '@opentrons/components' +import { + isTimeFormatMinutesSeconds, + temperatureRangeFieldValue, +} from '../../../../../../steplist/fieldLevel/errors' +import { + maskToFloat, + maskToInteger, + maskToTime, +} from '../../../../../../steplist/fieldLevel/processing' +import { uuid } from '../../../../../../utils' +import { getTimeFromString, getStepIndex } from './utils' + +import type { ThermocyclerStepTypeGeneral } from './ThermocyclerProfileModal' +import type { ThermocyclerStepType } from './ThermocyclerStep' + +export interface ThermocyclerCycleType { + id: string + title: string + steps: ThermocyclerStepType[] + type: 'profileCycle' + repetitions: string +} + +interface CycleStepValues { + value: string | null + error: string | null + wasAccessed?: boolean +} +interface CycleStepType { + name: CycleStepValues + temp: CycleStepValues + time: CycleStepValues +} + +interface ThermocyclerCycleProps { + steps: ThermocyclerStepTypeGeneral[] + setSteps: React.Dispatch> + setShowCreateNewCycle: React.Dispatch> + step?: ThermocyclerCycleType + backgroundColor?: string + readOnly?: boolean + setIsInEdit: React.Dispatch> +} + +export function ThermocyclerCycle(props: ThermocyclerCycleProps): JSX.Element { + const { + setShowCreateNewCycle, + step, + steps, + setSteps, + backgroundColor = COLORS.grey30, + setIsInEdit, + readOnly = true, + } = props + const { i18n, t } = useTranslation(['application', 'form']) + const [hover, setHover] = useState(false) + const [showEdit, setShowEditCurrentCycle] = useState(!readOnly) + + const [orderedCycleStepIds, setOrderedCycleStepIds] = useState( + step?.steps.map(cycleStep => cycleStep.id) ?? [] + ) + const [cycleStepsById, setCycleStepsById] = useState( + step?.steps.reduce>( + (acc, { id, title, temperature, durationMinutes, durationSeconds }) => { + return { + ...acc, + [id]: { + name: { value: title ?? null, error: null }, + temp: { + value: temperature ?? null, + error: null, + wasAccessed: false, + }, + time: { + value: + durationMinutes != null && durationSeconds != null + ? `${durationMinutes}:${durationSeconds}` + : null, + error: null, + wasAccessed: false, + }, + }, + } + }, + {} + ) ?? {} + ) + const [repetitions, setRepetitions] = useState( + step?.repetitions + ) + + const cycleId = step?.id ?? null + const isStepStateError = + Object.values(cycleStepsById).some(cycleStep => + Object.values(cycleStep).some( + ({ value, error }) => value == null || value === '' || error != null + ) + ) || + repetitions == null || + repetitions === '' + + const blankStep: CycleStepType = { + name: { + value: null, + error: null, + }, + temp: { + value: null, + error: null, + }, + time: { + value: null, + error: null, + }, + } + + useEffect(() => { + if (orderedCycleStepIds.length === 0) { + // prepopulate with blank step on mount if not editing + handleAddCycleStep() + setIsInEdit(true) + } + }, []) + + const handleAddCycleStep = (): void => { + const newStepId = uuid() + setOrderedCycleStepIds([...orderedCycleStepIds, newStepId]) + setCycleStepsById({ ...cycleStepsById, [newStepId]: blankStep }) + } + + const handleDeleteStep = (stepId: string): void => { + const filteredOrdredCycleStepIds = orderedCycleStepIds.filter( + id => id !== stepId + ) + setOrderedCycleStepIds(filteredOrdredCycleStepIds) + setCycleStepsById( + filteredOrdredCycleStepIds.reduce((acc, id) => { + return id !== stepId + ? { + ...acc, + [id]: cycleStepsById[id], + } + : acc + }, {}) + ) + } + const handleDeleteCycle = (): void => { + if (cycleId != null) { + setSteps( + steps.filter((s: any) => { + return s.id !== cycleId + }) + ) + } else { + setShowCreateNewCycle(false) + } + setIsInEdit(false) + } + const handleValueUpdate = ( + stepId: string, + field: 'name' | 'temp' | 'time', + value: string, + errorCheck?: (value: any) => string | null + ): void => { + setCycleStepsById({ + ...cycleStepsById, + [stepId]: { + ...cycleStepsById[stepId], + [field]: { + value, + error: errorCheck?.(value) ?? null, + }, + }, + }) + } + const handleSaveCycle = (): void => { + const orderedCycleSteps = orderedCycleStepIds.map(cycleStepId => { + const step = cycleStepsById[cycleStepId] + const { minutes, seconds } = getTimeFromString(step.time.value ?? '') + const cycleStepData: ThermocyclerStepType = { + durationMinutes: minutes, + durationSeconds: seconds, + id: cycleStepId, + temperature: step.temp.value ?? '', + title: step.name.value ?? '', + type: 'profileStep', + } + return cycleStepData + }) + const cycleData: ThermocyclerCycleType = { + id: cycleId ?? uuid(), + title: '', + steps: orderedCycleSteps, + type: 'profileCycle', + repetitions: repetitions ?? '', + } + const existingCycleIndex = steps.findIndex(step => step.id === cycleId) + if (existingCycleIndex >= 0) { + // editing a cycle that was already created + setSteps([ + ...steps.slice(0, existingCycleIndex), + cycleData, + ...steps.slice(existingCycleIndex + 1), + ]) + } else { + // append to end of steps + setSteps([...steps, cycleData]) + } + setShowCreateNewCycle(false) + setShowEditCurrentCycle(false) + setIsInEdit(false) + } + + const header = showEdit ? ( + + + + {cycleId != null ? getStepIndex(steps, cycleId) : steps.length + 1} + + + {i18n.format( + t('form:step_edit_form.field.thermocyclerProfile.cycle'), + 'capitalize' + )} + + + + + + {i18n.format( + t('form:step_edit_form.field.thermocyclerProfile.delete'), + 'capitalize' + )} + + + + + {i18n.format(t('save'), 'capitalize')} + + + + + ) : ( + { + setHover(true) + }} + onMouseLeave={() => { + setHover(false) + }} + > + + + {getStepIndex(steps, cycleId ?? '')} + + + {i18n.format( + t('form:step_edit_form.field.thermocyclerProfile.cycles', { + repetitions, + }), + 'capitalize' + )} + + + + {hover ? ( + { + setShowEditCurrentCycle(true) + setIsInEdit(true) + }} + > + + {i18n.format(t('edit'), 'capitalize')} + + + ) : null} + + + + + + ) + const bodyContent = ( + { + setHover(true) + }} + onMouseLeave={() => { + setHover(false) + }} + > + + {orderedCycleStepIds.map((cycleStepId, cycleStepIndex) => { + const stepState = cycleStepsById[cycleStepId] + return showEdit ? ( + + + ) => { + handleValueUpdate( + cycleStepId, + 'name', + e.target.value as string + ) + }} + /> + + + ) => { + handleValueUpdate( + cycleStepId, + 'temp', + maskToFloat(e.target.value), + temperatureRangeFieldValue(4, 96) + ) + }} + onBlur={() => { + setCycleStepsById({ + ...cycleStepsById, + [cycleStepId]: { + ...stepState, + temp: { + ...stepState.temp, + wasAccessed: true, + }, + }, + }) + }} + error={ + stepState.temp.wasAccessed ? stepState.temp.error : null + } + /> + + + ) => { + handleValueUpdate( + cycleStepId, + 'time', + maskToTime(e.target.value), + isTimeFormatMinutesSeconds + ) + }} + onBlur={() => { + setCycleStepsById({ + ...cycleStepsById, + [cycleStepId]: { + ...stepState, + time: { + ...stepState.time, + wasAccessed: true, + }, + }, + }) + }} + error={ + stepState.time.wasAccessed ? stepState.time.error : null + } + /> + + { + handleDeleteStep(cycleStepId) + }} + alignSelf={ALIGN_CENTER} + > + + + + ) : ( + + {`${getStepIndex(steps, cycleId ?? '')}.${ + cycleStepIndex + 1 + }`} + {`${ + stepState.name.value + }, ${stepState.temp.value}${t('units.degrees')}, ${ + stepState.time.value + }, `} + + ) + })} + + {showEdit ? ( + <> + + + {i18n.format( + t( + 'form:step_edit_form.field.thermocyclerProfile.add_cycle_step' + ), + 'capitalize' + )} + + + { + setRepetitions(maskToInteger(e.target.value)) + }} + /> + + ) : null} + + ) + + return ( + + {header} + {bodyContent} + + ) +} diff --git a/protocol-designer/src/pages/Designer/ProtocolSteps/StepForm/StepTools/ThermocyclerTools/ThermocyclerProfileModal.tsx b/protocol-designer/src/pages/Designer/ProtocolSteps/StepForm/StepTools/ThermocyclerTools/ThermocyclerProfileModal.tsx index 328125317e2..cb816041010 100644 --- a/protocol-designer/src/pages/Designer/ProtocolSteps/StepForm/StepTools/ThermocyclerTools/ThermocyclerProfileModal.tsx +++ b/protocol-designer/src/pages/Designer/ProtocolSteps/StepForm/StepTools/ThermocyclerTools/ThermocyclerProfileModal.tsx @@ -13,12 +13,18 @@ import { StyledText, } from '@opentrons/components' +import { ThermocyclerCycle } from './ThermocyclerCycle' import { ThermocyclerStep } from './ThermocyclerStep' import type { FormData } from '../../../../../../form-types' import type { FieldPropsByName } from '../../types' +import type { ThermocyclerCycleType } from './ThermocyclerCycle' import type { ThermocyclerStepType } from './ThermocyclerStep' +export type ThermocyclerStepTypeGeneral = + | ThermocyclerCycleType + | ThermocyclerStepType + interface ThermocyclerModalProps { formData: FormData propsForFields: FieldPropsByName @@ -33,10 +39,11 @@ export function ThermocyclerProfileModal( const [showCreateNewStep, setShowCreateNewStep] = useState(false) const [showCreateNewCycle, setShowCreateNewCycle] = useState(false) - const [steps, setSteps] = useState( + const [isInEdit, setIsInEdit] = useState(false) + const [steps, setSteps] = useState( formData.orderedProfileItems.map( (id: string) => formData.profileItemsById[id] - ) as ThermocyclerStepType[] + ) as ThermocyclerStepTypeGeneral[] ) const canAddStepOrProfile = !(showCreateNewCycle || showCreateNewStep) @@ -71,7 +78,10 @@ export function ThermocyclerProfileModal( {i18n.format(t('cancel'), 'capitalize')} - + {i18n.format(t('save'), 'capitalize')} @@ -111,24 +121,43 @@ export function ThermocyclerProfileModal( ) : ( // TODO (nd: 10/1/2024): add add profile cycle component - <>TODO: wire up cycle + ) })} {showCreateNewStep ? ( + ) : null} + {showCreateNewCycle ? ( + ) : null} - {showCreateNewCycle ? <>TODO: wire up cycle : null} ) : ( > - setShowCreateNewStep: (_: boolean) => void + steps: ThermocyclerStepTypeGeneral[] + setSteps: React.Dispatch> + setShowCreateNewStep: React.Dispatch> + setIsInEdit: React.Dispatch> step?: ThermocyclerStepType backgroundColor?: string - showHeader?: boolean readOnly?: boolean } export function ThermocyclerStep(props: ThermocyclerStepProps): JSX.Element { @@ -54,21 +56,22 @@ export function ThermocyclerStep(props: ThermocyclerStepProps): JSX.Element { steps, setSteps, backgroundColor = COLORS.grey30, - showHeader = true, readOnly = true, + setIsInEdit, } = props const { i18n, t } = useTranslation(['application', 'form']) const [hover, setHover] = useState(false) const [showEdit, setShowEditCurrentStep] = useState(!readOnly) const [stepState, setStepState] = useState({ name: { value: step?.title, error: null }, - temp: { value: step?.temperature, error: null }, + temp: { value: step?.temperature, error: null, wasAccessed: false }, time: { value: step?.durationMinutes != null && step?.durationSeconds != null ? `${step.durationMinutes}:${step.durationSeconds}` : undefined, error: null, + wasAccessed: false, }, }) const id = step?.id ?? null @@ -86,6 +89,7 @@ export function ThermocyclerStep(props: ThermocyclerStepProps): JSX.Element { } else { setShowCreateNewStep(false) } + setIsInEdit(false) } const handleValueUpdate = ( field: 'name' | 'temp' | 'time', @@ -101,14 +105,13 @@ export function ThermocyclerStep(props: ThermocyclerStepProps): JSX.Element { }) } const handleSaveStep = (): void => { - const stepId = uuid() const { minutes, seconds } = getTimeFromString(stepState.time.value ?? '') - const stepBaseData = { + const stepBaseData: ThermocyclerStepType = { durationMinutes: minutes, durationSeconds: seconds, - id: stepId, - temperature: stepState.temp.value, - title: stepState.name.value, + id: id ?? '', + temperature: stepState.temp.value ?? '', + title: stepState.name.value ?? '', type: 'profileStep', } @@ -117,14 +120,15 @@ export function ThermocyclerStep(props: ThermocyclerStepProps): JSX.Element { // editing a step already in steps setSteps([ ...steps.slice(0, existingStepIndex), - { ...stepBaseData, id }, + { ...stepBaseData, id: id ?? uuid() }, ...steps.slice(existingStepIndex + 1), ]) } else { - setSteps([...steps, { ...stepBaseData, id: stepId }]) + setSteps([...steps, { ...stepBaseData, id: uuid() }]) } setShowCreateNewStep(false) setShowEditCurrentStep(false) + setIsInEdit(false) } const header = showEdit ? ( @@ -207,6 +211,7 @@ export function ThermocyclerStep(props: ThermocyclerStepProps): JSX.Element { textDecoration={TYPOGRAPHY.textDecorationUnderline} onClick={() => { setShowEditCurrentStep(true) + setIsInEdit(true) }} > @@ -269,7 +274,13 @@ export function ThermocyclerStep(props: ThermocyclerStepProps): JSX.Element { temperatureRangeFieldValue(4, 96) ) }} - error={stepState.temp.error} + onBlur={() => { + setStepState({ + ...stepState, + temp: { ...stepState.temp, wasAccessed: true }, + }) + }} + error={stepState.temp.wasAccessed ? stepState.temp.error : null} /> { + setStepState({ + ...stepState, + time: { ...stepState.time, wasAccessed: true }, + }) + }} + error={stepState.time.wasAccessed ? stepState.time.error : null} /> @@ -303,7 +320,7 @@ export function ThermocyclerStep(props: ThermocyclerStepProps): JSX.Element { backgroundColor={backgroundColor} borderRadius={BORDERS.borderRadius4} > - {showHeader ? header : null} + {header} {showEdit ? editContent : null} ) diff --git a/protocol-designer/src/pages/Designer/ProtocolSteps/StepForm/StepTools/ThermocyclerTools/index.tsx b/protocol-designer/src/pages/Designer/ProtocolSteps/StepForm/StepTools/ThermocyclerTools/index.tsx index 071006c4d3f..834306b7b76 100644 --- a/protocol-designer/src/pages/Designer/ProtocolSteps/StepForm/StepTools/ThermocyclerTools/index.tsx +++ b/protocol-designer/src/pages/Designer/ProtocolSteps/StepForm/StepTools/ThermocyclerTools/index.tsx @@ -15,18 +15,13 @@ import { ThermocyclerState } from './ThermocyclerState' import type { StepFormProps } from '../../types' -type ThermocyclerContentType = - | 'thermocyclerState' - | 'thermocyclerProfile' - | null +type ThermocyclerContentType = 'thermocyclerState' | 'thermocyclerProfile' export function ThermocyclerTools(props: StepFormProps): JSX.Element { const { propsForFields, formData, toolboxStep } = props const { t } = useTranslation('form') - console.log(formData) const [contentType, setContentType] = useState( - // (formData.thermocyclerFormType ?? null) as ThermocyclerContentType (formData.thermocyclerFormType as ThermocyclerContentType) ?? 'thermocyclerState' ) From 1b356528a1d7e6dbfa302748a336b31600dac49e Mon Sep 17 00:00:00 2001 From: Seth Foster Date: Fri, 4 Oct 2024 15:00:12 -0400 Subject: [PATCH 07/27] refactor(api,shared-data): fix v10 command parsing (#16420) We actually missed some stuff when adding command schema v10, and we missed it in part because it's all over the place. This commit instead removes some of the duplicative json protocol parsing alongside adding better support for v10 protocols: - Loosen the definition of commands in protocol_schema_v8, including entirely removing the weird half-measure all-optional param parsing, so you don't have to add new things there when you add a new command parameter kind - Improve the formatting of the errors raised by json protocols that aren't valid because they have bad command, labware, or liquid schema IDs (because those are the ones we actually parse in python) Closes EXEC-753 --- .../protocol_reader/file_format_validator.py | 98 +- .../protocol_runner/json_translator.py | 26 +- .../protocol_runner/test_json_translator.py | 194 +-- shared-data/js/protocols.ts | 12 +- .../fixtures/8/simpleFlexV10CommandsV8.json | 1475 +++++++++++++++++ .../fixtures/8/simpleV10CommandsV8.json | 1473 ++++++++++++++++ .../opentrons_shared_data/command/__init__.py | 77 +- .../protocol/models/protocol_schema_v8.py | 76 +- .../tests/command/test_known_schema_ids.py | 9 + .../tests/protocol/test_protocol_schema_v8.py | 10 +- 10 files changed, 3256 insertions(+), 194 deletions(-) create mode 100644 shared-data/protocol/fixtures/8/simpleFlexV10CommandsV8.json create mode 100644 shared-data/protocol/fixtures/8/simpleV10CommandsV8.json create mode 100644 shared-data/python/tests/command/test_known_schema_ids.py diff --git a/api/src/opentrons/protocol_reader/file_format_validator.py b/api/src/opentrons/protocol_reader/file_format_validator.py index f13d1339041..df119ac3ffa 100644 --- a/api/src/opentrons/protocol_reader/file_format_validator.py +++ b/api/src/opentrons/protocol_reader/file_format_validator.py @@ -1,5 +1,5 @@ """File format validation interface.""" - +from __future__ import annotations from typing import Iterable @@ -29,6 +29,16 @@ class FileFormatValidationError(ProtocolFilesInvalidError): """Raised when a file does not conform to the format it's supposed to.""" + @classmethod + def _generic_json_failure( + cls, info: IdentifiedJsonMain, exc: Exception + ) -> FileFormatValidationError: + return cls( + message=f"{info.original_file.name} could not be read as a JSON protocol.", + detail={"kind": "bad-json-protocol"}, + wrapping=[PythonException(exc)], + ) + class FileFormatValidator: """File format validation interface.""" @@ -61,22 +71,80 @@ def validate_sync() -> None: await anyio.to_thread.run_sync(validate_sync) +def _handle_v8_json_protocol_validation_error( + info: IdentifiedJsonMain, pve: PydanticValidationError +) -> None: + for error in pve.errors(): + if error["loc"] == ("commandSchemaId",) and error["type"] == "type_error.enum": + # type_error.enum is for "this entry is not in this enum" and happens if you constrain a field by + # annotating it with Enum, as we now do for command schema IDs + raise FileFormatValidationError( + message=( + f"{info.original_file.name} could not be read as a JSON protocol, in part because its command schema " + "id is unknown. This protocol may have been exported from a future version of authorship software. " + "Updating your Opentrons software may help." + ), + detail={ + "kind": "bad-command-schema-id", + "command-schema-id": info.unvalidated_json.get( + "commandSchemaId", "" + ), + }, + wrapping=[PythonException(pve)], + ) from pve + if ( + error["loc"] == ("labwareDefinitionSchemaId",) + and error["type"] == "value_error.const" + ): + # value_error.const is for "this entry is not one of these const values", which is different from type_error.enum + # for I'm sure a very good reason, and happens if you constrain a field by annotating it with a Literal + raise FileFormatValidationError( + message=( + f"{info.original_file.name} could not be read as a JSON protocol, in part because its labware schema " + "id is unknown. This protocol may have been exported from a future version of authorship software. " + "Updating your Opentrons software may help." + ), + detail={ + "kind": "bad-labware-schema-id", + "labware-schema-id": info.unvalidated_json.get( + "labwareDefinitionSchemaId", "" + ), + }, + ) + if error["loc"] == ("liquidSchemaId",) and error["type"] == "value_error.const": + raise FileFormatValidationError( + message=( + f"{info.original_file.name} could not be read as a JSON protocol, in part because its liquid schema " + "id is unknown. This protocol may have been exported from a future version of authorship software. " + "Updating your Opentrons software may help." + ), + detail={ + "kind": "bad-liquid-schema-id", + "liquid-schema-id": info.unvalidated_json.get( + "liquidSchemaId", "" + ), + }, + ) + else: + raise FileFormatValidationError._generic_json_failure(info, pve) from pve + + async def _validate_json_protocol(info: IdentifiedJsonMain) -> None: def validate_sync() -> None: - try: - if info.schema_version == 8: + if info.schema_version == 8: + try: JsonProtocolV8.parse_obj(info.unvalidated_json) - elif info.schema_version == 7: - JsonProtocolV7.parse_obj(info.unvalidated_json) - elif info.schema_version == 6: - JsonProtocolV6.parse_obj(info.unvalidated_json) - else: - JsonProtocolUpToV5.parse_obj(info.unvalidated_json) - except PydanticValidationError as e: - raise FileFormatValidationError( - message=f"{info.original_file.name} could not be read as a JSON protocol.", - detail={"kind": "bad-json-protocol"}, - wrapping=[PythonException(e)], - ) from e + except PydanticValidationError as pve: + _handle_v8_json_protocol_validation_error(info, pve) + else: + try: + if info.schema_version == 7: + JsonProtocolV7.parse_obj(info.unvalidated_json) + elif info.schema_version == 6: + JsonProtocolV6.parse_obj(info.unvalidated_json) + else: + JsonProtocolUpToV5.parse_obj(info.unvalidated_json) + except PydanticValidationError as e: + raise FileFormatValidationError._generic_json_failure(info, e) from e await anyio.to_thread.run_sync(validate_sync) diff --git a/api/src/opentrons/protocol_runner/json_translator.py b/api/src/opentrons/protocol_runner/json_translator.py index 65410662e77..6c670baf97a 100644 --- a/api/src/opentrons/protocol_runner/json_translator.py +++ b/api/src/opentrons/protocol_runner/json_translator.py @@ -1,6 +1,6 @@ """Translation of JSON protocol commands into ProtocolEngine commands.""" -from typing import cast, List, Union -from pydantic import parse_obj_as +from typing import cast, List, Union, Iterator +from pydantic import parse_obj_as, ValidationError as PydanticValidationError from opentrons_shared_data.pipette.types import PipetteNameType from opentrons_shared_data.protocol.models import ( @@ -12,6 +12,7 @@ protocol_schema_v8, ) from opentrons_shared_data import command as command_schema +from opentrons_shared_data.errors.exceptions import InvalidProtocolData, PythonException from opentrons.types import MountType from opentrons.protocol_engine import ( @@ -196,7 +197,7 @@ class JsonTranslator: """Class that translates commands/liquids from PD/JSON to ProtocolEngine.""" def translate_liquids( - self, protocol: Union[ProtocolSchemaV6, ProtocolSchemaV7] + self, protocol: Union[ProtocolSchemaV6, ProtocolSchemaV7, ProtocolSchemaV8] ) -> List[Liquid]: """Takes json protocol v6 and translates liquids->protocol engine liquids.""" protocol_liquids = protocol.liquids or {} @@ -258,7 +259,8 @@ def _translate_v8_commands( self, protocol: ProtocolSchemaV8 ) -> List[pe_commands.CommandCreate]: """Translate commands in json protocol schema v8, which might be of different command schemas.""" - command_schema_ref = protocol.commandSchemaId + command_schema_ref = protocol.commandSchemaId.value + # these calls will raise if the command schema version is invalid or unknown command_schema_version = command_schema.schema_version_from_ref( command_schema_ref @@ -267,4 +269,18 @@ def _translate_v8_commands( command_schema_version ) - return [_translate_simple_command(command) for command in protocol.commands] + def translate_all_commands() -> Iterator[pe_commands.CommandCreate]: + for command in protocol.commands: + try: + yield _translate_simple_command(command) + except PydanticValidationError as pve: + raise InvalidProtocolData( + message=( + "The protocol is invalid because it contains an unknown or malformed command, " + f'"{command.commandType}".' + ), + detail={"kind": "invalid-command"}, + wrapping=[PythonException(pve)], + ) + + return list(translate_all_commands()) diff --git a/api/tests/opentrons/protocol_runner/test_json_translator.py b/api/tests/opentrons/protocol_runner/test_json_translator.py index 62181880dbc..a583fcbf1c4 100644 --- a/api/tests/opentrons/protocol_runner/test_json_translator.py +++ b/api/tests/opentrons/protocol_runner/test_json_translator.py @@ -85,17 +85,17 @@ protocol_schema_v8.Command( commandType="aspirate", key=None, - params=protocol_schema_v8.Params( - pipetteId="pipette-id-1", - labwareId="labware-id-2", - volume=1.23, - flowRate=4.56, - wellName="A1", - wellLocation=SD_WellLocation( - origin="bottom", - offset=OffsetVector(x=0, y=0, z=7.89), - ), - ), + params={ + "pipetteId": "pipette-id-1", + "labwareId": "labware-id-2", + "volume": 1.23, + "flowRate": 4.56, + "wellName": "A1", + "wellLocation": { + "origin": "bottom", + "offset": {"x": 0, "y": 0, "z": 7.89}, + }, + }, ), pe_commands.AspirateCreate( key=None, @@ -147,17 +147,17 @@ protocol_schema_v8.Command( commandType="dispense", key="dispense-key", - params=protocol_schema_v8.Params( - pipetteId="pipette-id-1", - labwareId="labware-id-2", - volume=1.23, - flowRate=4.56, - wellName="A1", - wellLocation=SD_WellLocation( - origin="bottom", - offset=OffsetVector(x=0, y=0, z=7.89), - ), - ), + params={ + "pipetteId": "pipette-id-1", + "labwareId": "labware-id-2", + "volume": 1.23, + "flowRate": 4.56, + "wellName": "A1", + "wellLocation": { + "origin": "bottom", + "offset": {"x": 0, "y": 0, "z": 7.89}, + }, + }, ), pe_commands.DispenseCreate( key="dispense-key", @@ -193,11 +193,11 @@ ), protocol_schema_v8.Command( commandType="dropTip", - params=protocol_schema_v8.Params( - pipetteId="pipette-id-1", - labwareId="labware-id-2", - wellName="A1", - ), + params={ + "pipetteId": "pipette-id-1", + "labwareId": "labware-id-2", + "wellName": "A1", + }, ), pe_commands.DropTipCreate( params=pe_commands.DropTipParams( @@ -230,11 +230,11 @@ ), protocol_schema_v8.Command( commandType="pickUpTip", - params=protocol_schema_v8.Params( - pipetteId="pipette-id-1", - labwareId="labware-id-2", - wellName="A1", - ), + params={ + "pipetteId": "pipette-id-1", + "labwareId": "labware-id-2", + "wellName": "A1", + }, ), pe_commands.PickUpTipCreate( params=pe_commands.PickUpTipParams( @@ -272,15 +272,15 @@ ), protocol_schema_v8.Command( commandType="touchTip", - params=protocol_schema_v8.Params( - pipetteId="pipette-id-1", - labwareId="labware-id-2", - wellName="A1", - wellLocation=SD_WellLocation( - origin="bottom", - offset=OffsetVector(x=0, y=0, z=-1.23), - ), - ), + params={ + "pipetteId": "pipette-id-1", + "labwareId": "labware-id-2", + "wellName": "A1", + "wellLocation": { + "origin": "bottom", + "offset": {"x": 0, "y": 0, "z": -1.23}, + }, + }, ), pe_commands.TouchTipCreate( params=pe_commands.TouchTipParams( @@ -307,9 +307,11 @@ ), protocol_schema_v8.Command( commandType="loadPipette", - params=protocol_schema_v8.Params( - pipetteId="pipette-id-1", mount="left", pipetteName="p10_single" - ), + params={ + "pipetteId": "pipette-id-1", + "mount": "left", + "pipetteName": "p10_single", + }, ), pe_commands.LoadPipetteCreate( params=pe_commands.LoadPipetteParams( @@ -337,11 +339,11 @@ ), protocol_schema_v8.Command( commandType="loadModule", - params=protocol_schema_v8.Params( - moduleId="module-id-1", - model="magneticModuleV2", - location=Location(slotName="3"), - ), + params={ + "moduleId": "module-id-1", + "model": "magneticModuleV2", + "location": {"slotName": "3"}, + }, ), pe_commands.LoadModuleCreate( params=pe_commands.LoadModuleParams( @@ -372,14 +374,14 @@ ), protocol_schema_v8.Command( commandType="loadLabware", - params=protocol_schema_v8.Params( - labwareId="labware-id-2", - version=1, - namespace="example", - loadName="foo_8_plate_33ul", - location=Location(moduleId="temperatureModuleId"), - displayName="Trash", - ), + params={ + "labwareId": "labware-id-2", + "version": 1, + "namespace": "example", + "loadName": "foo_8_plate_33ul", + "location": {"moduleId": "temperatureModuleId"}, + "displayName": "Trash", + }, ), pe_commands.LoadLabwareCreate( params=pe_commands.LoadLabwareParams( @@ -421,16 +423,16 @@ ), protocol_schema_v8.Command( commandType="blowout", - params=protocol_schema_v8.Params( - pipetteId="pipette-id-1", - labwareId="labware-id-2", - wellName="A1", - wellLocation=SD_WellLocation( - origin="bottom", - offset=OffsetVector(x=0, y=0, z=7.89), - ), - flowRate=1.23, - ), + params={ + "pipetteId": "pipette-id-1", + "labwareId": "labware-id-2", + "wellName": "A1", + "wellLocation": { + "origin": "bottom", + "offset": {"x": 0, "y": 0, "z": 7.89}, + }, + "flowRate": 1.23, + }, ), pe_commands.BlowOutCreate( params=pe_commands.BlowOutParams( @@ -456,7 +458,7 @@ ), protocol_schema_v8.Command( commandType="delay", - params=protocol_schema_v8.Params(waitForResume=True, message="hello world"), + params={"waitForResume": True, "message": "hello world"}, ), pe_commands.WaitForResumeCreate( params=pe_commands.WaitForResumeParams(message="hello world") @@ -473,7 +475,7 @@ ), protocol_schema_v8.Command( commandType="delay", - params=protocol_schema_v8.Params(seconds=12.34, message="hello world"), + params={"seconds": 12.34, "message": "hello world"}, ), pe_commands.WaitForDurationCreate( params=pe_commands.WaitForDurationParams( @@ -493,7 +495,7 @@ ), protocol_schema_v8.Command( commandType="waitForResume", - params=protocol_schema_v8.Params(message="hello world"), + params={"message": "hello world"}, ), pe_commands.WaitForResumeCreate( params=pe_commands.WaitForResumeParams(message="hello world") @@ -510,7 +512,7 @@ ), protocol_schema_v8.Command( commandType="waitForDuration", - params=protocol_schema_v8.Params(seconds=12.34, message="hello world"), + params={"seconds": 12.34, "message": "hello world"}, ), pe_commands.WaitForDurationCreate( params=pe_commands.WaitForDurationParams( @@ -540,12 +542,12 @@ ), protocol_schema_v8.Command( commandType="moveToCoordinates", - params=protocol_schema_v8.Params( - pipetteId="pipette-id-1", - coordinates=OffsetVector(x=1.1, y=2.2, z=3.3), - minimumZHeight=123.4, - forceDirect=True, - ), + params={ + "pipetteId": "pipette-id-1", + "coordinates": {"x": 1.1, "y": 2.2, "z": 3.3}, + "minimumZHeight": 123.4, + "forceDirect": True, + }, ), pe_commands.MoveToCoordinatesCreate( params=pe_commands.MoveToCoordinatesParams( @@ -593,20 +595,20 @@ ), protocol_schema_v8.Command( commandType="thermocycler/runProfile", - params=protocol_schema_v8.Params( - moduleId="module-id-2", - blockMaxVolumeUl=1.11, - profile=[ - ProfileStep( - celsius=2.22, - holdSeconds=3.33, - ), - ProfileStep( - celsius=4.44, - holdSeconds=5.55, - ), + params={ + "moduleId": "module-id-2", + "blockMaxVolumeUl": 1.11, + "profile": [ + { + "celsius": 2.22, + "holdSeconds": 3.33, + }, + { + "celsius": 4.44, + "holdSeconds": 5.55, + }, ], - ), + }, ), pe_commands.thermocycler.RunProfileCreate( params=pe_commands.thermocycler.RunProfileParams( @@ -645,11 +647,11 @@ protocol_schema_v8.Command( commandType="loadLiquid", key=None, - params=protocol_schema_v8.Params( - labwareId="labware-id-2", - liquidId="liquid-id-555", - volumeByWell={"A1": 32, "B2": 50}, - ), + params={ + "labwareId": "labware-id-2", + "liquidId": "liquid-id-555", + "volumeByWell": {"A1": 32, "B2": 50}, + }, ), pe_commands.LoadLiquidCreate( key=None, @@ -816,7 +818,7 @@ def _make_v8_json_protocol( ), labwareDefinitions=labware_definitions, labwareDefinitionSchemaId="opentronsLabwareSchemaV2", - commandSchemaId="opentronsCommandSchemaV8", + commandSchemaId=protocol_schema_v8.CommandSchemaId("opentronsCommandSchemaV8"), commands=commands, liquidSchemaId="opentronsLiquidSchemaV1", liquids=liquids, diff --git a/shared-data/js/protocols.ts b/shared-data/js/protocols.ts index e8effe36237..147c0b3125d 100644 --- a/shared-data/js/protocols.ts +++ b/shared-data/js/protocols.ts @@ -4,6 +4,7 @@ import Ajv from 'ajv' +import commandSchema10 from '../command/schemas/10.json' import commandSchema9 from '../command/schemas/9.json' import commandSchema8 from '../command/schemas/8.json' import commandSchema7 from '../command/schemas/7.json' @@ -30,6 +31,9 @@ const validateCommands8 = ( new Promise((resolve, reject) => { const requestedSchema = toValidate.commandSchemaId switch (requestedSchema) { + case 'opentronsCommandSchemaV10': + resolve(commandSchema10) + break case 'opentronsCommandSchemaV9': resolve(commandSchema9) break @@ -43,7 +47,13 @@ const validateCommands8 = ( keyword: 'Invalid command schema requested', dataPath: requestedSchema, schemaPath: '#/properties/commandSchemaId', - params: { allowedValues: ['opentronsCommandSchemaV8'] }, + params: { + allowedValues: [ + 'opentronsCommandSchemaV8', + 'opentronsCommandSchemaV9', + 'opentronsCommandSchemaV10', + ], + }, }, ]) break diff --git a/shared-data/protocol/fixtures/8/simpleFlexV10CommandsV8.json b/shared-data/protocol/fixtures/8/simpleFlexV10CommandsV8.json new file mode 100644 index 00000000000..fbd97d37b50 --- /dev/null +++ b/shared-data/protocol/fixtures/8/simpleFlexV10CommandsV8.json @@ -0,0 +1,1475 @@ +{ + "$otSharedSchema": "#/protocol/schemas/8", + "schemaVersion": 8, + "metadata": { + "protocolName": "Simple test protocol", + "author": "engineering ", + "description": "A short test protocol", + "created": 1223131231, + "tags": ["unitTest"] + }, + "robot": { + "model": "OT-3 Standard", + "deckId": "ot3_standard" + }, + "liquidSchemaId": "opentronsLiquidSchemaV1", + "liquids": { + "waterId": { + "displayName": "Water", + "description": "Liquid H2O", + "displayColor": "#7332a8" + } + }, + "labwareDefinitionSchemaId": "opentronsLabwareSchemaV2", + "labwareDefinitions": { + "opentrons/opentrons_1_trash_1100ml_fixed/1": { + "ordering": [["A1"]], + "metadata": { + "displayCategory": "trash", + "displayVolumeUnits": "mL", + "displayName": "Opentrons Fixed Trash", + "tags": [] + }, + "schemaVersion": 2, + "version": 1, + "namespace": "opentrons", + "dimensions": { + "xDimension": 172.86, + "yDimension": 165.86, + "zDimension": 82 + }, + "parameters": { + "format": "trash", + "isTiprack": false, + "loadName": "opentrons_1_trash_1100ml_fixed", + "isMagneticModuleCompatible": false, + "quirks": ["fixedTrash", "centerMultichannelOnWells"] + }, + "wells": { + "A1": { + "shape": "rectangular", + "yDimension": 165.67, + "xDimension": 107.11, + "totalLiquidVolume": 1100000, + "depth": 77, + "x": 82.84, + "y": 53.56, + "z": 5 + } + }, + "brand": { + "brand": "Opentrons" + }, + "groups": [ + { + "wells": ["A1"], + "metadata": {} + } + ], + "cornerOffsetFromSlot": { + "x": 0, + "y": 0, + "z": 0 + } + }, + "opentrons/opentrons_96_tiprack_10ul/1": { + "ordering": [ + ["A1", "B1", "C1", "D1", "E1", "F1", "G1", "H1"], + ["A2", "B2", "C2", "D2", "E2", "F2", "G2", "H2"], + ["A3", "B3", "C3", "D3", "E3", "F3", "G3", "H3"], + ["A4", "B4", "C4", "D4", "E4", "F4", "G4", "H4"], + ["A5", "B5", "C5", "D5", "E5", "F5", "G5", "H5"], + ["A6", "B6", "C6", "D6", "E6", "F6", "G6", "H6"], + ["A7", "B7", "C7", "D7", 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"circular", + "diameter": 3.27, + "totalLiquidVolume": 10, + "x": 59.38, + "y": 74.24, + "z": 25.49 + }, + "B6": { + "depth": 39.2, + "shape": "circular", + "diameter": 3.27, + "totalLiquidVolume": 10, + "x": 59.38, + "y": 65.24, + "z": 25.49 + }, + "C6": { + "depth": 39.2, + "shape": "circular", + "diameter": 3.27, + "totalLiquidVolume": 10, + "x": 59.38, + "y": 56.24, + "z": 25.49 + }, + "D6": { + "depth": 39.2, + "shape": "circular", + "diameter": 3.27, + "totalLiquidVolume": 10, + "x": 59.38, + "y": 47.24, + "z": 25.49 + }, + "E6": { + "depth": 39.2, + "shape": "circular", + "diameter": 3.27, + "totalLiquidVolume": 10, + "x": 59.38, + "y": 38.24, + "z": 25.49 + }, + "F6": { + "depth": 39.2, + "shape": "circular", + "diameter": 3.27, + "totalLiquidVolume": 10, + "x": 59.38, + "y": 29.24, + "z": 25.49 + }, + "G6": { + "depth": 39.2, + "shape": "circular", + "diameter": 3.27, + "totalLiquidVolume": 10, + "x": 59.38, + "y": 20.24, + "z": 25.49 + }, + "H6": { + "depth": 39.2, + "shape": 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"circular", + "diameter": 3.27, + "totalLiquidVolume": 10, + "x": 86.38, + "y": 38.24, + "z": 25.49 + }, + "F9": { + "depth": 39.2, + "shape": "circular", + "diameter": 3.27, + "totalLiquidVolume": 10, + "x": 86.38, + "y": 29.24, + "z": 25.49 + }, + "G9": { + "depth": 39.2, + "shape": "circular", + "diameter": 3.27, + "totalLiquidVolume": 10, + "x": 86.38, + "y": 20.24, + "z": 25.49 + }, + "H9": { + "depth": 39.2, + "shape": "circular", + "diameter": 3.27, + "totalLiquidVolume": 10, + "x": 86.38, + "y": 11.24, + "z": 25.49 + }, + "A10": { + "depth": 39.2, + "shape": "circular", + "diameter": 3.27, + "totalLiquidVolume": 10, + "x": 95.38, + "y": 74.24, + "z": 25.49 + }, + "B10": { + "depth": 39.2, + "shape": "circular", + "diameter": 3.27, + "totalLiquidVolume": 10, + "x": 95.38, + "y": 65.24, + "z": 25.49 + }, + "C10": { + "depth": 39.2, + "shape": "circular", + "diameter": 3.27, + "totalLiquidVolume": 10, + "x": 95.38, + "y": 56.24, + "z": 25.49 + }, + "D10": { + "depth": 39.2, + "shape": "circular", + "diameter": 3.27, + "totalLiquidVolume": 10, + "x": 95.38, + "y": 47.24, + "z": 25.49 + }, + "E10": { + "depth": 39.2, + "shape": "circular", + "diameter": 3.27, + "totalLiquidVolume": 10, + "x": 95.38, + "y": 38.24, + "z": 25.49 + }, + "F10": { + "depth": 39.2, + "shape": "circular", + "diameter": 3.27, + "totalLiquidVolume": 10, + "x": 95.38, + "y": 29.24, + "z": 25.49 + }, + "G10": { + "depth": 39.2, + "shape": "circular", + "diameter": 3.27, + "totalLiquidVolume": 10, + "x": 95.38, + "y": 20.24, + "z": 25.49 + }, + "H10": { + "depth": 39.2, + "shape": "circular", + "diameter": 3.27, + "totalLiquidVolume": 10, + "x": 95.38, + "y": 11.24, + "z": 25.49 + }, + "A11": { + "depth": 39.2, + "shape": "circular", + "diameter": 3.27, + "totalLiquidVolume": 10, + "x": 104.38, + "y": 74.24, + "z": 25.49 + }, + "B11": { + "depth": 39.2, + "shape": "circular", + "diameter": 3.27, + "totalLiquidVolume": 10, + "x": 104.38, + "y": 65.24, + "z": 25.49 + }, + "C11": { + "depth": 39.2, + "shape": "circular", + "diameter": 3.27, + "totalLiquidVolume": 10, + "x": 104.38, + "y": 56.24, + "z": 25.49 + }, + "D11": { + "depth": 39.2, + "shape": "circular", + "diameter": 3.27, + "totalLiquidVolume": 10, + "x": 104.38, + "y": 47.24, + "z": 25.49 + }, + "E11": { + "depth": 39.2, + "shape": "circular", + "diameter": 3.27, + "totalLiquidVolume": 10, + "x": 104.38, + "y": 38.24, + "z": 25.49 + }, + "F11": { + "depth": 39.2, + "shape": "circular", + "diameter": 3.27, + "totalLiquidVolume": 10, + "x": 104.38, + "y": 29.24, + "z": 25.49 + }, + "G11": { + "depth": 39.2, + "shape": "circular", + "diameter": 3.27, + "totalLiquidVolume": 10, + "x": 104.38, + "y": 20.24, + "z": 25.49 + }, + "H11": { + "depth": 39.2, + "shape": "circular", + "diameter": 3.27, + "totalLiquidVolume": 10, + "x": 104.38, + "y": 11.24, + "z": 25.49 + }, + "A12": { + "depth": 39.2, + "shape": "circular", + "diameter": 3.27, + "totalLiquidVolume": 10, + "x": 113.38, + "y": 74.24, + "z": 25.49 + }, + "B12": { + "depth": 39.2, + "shape": "circular", + "diameter": 3.27, + "totalLiquidVolume": 10, + "x": 113.38, + "y": 65.24, + "z": 25.49 + }, + "C12": { + "depth": 39.2, + "shape": "circular", + "diameter": 3.27, + "totalLiquidVolume": 10, + "x": 113.38, + "y": 56.24, + "z": 25.49 + }, + "D12": { + "depth": 39.2, + "shape": "circular", + "diameter": 3.27, + "totalLiquidVolume": 10, + "x": 113.38, + "y": 47.24, + "z": 25.49 + }, + "E12": { + "depth": 39.2, + "shape": "circular", + "diameter": 3.27, + "totalLiquidVolume": 10, + "x": 113.38, + "y": 38.24, + "z": 25.49 + }, + "F12": { + "depth": 39.2, + "shape": "circular", + "diameter": 3.27, + "totalLiquidVolume": 10, + "x": 113.38, + "y": 29.24, + "z": 25.49 + }, + "G12": { + "depth": 39.2, + "shape": "circular", + "diameter": 3.27, + "totalLiquidVolume": 10, + "x": 113.38, + "y": 20.24, + "z": 25.49 + }, + "H12": { + "depth": 39.2, + "shape": "circular", + "diameter": 3.27, + "totalLiquidVolume": 10, + "x": 113.38, + "y": 11.24, + "z": 25.49 + } + }, + "groups": [ + { + "metadata": {}, + "wells": [ + "A1", + "B1", + "C1", + "D1", + "E1", + "F1", + "G1", + "H1", + "A2", + "B2", + "C2", + "D2", + "E2", + "F2", + "G2", + "H2", + "A3", + "B3", + "C3", + "D3", + "E3", + "F3", + "G3", + "H3", + "A4", + "B4", + "C4", + "D4", + "E4", + "F4", + "G4", + "H4", + "A5", + "B5", + "C5", + "D5", + "E5", + "F5", + "G5", + "H5", + "A6", + "B6", + "C6", + "D6", + "E6", + "F6", + "G6", + "H6", + "A7", + "B7", + "C7", + "D7", + "E7", + "F7", + "G7", + "H7", + "A8", + "B8", + "C8", + "D8", + "E8", + "F8", + "G8", + "H8", + "A9", + "B9", + "C9", + "D9", + "E9", + "F9", + "G9", + "H9", + "A10", + "B10", + "C10", + "D10", + "E10", + "F10", + "G10", + "H10", + "A11", + "B11", + "C11", + "D11", + "E11", + "F11", + "G11", + "H11", + "A12", + "B12", + "C12", + "D12", + "E12", + "F12", + "G12", + "H12" + ] + } + ], + "parameters": { + "format": "96Standard", + "isTiprack": true, + "tipLength": 39.2, + "tipOverlap": 3.29, + "isMagneticModuleCompatible": false, + "loadName": "opentrons_96_tiprack_10ul" + }, + "namespace": "opentrons", + "version": 1, + "schemaVersion": 2, + "cornerOffsetFromSlot": { + "x": 0, + "y": 0, + "z": 0 + } + }, + "example/plate/1": { + "ordering": [ + ["A1", "B1", "C1", "D1"], + ["A2", "B2", "C2", "D2"] + ], + "brand": { + "brand": "foo", + "brandId": [] + }, + "metadata": { + "displayName": "Foo 8 Well Plate 33uL", + "displayCategory": "wellPlate", + "displayVolumeUnits": "µL" + }, + "dimensions": { + "xDimension": 127.75, + "yDimension": 85.5, + "zDimension": 100 + }, + "wells": { + "A1": { + "depth": 25, + "totalLiquidVolume": 33, + "shape": "circular", + "diameter": 10, + "x": 18.21, + "y": 75.43, + "z": 75 + }, + "B1": { + "depth": 25, + "totalLiquidVolume": 33, + "shape": "circular", + "diameter": 10, + "x": 18.21, + "y": 56.15, + "z": 75 + }, + "C1": { + "depth": 25, + "totalLiquidVolume": 33, + "shape": "circular", + "diameter": 10, + "x": 18.21, + "y": 36.87, + "z": 75 + }, + "D1": { + "depth": 25, + "totalLiquidVolume": 33, + "shape": "circular", + "diameter": 10, + "x": 18.21, + "y": 17.59, + "z": 75 + }, + "A2": { + "depth": 25, + "totalLiquidVolume": 33, + "shape": "circular", + "diameter": 10, + "x": 38.1, + "y": 75.43, + "z": 75 + }, + "B2": { + "depth": 25, + "totalLiquidVolume": 33, + "shape": "circular", + "diameter": 10, + "x": 38.1, + "y": 56.15, + "z": 75 + }, + "C2": { + "depth": 25, + "totalLiquidVolume": 33, + "shape": "circular", + "diameter": 10, + "x": 38.1, + "y": 36.87, + "z": 75 + }, + "D2": { + "depth": 25, + "totalLiquidVolume": 33, + "shape": "circular", + "diameter": 10, + "x": 38.1, + "y": 17.59, + "z": 75 + } + }, + "groups": [ + { + "metadata": {}, + "wells": ["A1", "B1", "C1", "A2", "B2", "C2"] + } + ], + "parameters": { + "format": "irregular", + "quirks": [], + "isTiprack": false, + "isMagneticModuleCompatible": false, + "loadName": "foo_8_plate_33ul" + }, + "namespace": "example", + "version": 1, + "schemaVersion": 2, + "cornerOffsetFromSlot": { + "x": 0, + "y": 0, + "z": 0 + } + } + }, + "commandSchemaId": "opentronsCommandSchemaV10", + "commands": [ + { + "commandType": "loadPipette", + "params": { + "pipetteId": "pipetteId", + "pipetteName": "p10_single", + "mount": "left" + } + }, + { + "commandType": "loadModule", + "params": { + "moduleId": "magneticModuleId", + "model": "magneticModuleV2", + "location": { "slotName": "3" } + } + }, + { + "commandType": "loadModule", + "params": { + "moduleId": "temperatureModuleId", + "model": "temperatureModuleV2", + "location": { "slotName": "1" } + } + }, + { + "commandType": "loadLabware", + "params": { + "labwareId": "sourcePlateId", + "loadName": "armadillo_96_wellplate_200ul_pcr_full_skirt", + "namespace": "opentrons", + "version": 1, + "location": { + "moduleId": "temperatureModuleId" + }, + "displayName": "Source Plate" + } + }, + { + "commandType": "loadLabware", + "params": { + "labwareId": "destPlateId", + "loadName": "armadillo_96_wellplate_200ul_pcr_full_skirt", + "namespace": "opentrons", + "version": 1, + "location": { + "moduleId": "magneticModuleId" + }, + "displayName": "Sample Collection Plate" + } + }, + { + "commandType": "loadLabware", + "params": { + "labwareId": "tipRackId", + "location": { "slotName": "8" }, + "loadName": "opentrons_96_tiprack_10ul", + "namespace": "opentrons", + "version": 1, + "displayName": "Opentrons 96 Tip Rack 10 µL" + } + }, + { + "commandType": "loadLabware", + "params": { + "labwareId": "fixedTrash", + "location": { + "slotName": "12" + }, + "loadName": "opentrons_1_trash_1100ml_fixed", + "namespace": "opentrons", + "version": 1, + "displayName": "Trash" + } + }, + { + "commandType": "loadLiquid", + "params": { + "liquidId": "waterId", + "labwareId": "sourcePlateId", + "volumeByWell": { + "A1": 100, + "B1": 100 + } + } + }, + { + "commandType": "home", + "params": {} + }, + { + "commandType": "pickUpTip", + "params": { + "pipetteId": "pipetteId", + "labwareId": "tipRackId", + "wellName": "B1" + } + }, + { + "commandType": "aspirate", + "params": { + "pipetteId": "pipetteId", + "labwareId": "sourcePlateId", + "wellName": "A1", + "volume": 5, + "flowRate": 3, + "wellLocation": { + "origin": "bottom", + "offset": { "x": 0, "y": 0, "z": 2 } + } + } + }, + { + "commandType": "waitForDuration", + "params": { + "seconds": 42 + } + }, + { + "commandType": "dispense", + "params": { + "pipetteId": "pipetteId", + "labwareId": "destPlateId", + "wellName": "B1", + "volume": 4.5, + "flowRate": 2.5, + "wellLocation": { + "origin": "bottom", + "offset": { "x": 0, "y": 0, "z": 1 } + } + } + }, + { + "commandType": "touchTip", + "params": { + "pipetteId": "pipetteId", + "labwareId": "destPlateId", + "wellName": "B1", + "wellLocation": { + "origin": "bottom", + "offset": { "x": 0, "y": 0, "z": 11 } + } + } + }, + { + "commandType": "blowout", + "params": { + "pipetteId": "pipetteId", + "labwareId": "destPlateId", + "wellName": "B1", + "flowRate": 2, + "wellLocation": { + "origin": "bottom", + "offset": { "x": 0, "y": 0, "z": 12 } + } + } + }, + { + "commandType": "moveToCoordinates", + "params": { + "pipetteId": "pipetteId", + "coordinates": { "x": 100, "y": 100, "z": 100 } + } + }, + { + "commandType": "moveToWell", + "params": { + "pipetteId": "pipetteId", + "labwareId": "destPlateId", + "wellName": "B2" + } + }, + { + "commandType": "moveToWell", + "params": { + "pipetteId": "pipetteId", + "labwareId": "destPlateId", + "wellName": "B2", + "wellLocation": { + "origin": "bottom", + "offset": { "x": 2, "y": 3, "z": 10 } + }, + "minimumZHeight": 35, + "forceDirect": true + } + }, + { + "commandType": "dropTip", + "params": { + "pipetteId": "pipetteId", + "labwareId": "fixedTrash", + "wellName": "A1" + } + }, + { + "commandType": "waitForResume", + "params": { + "message": "pause command" + } + }, + { + "commandType": "moveToCoordinates", + "params": { + "pipetteId": "pipetteId", + "coordinates": { "x": 0, "y": 0, "z": 0 }, + "minimumZHeight": 35, + "forceDirect": true + } + }, + { + "commandType": "moveRelative", + "params": { + "pipetteId": "pipetteId", + "axis": "x", + "distance": 1 + } + }, + { + "commandType": "moveRelative", + "params": { + "pipetteId": "pipetteId", + "axis": "y", + "distance": 0.1 + } + }, + { + "commandType": "savePosition", + "params": { + "pipetteId": "pipetteId" + } + }, + { + "commandType": "moveRelative", + "params": { + "pipetteId": "pipetteId", + "axis": "z", + "distance": 10 + } + }, + { + "commandType": "savePosition", + "params": { + "pipetteId": "pipetteId", + "positionId": "positionId" + } + } + ], + "commandAnnotationSchemaId": "opentronsCommandAnnotationSchemaV1", + "commandAnnotations": [ + { + "commandKeys": [ + "1abc123", + "2abc123", + "3abc123", + "4abc123", + "5abc123", + "6abc123", + "7abc123" + ], + "annotationType": "custom" + } + ] +} diff --git a/shared-data/python/opentrons_shared_data/command/__init__.py b/shared-data/python/opentrons_shared_data/command/__init__.py index f1b58056638..a0d75a8aaa6 100644 --- a/shared-data/python/opentrons_shared_data/command/__init__.py +++ b/shared-data/python/opentrons_shared_data/command/__init__.py @@ -1,27 +1,37 @@ """opentrons_shared_data.command: functions command schemas.""" from pathlib import Path +from functools import cache import json import os import re +from logging import getLogger -from opentrons_shared_data.errors.exceptions import InvalidProtocolData, PythonException +from opentrons_shared_data.errors.exceptions import ( + InvalidProtocolData, + PythonException, + InvalidStoredData, +) from ..load import load_shared_data, get_shared_data_root +LOG = getLogger(__name__) + SCHEMA_REF_VERSION_RE = re.compile(r"opentronsCommandSchemaV(\d+)") def get_newest_schema_version() -> str: """Get the version string of the most modern command schema currently in shared-data.""" - command_schemas_dir = get_shared_data_root() / "command" / "schemas" - command_schemas = os.listdir(command_schemas_dir) - all_schema_versions = [] - for schema_file_name in command_schemas: - schema_version_match = re.match(r"(\d+).json", schema_file_name) - if schema_version_match is not None: - all_schema_versions.append(int(schema_version_match.group(1))) + schema_ids = known_schema_ids() + max_version = 0 + for schema_id in schema_ids: + ref_version_match = SCHEMA_REF_VERSION_RE.match(schema_id) + if not ref_version_match: + continue + ref_version = int(ref_version_match.group(1)) + if ref_version > max_version: + max_version = ref_version - return str(max(all_schema_versions)) + return str(max_version) def load_schema_string(version: str) -> str: @@ -50,3 +60,52 @@ def schema_version_from_ref(ref: str) -> str: detail={"ref": ref, "type": "bad-schema-ref", "schema-kind": "command"}, ) return version.group(1) + + +def _schema_id_from_file(schema_file_name: str) -> str: + schema_version_match = re.match(r"^.*(\d+).json$", schema_file_name) + if schema_version_match is None: + raise InvalidStoredData( + message=f"Command schema {schema_file_name} is not named appropriately for its version", + detail={"type": "bad-schema-name", "schema-kind": "command"}, + ) + try: + schema_content = json.load(open(schema_file_name)) + except json.JSONDecodeError as jde: + raise InvalidStoredData( + message=f"Command schema {schema_file_name} is not valid json", + detail={"type": "bad-schema-json", "schema-kind": "command"}, + wrapping=[PythonException(jde)], + ) from jde + + try: + schema_id: str = schema_content["$id"] + except KeyError as ke: + raise InvalidStoredData( + message=f"Command schema {schema_file_name} has no $id", + detail={"type": "bad-schema-json", "schema-kind": "command"}, + wrapping=[PythonException(ke)], + ) from ke + if not SCHEMA_REF_VERSION_RE.match(schema_id): + raise InvalidStoredData( + message=f"Command schema {schema_file_name} has an invalid id {schema_id} that does not match opentronsCommandSchema#" + ) + return schema_id + + +@cache +def known_schema_ids() -> list[str]: + """Get a list of all known command schema IDs.""" + command_schemas_dir = get_shared_data_root() / "command" / "schemas" + command_schemas = os.listdir(command_schemas_dir) + all_schema_ids = [] + for schema_file_name in command_schemas: + try: + all_schema_ids.append( + _schema_id_from_file(str(command_schemas_dir / schema_file_name)) + ) + except Exception: + LOG.exception( + f"Could not load command schema from {str(command_schemas_dir/schema_file_name)}, skipping" + ) + return all_schema_ids diff --git a/shared-data/python/opentrons_shared_data/protocol/models/protocol_schema_v8.py b/shared-data/python/opentrons_shared_data/protocol/models/protocol_schema_v8.py index ce5b814d73f..11beddb96c0 100644 --- a/shared-data/python/opentrons_shared_data/protocol/models/protocol_schema_v8.py +++ b/shared-data/python/opentrons_shared_data/protocol/models/protocol_schema_v8.py @@ -1,80 +1,23 @@ -from pydantic import BaseModel, Field, Extra -from typing import Any, List, Optional, Dict, Union +from enum import Enum +from typing import Any, List, Optional, Dict from typing_extensions import Literal +from pydantic import BaseModel, Field, Extra + from opentrons_shared_data.labware.labware_definition import LabwareDefinition +from opentrons_shared_data.command import known_schema_ids from .shared_models import ( Liquid, - Location, - ProfileStep, - WellLocation, - OffsetVector, Metadata, DesignerApplication, Robot, - NozzleConfigurationParams, ) -# TODO (tamar 3/15/22): split apart all the command payloads when we tackle #9583 -class Params(BaseModel): - slotName: Optional[str] - axes: Optional[List[str]] - pipetteId: Optional[str] - mount: Optional[str] - moduleId: Optional[str] - location: Optional[Union[Location, Literal["offDeck"]]] - labwareId: Optional[str] - displayName: Optional[str] - liquidId: Optional[str] - volumeByWell: Optional[Dict[str, Any]] - wellName: Optional[str] - volume: Optional[float] - flowRate: Optional[float] - wellLocation: Optional[WellLocation] - waitForResume: Optional[Literal[True]] - seconds: Optional[float] - minimumZHeight: Optional[float] - forceDirect: Optional[bool] - speed: Optional[float] - message: Optional[str] - coordinates: Optional[OffsetVector] - axis: Optional[str] - distance: Optional[float] - positionId: Optional[str] - temperature: Optional[float] - celsius: Optional[float] - blockMaxVolumeUl: Optional[float] - rpm: Optional[float] - height: Optional[float] - offset: Optional[OffsetVector] - profile: Optional[List[ProfileStep]] - radius: Optional[float] - newLocation: Optional[Union[Location, Literal["offDeck"]]] - strategy: Optional[str] - # schema v7 add-ons - homeAfter: Optional[bool] - alternateDropLocation: Optional[bool] - holdTimeSeconds: Optional[float] - maintenancePosition: Optional[str] - pipetteName: Optional[str] - model: Optional[str] - loadName: Optional[str] - namespace: Optional[str] - version: Optional[int] - pushOut: Optional[float] - pickUpOffset: Optional[OffsetVector] - dropOffset: Optional[OffsetVector] - # schema v8 add-ons - addressableAreaName: Optional[str] - configurationParams: Optional[NozzleConfigurationParams] - stayAtHighestPossibleZ: Optional[bool] - - class Command(BaseModel): commandType: str - params: Params + params: Dict[str, Any] key: Optional[str] @@ -86,6 +29,11 @@ class Config: extra = Extra.allow +CommandSchemaId = Enum( # type: ignore[misc] + "CommandSchemaId", ((schema_id, schema_id) for schema_id in known_schema_ids()) +) + + class ProtocolSchemaV8(BaseModel): otSharedSchema: Literal["#/protocol/schemas/8"] = Field( ..., @@ -100,7 +48,7 @@ class ProtocolSchemaV8(BaseModel): liquids: Dict[str, Liquid] labwareDefinitionSchemaId: Literal["opentronsLabwareSchemaV2"] labwareDefinitions: Dict[str, LabwareDefinition] - commandSchemaId: Literal["opentronsCommandSchemaV8", "opentronsCommandSchemaV9"] + commandSchemaId: CommandSchemaId commands: List[Command] commandAnnotationSchemaId: Literal["opentronsCommandAnnotationSchemaV1"] commandAnnotations: List[CommandAnnotation] diff --git a/shared-data/python/tests/command/test_known_schema_ids.py b/shared-data/python/tests/command/test_known_schema_ids.py new file mode 100644 index 00000000000..6ec282428ac --- /dev/null +++ b/shared-data/python/tests/command/test_known_schema_ids.py @@ -0,0 +1,9 @@ +from opentrons_shared_data.load import get_shared_data_root +from opentrons_shared_data.command import known_schema_ids + + +def test_known_schema_ids() -> None: + schema_paths = get_shared_data_root() / "command" / "schemas" + names = [filename.stem for filename in schema_paths.iterdir()] + ids = [f"opentronsCommandSchemaV{version}" for version in names] + assert sorted(ids) == sorted(known_schema_ids()) diff --git a/shared-data/python/tests/protocol/test_protocol_schema_v8.py b/shared-data/python/tests/protocol/test_protocol_schema_v8.py index 0928441d328..63d00db571d 100644 --- a/shared-data/python/tests/protocol/test_protocol_schema_v8.py +++ b/shared-data/python/tests/protocol/test_protocol_schema_v8.py @@ -11,10 +11,12 @@ def test_v8_types(defpath): def_data = load_shared_data(defpath) def_model = protocol_schema_v8.ProtocolSchemaV8.parse_raw(def_data) - def_dict_from_model = def_model.dict( - exclude_unset=True, - # 'schemaVersion' in python is '$schemaVersion' in JSON - by_alias=True, + def_dict_from_model = json.loads( + def_model.json( + exclude_unset=True, + # 'schemaVersion' in python is '$schemaVersion' in JSON + by_alias=True, + ) ) expected_def_dict = json.loads(def_data) assert def_dict_from_model == expected_def_dict From 04842958a19a53dc7ee054c98ebd686c2090e1ac Mon Sep 17 00:00:00 2001 From: Josh McVey Date: Fri, 4 Oct 2024 14:57:43 -0500 Subject: [PATCH 08/27] test(analyses): 8.0.0 testing protocols into analyses battery (#16407) # Overview Get these into edge ASAP! - [x] Josh reviewed the snapshots PR making sure that protocols with **X** had errors in the snapshot and **S** do not. Not much else to review. We need these in so that PRs to edge are also running against these snapshots. --------- Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: y3rsh <502770+y3rsh@users.noreply.github.com> --- analyses-snapshot-testing/Makefile | 23 + analyses-snapshot-testing/README.md | 20 + .../automation/data/protocols.py | 81 + .../data/protocols_with_overrides.py | 69 + .../citools/Dockerfile.server | 31 + .../protocols/Flex_S_v2_20_1000M_Simple.py | 93 + ...S_v2_20_8_None_PARTIAL_COLUMN_HappyPath.py | 109 + .../Flex_S_v2_20_8_None_SINGLE_HappyPath.py | 131 + ...S_v2_20_8_None_SINGLE_TubeRackCollision.py | 65 + .../Flex_S_v2_20_8_PARTIAL_COLUMN_Overhang.py | 150 + .../Flex_S_v2_20_8_TipsDontMatchWells.py | 87 + .../protocols/Flex_S_v2_20_96_AllCorners.py | 296 + .../files/protocols/Flex_S_v2_20_96_LLD.py | 93 + .../Flex_S_v2_20_96_None_COLUMN_HappyPath.py | 121 + .../Flex_S_v2_20_96_None_Column3_SINGLE_.py | 118 + .../Flex_S_v2_20_96_None_ROW_HappyPath.py | 121 + ...lex_S_v2_20_96_None_SINGLE_4Corners50ul.py | 66 + ...v2_20_96_None_SINGLE_HappyPathNorthSide.py | 143 + ...v2_20_96_None_SINGLE_HappyPathSouthSide.py | 143 + ..._v2_20_96_None_SINGLE_TubeRackCollision.py | 68 + .../protocols/Flex_S_v2_20_96_Reservoir.py | 91 + .../files/protocols/Flex_S_v2_20_P50_LPD.py | 122 + .../Flex_S_v2_20_P50_LPD_wet_tip_scenarios.py | 169 + .../Flex_S_v2_20_P50_touch_tip_directly.py | 66 + .../protocols/Flex_S_v2_20_P8X1000_P50_LLD.py | 106 + ..._v2_20_96_None_Overrides_TooTallLabware.py | 504 + ...v2_20_96_and_8_Overrides_InvalidConfigs.py | 185 + ...e_PARTIAL_COLUMN_HappyPathMixedTipRacks.py | 111 + .../OT2_S_v2_20_8_None_SINGLE_HappyPath.py | 135 + ...S_v2_20_8_None_SINGLE_TubeRackCollision.py | 64 + ...T2_S_v2_20_P20M_PARTIAL_COLUMN_Overhang.py | 155 + .../protocols/OT2_S_v2_20_P20M_Simple.py | 90 + ...2_S_v2_20_P300M_PARTIAL_COLUMN_Overhang.py | 151 + .../protocols/OT2_S_v2_20_P300M_Simple.py | 94 + .../protocols/OT2_S_v2_20_P50_touch_tip.py | 52 + .../OT2_X_v2_20_8_Overrides_InvalidConfigs.py | 151 + .../files/templates/basic_flex_rtp_v1.1.py | 522 + ...s_TooTallLabware_Override_south_west].json | 1500 + ...es_TooTallLabware_Override_north_row].json | 1500 + ...][Flex_S_v2_20_96_None_ROW_HappyPath].json | 6224 +++ ...c2386b92][Flex_S_v2_20_96_AllCorners].json | 33713 ++++++++++++++++ ...a9c68b][Flex_S_v2_20_P8X1000_P50_LLD].json | 6191 +++ ...errides_TooTallLabware_Override_west].json | 1500 + ...ooTallLabware_Override_mix_collision].json | 2746 ++ ...ide_distribute_destination_collision].json | 3930 ++ ...e_Override_transfer_source_collision].json | 3897 ++ ..._TooTallLabware_Override_east_column].json | 1500 + ..._S_v2_20_96_None_SINGLE_4Corners50ul].json | 3036 ++ ...20_96_None_SINGLE_HappyPathNorthSide].json | 9380 +++++ ...allLabware_Override_bottom_left_edge].json | 1268 + ...allLabware_Override_bottom_left_edge].json | 1268 + ...es_TooTallLabware_Override_south_row].json | 1500 + ...ARTIAL_COLUMN_HappyPathMixedTipRacks].json | 19487 +++++++++ ...Override_eight_partial_column_no_end].json | 1260 + ...ide_eight_partial_column_bottom_left].json | 1296 + ...ooTallLabware_Override_c3_right_edge].json | 1268 + ...Override_eight_partial_column_no_end].json | 2414 ++ ...Override_ninety_six_partial_column_2].json | 1260 + ...Override_ninety_six_partial_column_1].json | 1260 + ...s_TooTallLabware_Override_south_east].json | 1500 + ...errides_TooTallLabware_Override_east].json | 1500 + ...lex_S_v2_20_96_None_COLUMN_HappyPath].json | 6224 +++ ...de_consolidate_destination_collision].json | 3963 ++ ...2_20_8_None_PARTIAL_COLUMN_HappyPath].json | 5041 +++ ...lidConfigs_Override_return_tip_error].json | 4939 +++ ..._TooTallLabware_Override_west_column].json | 1500 + ...rrides_TooTallLabware_Override_south].json | 1500 + ...figs_Override_drop_tip_with_location].json | 3785 ++ ...de_eight_partial_column_bottom_right].json | 2480 ++ ...s_TooTallLabware_Override_north_west].json | 1500 + ...20_96_None_SINGLE_HappyPathSouthSide].json | 9380 +++++ ...ide_eight_partial_column_bottom_left].json | 2450 ++ ...lidConfigs_Override_return_tip_error].json | 3785 ++ ...figs_Override_drop_tip_with_location].json | 4939 +++ ...rride_transfer_destination_collision].json | 3930 ++ ...rrides_TooTallLabware_Override_north].json | 1500 + ...llLabware_Override_bottom_right_edge].json | 1268 + ...Flex_S_v2_20_8_None_SINGLE_HappyPath].json | 7137 ++++ ...de_eight_partial_column_bottom_right].json | 1326 + ...hot[d2c818bf00][Flex_S_v2_20_P50_LPD].json | 5125 +++ ...[OT2_S_v2_20_8_None_SINGLE_HappyPath].json | 8190 ++++ ...Override_ninety_six_partial_column_3].json | 1260 + ...des_TooTallLabware_Override_top_edge].json | 1268 + ...Flex_S_v2_20_96_None_Column3_SINGLE_].json | 26859 ++++++++++++ ...verride_consolidate_source_collision].json | 3897 ++ ...Override_distribute_source_collision].json | 3897 ++ 86 files changed, 232337 insertions(+) create mode 100644 analyses-snapshot-testing/citools/Dockerfile.server create mode 100644 analyses-snapshot-testing/files/protocols/Flex_S_v2_20_1000M_Simple.py create mode 100644 analyses-snapshot-testing/files/protocols/Flex_S_v2_20_8_None_PARTIAL_COLUMN_HappyPath.py create mode 100644 analyses-snapshot-testing/files/protocols/Flex_S_v2_20_8_None_SINGLE_HappyPath.py create mode 100644 analyses-snapshot-testing/files/protocols/Flex_S_v2_20_8_None_SINGLE_TubeRackCollision.py create mode 100644 analyses-snapshot-testing/files/protocols/Flex_S_v2_20_8_PARTIAL_COLUMN_Overhang.py create mode 100644 analyses-snapshot-testing/files/protocols/Flex_S_v2_20_8_TipsDontMatchWells.py create mode 100644 analyses-snapshot-testing/files/protocols/Flex_S_v2_20_96_AllCorners.py create mode 100644 analyses-snapshot-testing/files/protocols/Flex_S_v2_20_96_LLD.py create mode 100644 analyses-snapshot-testing/files/protocols/Flex_S_v2_20_96_None_COLUMN_HappyPath.py create mode 100644 analyses-snapshot-testing/files/protocols/Flex_S_v2_20_96_None_Column3_SINGLE_.py create mode 100644 analyses-snapshot-testing/files/protocols/Flex_S_v2_20_96_None_ROW_HappyPath.py create mode 100644 analyses-snapshot-testing/files/protocols/Flex_S_v2_20_96_None_SINGLE_4Corners50ul.py create mode 100644 analyses-snapshot-testing/files/protocols/Flex_S_v2_20_96_None_SINGLE_HappyPathNorthSide.py create mode 100644 analyses-snapshot-testing/files/protocols/Flex_S_v2_20_96_None_SINGLE_HappyPathSouthSide.py create mode 100644 analyses-snapshot-testing/files/protocols/Flex_S_v2_20_96_None_SINGLE_TubeRackCollision.py create mode 100644 analyses-snapshot-testing/files/protocols/Flex_S_v2_20_96_Reservoir.py create mode 100644 analyses-snapshot-testing/files/protocols/Flex_S_v2_20_P50_LPD.py create mode 100644 analyses-snapshot-testing/files/protocols/Flex_S_v2_20_P50_LPD_wet_tip_scenarios.py create mode 100644 analyses-snapshot-testing/files/protocols/Flex_S_v2_20_P50_touch_tip_directly.py create mode 100644 analyses-snapshot-testing/files/protocols/Flex_S_v2_20_P8X1000_P50_LLD.py create mode 100644 analyses-snapshot-testing/files/protocols/Flex_X_v2_20_96_None_Overrides_TooTallLabware.py create mode 100644 analyses-snapshot-testing/files/protocols/Flex_X_v2_20_96_and_8_Overrides_InvalidConfigs.py create mode 100644 analyses-snapshot-testing/files/protocols/OT2_S_v2_20_8_None_PARTIAL_COLUMN_HappyPathMixedTipRacks.py create mode 100644 analyses-snapshot-testing/files/protocols/OT2_S_v2_20_8_None_SINGLE_HappyPath.py create mode 100644 analyses-snapshot-testing/files/protocols/OT2_S_v2_20_8_None_SINGLE_TubeRackCollision.py create mode 100644 analyses-snapshot-testing/files/protocols/OT2_S_v2_20_P20M_PARTIAL_COLUMN_Overhang.py create mode 100644 analyses-snapshot-testing/files/protocols/OT2_S_v2_20_P20M_Simple.py create mode 100644 analyses-snapshot-testing/files/protocols/OT2_S_v2_20_P300M_PARTIAL_COLUMN_Overhang.py create mode 100644 analyses-snapshot-testing/files/protocols/OT2_S_v2_20_P300M_Simple.py create mode 100644 analyses-snapshot-testing/files/protocols/OT2_S_v2_20_P50_touch_tip.py create mode 100644 analyses-snapshot-testing/files/protocols/OT2_X_v2_20_8_Overrides_InvalidConfigs.py create mode 100644 analyses-snapshot-testing/files/templates/basic_flex_rtp_v1.1.py create mode 100644 analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[09676b9f7e][Flex_X_v2_20_96_None_Overrides_TooTallLabware_Override_south_west].json create mode 100644 analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[0b42cfc151][Flex_X_v2_20_96_None_Overrides_TooTallLabware_Override_north_row].json create mode 100644 analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[109b7ad1f0][Flex_S_v2_20_96_None_ROW_HappyPath].json create mode 100644 analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[10c2386b92][Flex_S_v2_20_96_AllCorners].json create mode 100644 analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[13e5a9c68b][Flex_S_v2_20_P8X1000_P50_LLD].json create mode 100644 analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[196ec488f7][Flex_X_v2_20_96_None_Overrides_TooTallLabware_Override_west].json create mode 100644 analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[255d014c70][Flex_X_v2_20_96_None_Overrides_TooTallLabware_Override_mix_collision].json create mode 100644 analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[29e143f047][Flex_X_v2_20_96_None_Overrides_TooTallLabware_Override_distribute_destination_collision].json create mode 100644 analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[29eec5a85a][Flex_X_v2_20_96_None_Overrides_TooTallLabware_Override_transfer_source_collision].json create mode 100644 analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[2cc8efae68][Flex_X_v2_20_96_None_Overrides_TooTallLabware_Override_east_column].json create mode 100644 analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[30c05024e8][Flex_S_v2_20_96_None_SINGLE_4Corners50ul].json create mode 100644 analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[31d1aec819][Flex_S_v2_20_96_None_SINGLE_HappyPathNorthSide].json create mode 100644 analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[376765183a0][Flex_X_v2_20_96_None_Overrides_TooTallLabware_Override_bottom_left_edge].json create mode 100644 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mode 100644 analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[549cc904ac][Flex_X_v2_20_96_None_Overrides_TooTallLabware_Override_c3_right_edge].json create mode 100644 analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[54b0b509cd][OT2_X_v2_20_8_Overrides_InvalidConfigs_Override_eight_partial_column_no_end].json create mode 100644 analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[5edb9b4de3][Flex_X_v2_20_96_and_8_Overrides_InvalidConfigs_Override_ninety_six_partial_column_2].json create mode 100644 analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[6122c72996][Flex_X_v2_20_96_and_8_Overrides_InvalidConfigs_Override_ninety_six_partial_column_1].json create mode 100644 analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[675d2c2562][Flex_X_v2_20_96_None_Overrides_TooTallLabware_Override_south_east].json create mode 100644 analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[68614da0b3][Flex_X_v2_20_96_None_Overrides_TooTallLabware_Override_east].json create mode 100644 analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[6c20d6c570][Flex_S_v2_20_96_None_COLUMN_HappyPath].json create mode 100644 analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[6e2f6f10c5][Flex_X_v2_20_96_None_Overrides_TooTallLabware_Override_consolidate_destination_collision].json create mode 100644 analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[733c9cdf62][Flex_S_v2_20_8_None_PARTIAL_COLUMN_HappyPath].json create mode 100644 analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[7583faec7c][OT2_X_v2_20_8_Overrides_InvalidConfigs_Override_return_tip_error].json create mode 100644 analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[7e7a90041b][Flex_X_v2_20_96_None_Overrides_TooTallLabware_Override_west_column].json create mode 100644 analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[8a663305c4][Flex_X_v2_20_96_None_Overrides_TooTallLabware_Override_south].json create mode 100644 analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[8b07e799f6][Flex_X_v2_20_96_and_8_Overrides_InvalidConfigs_Override_drop_tip_with_location].json create mode 100644 analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[93b724671e][OT2_X_v2_20_8_Overrides_InvalidConfigs_Override_eight_partial_column_bottom_right].json create mode 100644 analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[a0b755a1a1][Flex_X_v2_20_96_None_Overrides_TooTallLabware_Override_north_west].json create mode 100644 analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[a8528e52b4][Flex_S_v2_20_96_None_SINGLE_HappyPathSouthSide].json create mode 100644 analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[acefe91275][OT2_X_v2_20_8_Overrides_InvalidConfigs_Override_eight_partial_column_bottom_left].json create mode 100644 analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[afd5d372a9][Flex_X_v2_20_96_and_8_Overrides_InvalidConfigs_Override_return_tip_error].json create mode 100644 analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[b79134ab8a][OT2_X_v2_20_8_Overrides_InvalidConfigs_Override_drop_tip_with_location].json create mode 100644 analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[bc049301c1][Flex_X_v2_20_96_None_Overrides_TooTallLabware_Override_transfer_destination_collision].json create mode 100644 analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[c0435f08da][Flex_X_v2_20_96_None_Overrides_TooTallLabware_Override_north].json create mode 100644 analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[c343dfb5a0][Flex_X_v2_20_96_None_Overrides_TooTallLabware_Override_bottom_right_edge].json create mode 100644 analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[cc26c104b4][Flex_S_v2_20_8_None_SINGLE_HappyPath].json create mode 100644 analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[d0154b1493][Flex_X_v2_20_96_and_8_Overrides_InvalidConfigs_Override_eight_partial_column_bottom_right].json create mode 100644 analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[d2c818bf00][Flex_S_v2_20_P50_LPD].json create mode 100644 analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[d979799443][OT2_S_v2_20_8_None_SINGLE_HappyPath].json create mode 100644 analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[db1fae41ec][Flex_X_v2_20_96_and_8_Overrides_InvalidConfigs_Override_ninety_six_partial_column_3].json create mode 100644 analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[e84e23a4ea][Flex_X_v2_20_96_None_Overrides_TooTallLabware_Override_top_edge].json create mode 100644 analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[e8f451df45][Flex_S_v2_20_96_None_Column3_SINGLE_].json create mode 100644 analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[ed26635ff7][Flex_X_v2_20_96_None_Overrides_TooTallLabware_Override_consolidate_source_collision].json create mode 100644 analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[f86713b4d4][Flex_X_v2_20_96_None_Overrides_TooTallLabware_Override_distribute_source_collision].json diff --git a/analyses-snapshot-testing/Makefile b/analyses-snapshot-testing/Makefile index e0aa23a8415..fff00bbe3c1 100644 --- a/analyses-snapshot-testing/Makefile +++ b/analyses-snapshot-testing/Makefile @@ -89,3 +89,26 @@ build-opentrons-analysis: .PHONY: generate-protocols generate-protocols: python -m pipenv run python -m automation.data.protocol_registry + + +OPENTRONS_VERSION ?= edge +export OPENTRONS_VERSION + +.PHONY: build-rs +build-rs: + @echo "Building docker image for opentrons-robot-server:$(OPENTRONS_VERSION)" + @echo "Cache is always busted to ensure latest version of the code is used" + @echo "If you want to build a different version, run 'make build-rs OPENTRONS_VERSION=chore_release-8.0.0'" + docker build --build-arg OPENTRONS_VERSION=$(OPENTRONS_VERSION) --build-arg CACHEBUST=$(CACHEBUST) -t opentrons-robot-server:$(OPENTRONS_VERSION) -f citools/Dockerfile.server . + +.PHONY: run-flex +run-flex: + @echo "Running opentrons-robot-server:$(OPENTRONS_VERSION)" + @echo "If you want to run a different version, run 'make run-flex OPENTRONS_VERSION=chore_release-8.0.0'" + docker run -p 31950:31950 --env-file ../robot-server/dev-flex.env opentrons-robot-server:$(OPENTRONS_VERSION) + +.PHONY: run-ot2 +run-ot2: + @echo "Running opentrons-robot-server:$(OPENTRONS_VERSION)" + @echo "If you want to run a different version, run 'make run-ot2 OPENTRONS_VERSION=chore_release-8.0.0'" + docker run -p 31950:31950 --env-file ../robot-server/dev.env opentrons-robot-server:$(OPENTRONS_VERSION) diff --git a/analyses-snapshot-testing/README.md b/analyses-snapshot-testing/README.md index 1ed330efefe..51a8e194ca1 100644 --- a/analyses-snapshot-testing/README.md +++ b/analyses-snapshot-testing/README.md @@ -14,6 +14,12 @@ - In CI this is the `SNAPSHOT_REF`. This is the branch or tag of the test code/snapshots that analyses generated will be compared to. - The `ANALYSIS_REF` is the branch or tag that you want analyses generated from. +## Build the opentrons-analysis image + +> This ALWAYS gets the remote code pushed to Opentrons/opentrons for the specified ANALYSIS_REF + +`make build-opentrons-analysis ANALYSIS_REF=chore_release-8.0.0` + ## Running the tests locally - Compare the current branch snapshots to analyses generated from the edge branch @@ -38,3 +44,17 @@ - `make snapshot-test PROTOCOL_NAMES=Flex_S_v2_19_Illumina_DNA_PCR_Free OVERRIDE_PROTOCOL_NAMES=none` - `make snapshot-test PROTOCOL_NAMES=none OVERRIDE_PROTOCOL_NAMES=Flex_X_v2_18_NO_PIPETTES_Overrides_BadTypesInRTP` - `make snapshot-test PROTOCOL_NAMES="Flex_S_v2_19_Illumina_DNA_PCR_Free,OT2_S_v2_18_P300M_P20S_HS_TC_TM_SmokeTestV3" OVERRIDE_PROTOCOL_NAMES=none` + +## Running a Flex just like `make -C robot-server dev-flex` + +> This ALWAYS gets the remote code pushed to Opentrons/opentrons for the specified OPENTRONS_VERSION + +```shell +cd analyses-snapshot-testing \ +&& make build-rs OPENTRONS_VERSION=chore_release-8.0.0 \ +&& make run-rs OPENTRONS_VERSION=chore_release-8.0.0` +``` + +### Default OPENTRONS_VERSION=edge in the Makefile so you can omit it if you want latest edge + +`cd analyses-snapshot-testing && make build-rs && make run-rs` diff --git a/analyses-snapshot-testing/automation/data/protocols.py b/analyses-snapshot-testing/automation/data/protocols.py index 580c9183d9d..ada74a736e0 100644 --- a/analyses-snapshot-testing/automation/data/protocols.py +++ b/analyses-snapshot-testing/automation/data/protocols.py @@ -641,6 +641,74 @@ class Protocols: robot="Flex", ) + # analyses-snapshot-testing/files/protocols/Flex_S_v2_20_8_None_PARTIAL_COLUMN_HappyPath.py + Flex_S_v2_20_8_None_PARTIAL_COLUMN_HappyPath: Protocol = Protocol( + file_stem="Flex_S_v2_20_8_None_PARTIAL_COLUMN_HappyPath", + file_extension="py", + robot="Flex", + ) + # analyses-snapshot-testing/files/protocols/Flex_S_v2_20_8_None_SINGLE_HappyPath.py + Flex_S_v2_20_8_None_SINGLE_HappyPath: Protocol = Protocol( + file_stem="Flex_S_v2_20_8_None_SINGLE_HappyPath", + file_extension="py", + robot="Flex", + ) + # analyses-snapshot-testing/files/protocols/Flex_S_v2_20_96_AllCorners.py + Flex_S_v2_20_96_AllCorners: Protocol = Protocol( + file_stem="Flex_S_v2_20_96_AllCorners", + file_extension="py", + robot="Flex", + ) + # analyses-snapshot-testing/files/protocols/Flex_S_v2_20_96_None_COLUMN_HappyPath.py + Flex_S_v2_20_96_None_COLUMN_HappyPath: Protocol = Protocol( + file_stem="Flex_S_v2_20_96_None_COLUMN_HappyPath", + file_extension="py", + robot="Flex", + ) + # analyses-snapshot-testing/files/protocols/Flex_S_v2_20_96_None_Column3_SINGLE_.py + Flex_S_v2_20_96_None_Column3_SINGLE_: Protocol = Protocol( + file_stem="Flex_S_v2_20_96_None_Column3_SINGLE_", + file_extension="py", + robot="Flex", + ) + # analyses-snapshot-testing/files/protocols/Flex_S_v2_20_96_None_ROW_HappyPath.py + Flex_S_v2_20_96_None_ROW_HappyPath: Protocol = Protocol( + file_stem="Flex_S_v2_20_96_None_ROW_HappyPath", + file_extension="py", + robot="Flex", + ) + # analyses-snapshot-testing/files/protocols/Flex_S_v2_20_96_None_SINGLE_4Corners50ul.py + Flex_S_v2_20_96_None_SINGLE_4Corners50ul: Protocol = Protocol( + file_stem="Flex_S_v2_20_96_None_SINGLE_4Corners50ul", + file_extension="py", + robot="Flex", + ) + # analyses-snapshot-testing/files/protocols/Flex_S_v2_20_96_None_SINGLE_HappyPathNorthSide.py + Flex_S_v2_20_96_None_SINGLE_HappyPathNorthSide: Protocol = Protocol( + file_stem="Flex_S_v2_20_96_None_SINGLE_HappyPathNorthSide", + file_extension="py", + robot="Flex", + ) + # analyses-snapshot-testing/files/protocols/Flex_S_v2_20_96_None_SINGLE_HappyPathSouthSide.py + Flex_S_v2_20_96_None_SINGLE_HappyPathSouthSide: Protocol = Protocol( + file_stem="Flex_S_v2_20_96_None_SINGLE_HappyPathSouthSide", + file_extension="py", + robot="Flex", + ) + + # analyses-snapshot-testing/files/protocols/Flex_S_v2_20_P8X1000_P50_LLD.py + Flex_S_v2_20_P8X1000_P50_LLD: Protocol = Protocol( + file_stem="Flex_S_v2_20_P8X1000_P50_LLD", + file_extension="py", + robot="Flex", + ) + # analyses-snapshot-testing/files/protocols/Flex_S_v2_20_P50_LPD.py + Flex_S_v2_20_P50_LPD: Protocol = Protocol( + file_stem="Flex_S_v2_20_P50_LPD", + file_extension="py", + robot="Flex", + ) + OT2_X_v2_18_None_None_duplicateRTPVariableName: Protocol = Protocol( file_stem="OT2_X_v2_18_None_None_duplicateRTPVariableName", file_extension="py", @@ -677,6 +745,19 @@ class Protocols: robot="OT2", ) + # analyses-snapshot-testing/files/protocols/OT2_S_v2_20_8_None_PARTIAL_COLUMN_HappyPathMixedTipRacks.py + OT2_S_v2_20_8_None_PARTIAL_COLUMN_HappyPathMixedTipRacks: Protocol = Protocol( + file_stem="OT2_S_v2_20_8_None_PARTIAL_COLUMN_HappyPathMixedTipRacks", + file_extension="py", + robot="OT2", + ) + # analyses-snapshot-testing/files/protocols/OT2_S_v2_20_8_None_SINGLE_HappyPath.py + OT2_S_v2_20_8_None_SINGLE_HappyPath: Protocol = Protocol( + file_stem="OT2_S_v2_20_8_None_SINGLE_HappyPath", + file_extension="py", + robot="OT2", + ) + ########################################################################################################## # Begin Protocol Library Protocols ####################################################################### ########################################################################################################## diff --git a/analyses-snapshot-testing/automation/data/protocols_with_overrides.py b/analyses-snapshot-testing/automation/data/protocols_with_overrides.py index ff4a900e58d..5018a848c31 100644 --- a/analyses-snapshot-testing/automation/data/protocols_with_overrides.py +++ b/analyses-snapshot-testing/automation/data/protocols_with_overrides.py @@ -38,3 +38,72 @@ class ProtocolsWithOverrides: override_variable_name="type_to_test", overrides=["str_default_no_matching_choices", "float_default_no_matching_choices", "int_default_no_matching_choices"], ) + + # analyses-snapshot-testing/files/protocols/Flex_X_v2_20_96_and_8_Overrides_InvalidConfigs.py + + Flex_X_v2_20_96_and_8_Overrides_InvalidConfigs: ProtocolWithOverrides = ProtocolWithOverrides( + file_stem="Flex_X_v2_20_96_and_8_Overrides_InvalidConfigs", + file_extension="py", + robot="Flex", + override_variable_name="key", + overrides=[ + "ninety_six_partial_column_1", + "ninety_six_partial_column_2", + "ninety_six_partial_column_3", + "eight_partial_column_bottom_left", + "eight_partial_column_bottom_right", + "eight_partial_column_no_end", + "return_tip_error", + "drop_tip_with_location", + ], + ) + + # analyses-snapshot-testing/files/protocols/Flex_X_v2_20_96_None_Overrides_TooTallLabware.py + + Flex_X_v2_20_96_None_Overrides_TooTallLabware: ProtocolWithOverrides = ProtocolWithOverrides( + file_stem="Flex_X_v2_20_96_None_Overrides_TooTallLabware", + file_extension="py", + robot="Flex", + override_variable_name="key", + overrides=[ + "transfer_source_collision", + "transfer_destination_collision", + "c3_right_edge", + "north", + "north_west", + "west", + "south_west", + "south", + "south_east", + "east", + "east_column", + "west_column", + "north_row", + "south_row", + "top_edge", + "bottom_left_edge", + "bottom_left_edge", + "bottom_right_edge", + "mix_collision", + "consolidate_source_collision", + "consolidate_destination_collision", + "distribute_source_collision", + "distribute_destination_collision", + ], + ) + + # analyses-snapshot-testing/files/protocols/OT2_X_v2_20_8_Overrides_InvalidConfigs.py + + OT2_X_v2_20_8_Overrides_InvalidConfigs: ProtocolWithOverrides = ProtocolWithOverrides( + file_stem="OT2_X_v2_20_8_Overrides_InvalidConfigs", + file_extension="py", + robot="Flex", + override_variable_name="key", + overrides=[ + "eight_partial_column_bottom_left", + "eight_partial_column_bottom_right", + "eight_partial_column_no_end", + "return_tip_error", + "drop_tip_with_location", + ], + ) diff --git a/analyses-snapshot-testing/citools/Dockerfile.server b/analyses-snapshot-testing/citools/Dockerfile.server new file mode 100644 index 00000000000..6d4d9edcda3 --- /dev/null +++ b/analyses-snapshot-testing/citools/Dockerfile.server @@ -0,0 +1,31 @@ +# Use Python 3.10 as the base image +FROM python:3.10-slim-bullseye + +# Update packages and install dependencies +RUN apt-get update && \ + apt-get upgrade -y && \ + apt-get install -y git libsystemd-dev build-essential pkg-config network-manager + +# Define build arguments +ARG OPENTRONS_VERSION=edge + +# Set the working directory +WORKDIR /opentrons + +# Clone the Opentrons repository +ARG CACHEBUST=1 +RUN git clone --branch $OPENTRONS_VERSION --depth 1 https://github.com/Opentrons/opentrons . + +# Install dependencies +RUN make setup-py -j + +WORKDIR /opentrons/robot-server + +# Set the port via environment variable +ENV PORT=31950 + +# Expose the port +EXPOSE ${PORT} + +# Default command +CMD ["sh", "-c", "python -m pipenv run uvicorn robot_server.app:app --host 0.0.0.0 --port ${PORT} --ws wsproto --lifespan on"] diff --git a/analyses-snapshot-testing/files/protocols/Flex_S_v2_20_1000M_Simple.py b/analyses-snapshot-testing/files/protocols/Flex_S_v2_20_1000M_Simple.py new file mode 100644 index 00000000000..36fe24def92 --- /dev/null +++ b/analyses-snapshot-testing/files/protocols/Flex_S_v2_20_1000M_Simple.py @@ -0,0 +1,93 @@ +from opentrons.protocol_api import PARTIAL_COLUMN + +metadata = { + "protocolName": "flex_8channel_1000 Simple", + "description": "A protocol that demonstrates safe actions with flex_8channel_1000", + "author": "Josh McVey", +} + +requirements = { + "robotType": "Flex", + "apiLevel": "2.20", +} + + +def comment_tip_rack_status(ctx, tip_rack): + """ + Print out the tip status for each row in a tip rack. + Each row (A-H) will print the well statuses for columns 1-12 in a single comment, + with a '🟢' for present tips and a '❌' for missing tips. + """ + range_A_to_H = [chr(i) for i in range(ord("A"), ord("H") + 1)] + range_1_to_12 = range(1, 13) + + ctx.comment(f"Tip rack in {tip_rack.parent}") + + for row in range_A_to_H: + status_line = f"{row}: " + for col in range_1_to_12: + well = f"{row}{col}" + has_tip = tip_rack.wells_by_name()[well].has_tip + status_emoji = "🟢" if has_tip else "❌" + status_line += f"{well} {status_emoji} " + + # Print the full status line for the row + ctx.comment(status_line) + + +def run(protocol): + + trash = protocol.load_trash_bin("A3") # must load trash bin + tip_rack = protocol.load_labware( + load_name="opentrons_flex_96_tiprack_1000ul", + label="Tip Rack", + location="A1", + ) + + pipette = protocol.load_instrument(instrument_name="flex_8channel_1000", mount="left", tip_racks=[tip_rack]) + + source_labware_C2 = protocol.load_labware( + load_name="nest_1_reservoir_290ml", + label="Source Reservoir", + location="C2", + ) + + destination_labware_D2 = protocol.load_labware( + load_name="nest_96_wellplate_100ul_pcr_full_skirt", + label="PCR Plate", + location="2", + ) + + volume = 100 + pipette.pick_up_tip() + comment_tip_rack_status(protocol, tip_rack) + pipette.aspirate(volume=volume, location=destination_labware_D2["H1"]) + pipette.dispense(volume=volume, location=destination_labware_D2["H2"]) + for i in range(1, 13): + protocol.comment(f"Touching tip to {destination_labware_D2[f'H{i}']}") + pipette.touch_tip(location=destination_labware_D2[f"H{i}"]) + + pipette.blow_out(location=destination_labware_D2["H1"]) + pipette.mix(repetitions=3, volume=volume, location=destination_labware_D2["H1"]) + pipette.drop_tip() + + range_A_to_H = [chr(i) for i in range(ord("A"), ord("H") + 1)] + column1 = [destination_labware_D2[f"{row}1"] for row in range_A_to_H] + column2 = [destination_labware_D2[f"{row}2"] for row in range_A_to_H] + column3 = [destination_labware_D2[f"{row}3"] for row in range_A_to_H] + column4 = [destination_labware_D2[f"{row}4"] for row in range_A_to_H] + column5 = [destination_labware_D2[f"{row}5"] for row in range_A_to_H] + column6 = [destination_labware_D2[f"{row}6"] for row in range_A_to_H] + column7 = [destination_labware_D2[f"{row}7"] for row in range_A_to_H] + + protocol.comment(f"Transferring {volume}uL from column 1 to column 2") + pipette.transfer(volume=volume, source=column1, dest=column2) + comment_tip_rack_status(protocol, tip_rack) + + volume = 50 + protocol.comment(f"Distribute {volume}uL from column 2 to column 3 and 4") + pipette.distribute(volume=volume, source=column2, dest=column3 + column4) + comment_tip_rack_status(protocol, tip_rack) + protocol.comment(f"Consolidate {volume}uL from column 5 and 6 to column 7") + pipette.consolidate(volume=volume, source=column5 + column6, dest=column7) + comment_tip_rack_status(protocol, tip_rack) diff --git a/analyses-snapshot-testing/files/protocols/Flex_S_v2_20_8_None_PARTIAL_COLUMN_HappyPath.py b/analyses-snapshot-testing/files/protocols/Flex_S_v2_20_8_None_PARTIAL_COLUMN_HappyPath.py new file mode 100644 index 00000000000..cde6baf358f --- /dev/null +++ b/analyses-snapshot-testing/files/protocols/Flex_S_v2_20_8_None_PARTIAL_COLUMN_HappyPath.py @@ -0,0 +1,109 @@ +from opentrons.protocol_api import PARTIAL_COLUMN + +metadata = { + "protocolName": "8 Channel PARTIAL_COLUMN Happy Path A1 or H1", + "description": "Tip Rack South Clearance for the 8 Channel pipette and a SINGLE partial tip configuration.", +} + +requirements = { + "robotType": "Flex", + "apiLevel": "2.20", +} + + +def run(protocol): + + trash = protocol.load_trash_bin("A3") # must load trash bin + + thermocycler = protocol.load_module("thermocycler module gen2") + + partial_tip_rack = protocol.load_labware( + load_name="opentrons_flex_96_tiprack_50ul", + label="Partial Tip Rack", + location="B3", + ) + + pipette = protocol.load_instrument(instrument_name="flex_8channel_50", mount="right") + # mount on the right and you will get an error. + + pipette.configure_nozzle_layout( + style=PARTIAL_COLUMN, + start="H1", + end="B1", # 2 Tips + tip_racks=[partial_tip_rack], + ) + + source_labware_B2 = protocol.load_labware( + load_name="nest_96_wellplate_100ul_pcr_full_skirt", + label="B2 Source Labware", + location="B2", + ) + + destination_labware_C2 = protocol.load_labware( + load_name="nest_96_wellplate_100ul_pcr_full_skirt", + label="C2 Destination Labware", + location="C2", + ) + + volume = 10 # Default volume for actions that require it + + # ############################# + # # Pipette do work + # # leading nozzle + # # index in based on eh number of tips in my current configuration + # pipette.transfer(volume, source_labware_B2["B6"], destination_labware_C2["A6"]) + + # pipette.pick_up_tip() + # pipette.touch_tip(source_labware_B2["B1"]) + # pipette.drop_tip() + # pipette.pick_up_tip() + # pipette.home() + # pipette.drop_tip() + + # pipette.pick_up_tip() + # well = source_labware_B2["D1"] + # # directly from docs http://sandbox.docs.opentrons.com/edge/v2/new_protocol_api.html#opentrons.protocol_api.InstrumentContext.prepare_to_aspirate + # pipette.move_to(well.bottom(z=2)) + # pipette.mix(10, 10) + # pipette.move_to(well.top(z=5)) + # pipette.blow_out() + # pipette.prepare_to_aspirate() + # pipette.move_to(well.bottom(z=2)) + # pipette.aspirate(10, well.bottom(z=2)) + # pipette.dispense(10) + # pipette.drop_tip() + + # ############################ + # # Change the pipette configuration + + # pipette.configure_nozzle_layout( + # style=PARTIAL_COLUMN, + # start="H1", + # end="B1", # 7 Tips + # tip_racks=[partial_tip_rack], + # ) + + ############################# + # Pipette do work + + pipette.transfer(volume, source_labware_B2["A6"], destination_labware_C2["A6"]) + + pipette.pick_up_tip() + pipette.touch_tip(source_labware_B2["B1"]) + pipette.drop_tip() + pipette.pick_up_tip() + pipette.home() + pipette.drop_tip() + + pipette.pick_up_tip() + well = source_labware_B2["D1"] + # directly from docs http://sandbox.docs.opentrons.com/edge/v2/new_protocol_api.html#opentrons.protocol_api.InstrumentContext.prepare_to_aspirate + pipette.move_to(well.bottom(z=2)) + pipette.mix(10, 10) + pipette.move_to(well.top(z=5)) + pipette.blow_out() + pipette.prepare_to_aspirate() + pipette.move_to(well.bottom(z=2)) + pipette.aspirate(10, well.bottom(z=2)) + pipette.dispense(10) + pipette.drop_tip() diff --git a/analyses-snapshot-testing/files/protocols/Flex_S_v2_20_8_None_SINGLE_HappyPath.py b/analyses-snapshot-testing/files/protocols/Flex_S_v2_20_8_None_SINGLE_HappyPath.py new file mode 100644 index 00000000000..95493eb0ab3 --- /dev/null +++ b/analyses-snapshot-testing/files/protocols/Flex_S_v2_20_8_None_SINGLE_HappyPath.py @@ -0,0 +1,131 @@ +from opentrons.protocol_api import SINGLE + +metadata = { + "protocolName": "8 Channel SINGLE Happy Path A1 or H1", + "description": "Tip Rack South Clearance for the 8 Channel pipette and a SINGLE partial tip configuration.", +} + +requirements = { + "robotType": "Flex", + "apiLevel": "2.20", +} + + +def run(protocol): + + trash = protocol.load_trash_bin("A3") # must load trash bin + + partial_tip_rack = protocol.load_labware( + load_name="opentrons_flex_96_tiprack_50ul", + label="Partial Tip Rack", + location="B3", + ) + + thermocycler = protocol.load_module("thermocycler module gen2") + + pipette = protocol.load_instrument(instrument_name="flex_8channel_50", mount="right") + # mount on the right and you will get an error. + + # On the 8-channel SINGLE + # start="A1" Means the South nozzle will pickup from the NW corner of the tip rack + # start="H1" Means the North nozzle will pickup from the SW corner of the tip rack + pipette.configure_nozzle_layout( + style=SINGLE, + start="A1", # Which tip to start with + tip_racks=[partial_tip_rack], + ) + + source_labware_B2 = protocol.load_labware( + load_name="nest_96_wellplate_100ul_pcr_full_skirt", + label="B2 Source Labware", + location="B2", + ) + + destination_labware_C2 = protocol.load_labware( + load_name="nest_96_wellplate_100ul_pcr_full_skirt", + label="C2 Destination Labware", + location="C2", + ) + + volume = 10 # Default volume for actions that require it + + ############################# + # Pipette do work + pipette.consolidate( + [volume, volume], + [source_labware_B2["A3"], source_labware_B2["A4"]], + destination_labware_C2["A3"], + ) + + pipette.transfer(volume, source_labware_B2["A6"], destination_labware_C2["A6"]) + + pipette.distribute( + 5, + source_labware_B2["A7"], + [destination_labware_C2["A7"], destination_labware_C2["A8"]], + ) + + pipette.pick_up_tip() + pipette.touch_tip(source_labware_B2["B1"]) + pipette.drop_tip() + pipette.pick_up_tip() + pipette.home() + pipette.drop_tip() + + pipette.pick_up_tip() + well = source_labware_B2["D1"] + # directly from docs http://sandbox.docs.opentrons.com/edge/v2/new_protocol_api.html#opentrons.protocol_api.InstrumentContext.prepare_to_aspirate + pipette.move_to(well.bottom(z=2)) + pipette.mix(10, 10) + pipette.move_to(well.top(z=5)) + pipette.blow_out() + pipette.prepare_to_aspirate() + pipette.move_to(well.bottom(z=2)) + pipette.aspirate(10, well.bottom(z=2)) + pipette.dispense(10) + pipette.drop_tip() + + ############################ + # Change the pipette configuration + + pipette.configure_nozzle_layout( + style=SINGLE, + start="H1", # Which tip to start with + tip_racks=[partial_tip_rack], + ) + + ############################# + # Pipette do work + pipette.consolidate( + [volume, volume], + [source_labware_B2["A3"], source_labware_B2["A4"]], + destination_labware_C2["A3"], + ) + + pipette.transfer(volume, source_labware_B2["A6"], destination_labware_C2["A6"]) + + pipette.distribute( + 5, + source_labware_B2["A7"], + [destination_labware_C2["A7"], destination_labware_C2["A8"]], + ) + + pipette.pick_up_tip() + pipette.touch_tip(source_labware_B2["B1"]) + pipette.drop_tip() + pipette.pick_up_tip() + pipette.home() + pipette.drop_tip() + + pipette.pick_up_tip() + well = source_labware_B2["D1"] + # directly from docs http://sandbox.docs.opentrons.com/edge/v2/new_protocol_api.html#opentrons.protocol_api.InstrumentContext.prepare_to_aspirate + pipette.move_to(well.bottom(z=2)) + pipette.mix(10, 10) + pipette.move_to(well.top(z=5)) + pipette.blow_out() + pipette.prepare_to_aspirate() + pipette.move_to(well.bottom(z=2)) + pipette.aspirate(10, well.bottom(z=2)) + pipette.dispense(10) + pipette.drop_tip() diff --git a/analyses-snapshot-testing/files/protocols/Flex_S_v2_20_8_None_SINGLE_TubeRackCollision.py b/analyses-snapshot-testing/files/protocols/Flex_S_v2_20_8_None_SINGLE_TubeRackCollision.py new file mode 100644 index 00000000000..4f7a21d58bb --- /dev/null +++ b/analyses-snapshot-testing/files/protocols/Flex_S_v2_20_8_None_SINGLE_TubeRackCollision.py @@ -0,0 +1,65 @@ +from opentrons.protocol_api import SINGLE + +metadata = { + "protocolName": "8Channel SINGLE Pickup tuberack collision", +} + +requirements = { + "robotType": "Flex", + "apiLevel": "2.20", +} + + +def comment_tip_rack_status(ctx, tip_rack): + """ + Print out the tip status for each row in a tip rack. + Each row (A-H) will print the well statuses for columns 1-12 in a single comment, + with a '🟢' for present tips and a '❌' for missing tips. + """ + range_A_to_H = [chr(i) for i in range(ord("A"), ord("H") + 1)] + range_1_to_12 = range(1, 13) + + ctx.comment(f"Tip rack in {tip_rack.parent}") + + for row in range_A_to_H: + status_line = f"{row}: " + for col in range_1_to_12: + well = f"{row}{col}" + has_tip = tip_rack.wells_by_name()[well].has_tip + status_emoji = "🟢" if has_tip else "❌" + status_line += f"{well} {status_emoji} " + + # Print the full status line for the row + ctx.comment(status_line) + + +def run(protocol): + + trash = protocol.load_trash_bin("A3") # must load trash bin + + partial_tip_rack = protocol.load_labware( + load_name="opentrons_flex_96_tiprack_50ul", + label="Partial Tip Rack", + location="D2", + ) + + tube_rack = protocol.load_labware( + load_name="opentrons_10_tuberack_falcon_4x50ml_6x15ml_conical", + label="Tube Rack", + location="B2", + ) + + pipette = protocol.load_instrument(instrument_name="flex_8channel_50", mount="left") + + pipette.configure_nozzle_layout( + style=SINGLE, + start="H1", + tip_racks=[partial_tip_rack], + ) + + pipette.pick_up_tip() + comment_tip_rack_status(protocol, partial_tip_rack) + # can the flex_8channel_50 with 50μl tips really reach the bottom of the tube? + pipette.aspirate(30, tube_rack["A1"].bottom()) + pipette.dispense(30, tube_rack["A2"].bottom()) + pipette.drop_tip() diff --git a/analyses-snapshot-testing/files/protocols/Flex_S_v2_20_8_PARTIAL_COLUMN_Overhang.py b/analyses-snapshot-testing/files/protocols/Flex_S_v2_20_8_PARTIAL_COLUMN_Overhang.py new file mode 100644 index 00000000000..b1bcf5ed77b --- /dev/null +++ b/analyses-snapshot-testing/files/protocols/Flex_S_v2_20_8_PARTIAL_COLUMN_Overhang.py @@ -0,0 +1,150 @@ +from opentrons.protocol_api import PARTIAL_COLUMN + +metadata = { + "protocolName": "8 Channel PARTIAL_COLUMN Overhang", + "description": "A protocol that demonstrates overhang into a slot with a partial column configuration.", + "author": "Josh McVey", +} + +requirements = { + "robotType": "Flex", + "apiLevel": "2.20", +} + + +def comment_tip_rack_status(ctx, tip_rack): + """ + Print out the tip status for each row in a tip rack. + Each row (A-H) will print the well statuses for columns 1-12 in a single comment, + with a '🟢' for present tips and a '❌' for missing tips. + """ + range_A_to_H = [chr(i) for i in range(ord("A"), ord("H") + 1)] + range_1_to_12 = range(1, 13) + + ctx.comment(f"Tip rack in {tip_rack.parent}") + + for row in range_A_to_H: + status_line = f"{row}: " + for col in range_1_to_12: + well = f"{row}{col}" + has_tip = tip_rack.wells_by_name()[well].has_tip + status_emoji = "🟢" if has_tip else "❌" + status_line += f"{well} {status_emoji} " + + # Print the full status line for the row + ctx.comment(status_line) + + +def run(protocol): + + trash = protocol.load_trash_bin("A3") # must load trash bin + + thermocycler = protocol.load_module("thermocycler module gen2") + + partial_tip_rack = protocol.load_labware( + load_name="opentrons_flex_96_tiprack_50ul", + label="Partial Tip Rack", + location="B3", + ) + + pipette = protocol.load_instrument(instrument_name="flex_8channel_50", mount="right") + + pipette.configure_nozzle_layout( + style=PARTIAL_COLUMN, + start="H1", + end="D1", # 5 Tips + tip_racks=[partial_tip_rack], + ) + + source_labware_B2 = protocol.load_labware( + load_name="nest_1_reservoir_290ml", + label="B2 Source Reservoir", + location="B2", + ) + + destination_labware_C2 = protocol.load_labware( + load_name="nest_96_wellplate_100ul_pcr_full_skirt", + label="C2 Destination Labware", + location="C2", + ) + + volume = 10 # Default volume for actions that require it + + # Known issue in 8.0.0 + # if you target A1 of the labware in C2 + # nozzle H1 - the front-most nozzle will go to A1 + # this means that tips will be out of the slot + # they will over hang into the B2 + # no error is raised + # but a collision will occur with the labware in slot B2 + # the overhanging tips will collide with the labware in B2 + + # If we ever do detect and error for this + # Take all these examples into a negative Overrides test + + volume = 20 + pipette.pick_up_tip() + comment_tip_rack_status(protocol, partial_tip_rack) + # bad - 4 tips will overhang into B2 + pipette.aspirate(volume=5, location=destination_labware_C2["A1"]) + # bad - 3 tips will overhang into B2 + pipette.aspirate(volume=5, location=destination_labware_C2["B1"]) + # bad - 2 tips will overhang into B2 + pipette.aspirate(volume=5, location=destination_labware_C2["C1"]) + # bad - 1 tip will overhang into B2 + pipette.aspirate(volume=5, location=destination_labware_C2["D1"]) + # this is safe + pipette.aspirate(volume=5, location=destination_labware_C2["E1"]) + + # this is safe - from a reservoir + # must aspirate before dispense + pipette.aspirate(volume=volume, location=source_labware_B2["A1"]) + # bad - bad - 4 tips will overhang into B2 + pipette.dispense(volume=volume, location=destination_labware_C2["A1"]) + # this is safe - from a reservoir + # must aspirate before dispense + pipette.aspirate(volume=volume, location=source_labware_B2["A1"]) + # bad - bad - 3 tips will overhang into B2 + pipette.dispense(volume=volume, location=destination_labware_C2["B2"]) + # this is safe - from a reservoir + # must aspirate before dispense + pipette.aspirate(volume=volume, location=source_labware_B2["A1"]) + # bad - bad - 2 tips will overhang into B2 + pipette.dispense(volume=volume, location=destination_labware_C2["C3"]) + # this is safe - from a reservoir + # must aspirate before dispense + pipette.aspirate(volume=volume, location=source_labware_B2["A1"]) + # bad - bad - 1 tip will overhang into B2 + pipette.dispense(volume=volume, location=destination_labware_C2["D4"]) + # this is safe - from a reservoir + # must aspirate before dispense + pipette.aspirate(volume=volume, location=source_labware_B2["A1"]) + # this is safe - 0 tips will overhang into B2 + pipette.dispense(volume=volume, location=destination_labware_C2["E5"]) + # bad - has overhang into B2 - 4 tips + pipette.touch_tip(location=destination_labware_C2["A1"]) + # bad - has overhang into B2 - 4 tips + pipette.blow_out(location=destination_labware_C2["A1"]) + # bad - has overhang into B2 - 4 tips + pipette.mix(repetitions=3, volume=volume, location=destination_labware_C2["A2"]) + # bad - aspirate and dispense have overhang into B2 + pipette.drop_tip() + pipette.transfer(volume=volume, source=destination_labware_C2["A1"], dest=destination_labware_C2["A2"]) + # bad - aspirate has 3 tip overhang but not dispense + pipette.transfer(volume=volume, source=destination_labware_C2["B1"], dest=destination_labware_C2["E1"]) + # bad - aspirate is safe but dispense has 2 tip overhang + pipette.transfer(volume=volume, source=destination_labware_C2["E1"], dest=destination_labware_C2["C3"]) + # bad - source and destinations have overhang + pipette.distribute(volume=20, source=destination_labware_C2["D2"], dest=[destination_labware_C2["D3"], destination_labware_C2["D4"]]) + # bad - source has overhang but destinations are safe + pipette.distribute(volume=20, source=destination_labware_C2["D2"], dest=[destination_labware_C2["E3"], destination_labware_C2["E4"]]) + # bad - source has no overhang but 1 destination does + pipette.distribute(volume=20, source=destination_labware_C2["E6"], dest=[destination_labware_C2["A7"], destination_labware_C2["E7"]]) + # bad - source has no overhang but 2 destinations do + pipette.distribute(volume=20, source=destination_labware_C2["E7"], dest=[destination_labware_C2["A8"], destination_labware_C2["A9"]]) + # bad - all sources and destination have overhang + pipette.consolidate(volume=5, source=[destination_labware_C2["A9"], destination_labware_C2["A10"]], dest=destination_labware_C2["A11"]) + # bad - 1 source has overhang but destination is safe + pipette.consolidate(volume=5, source=[destination_labware_C2["A9"], destination_labware_C2["E10"]], dest=destination_labware_C2["E11"]) + # bad - sources are safe but destination has overhang + pipette.consolidate(volume=5, source=[destination_labware_C2["E9"], destination_labware_C2["E10"]], dest=destination_labware_C2["A12"]) diff --git a/analyses-snapshot-testing/files/protocols/Flex_S_v2_20_8_TipsDontMatchWells.py b/analyses-snapshot-testing/files/protocols/Flex_S_v2_20_8_TipsDontMatchWells.py new file mode 100644 index 00000000000..a6ecaf02340 --- /dev/null +++ b/analyses-snapshot-testing/files/protocols/Flex_S_v2_20_8_TipsDontMatchWells.py @@ -0,0 +1,87 @@ +from opentrons.protocol_api import SINGLE, ALL + +metadata = { + "protocolName": "8channel 50 into a 48 well plate", + "description": "the nozzles on the pipette do not match the target labware wells", + "author": "Josh McVey", +} + +requirements = { + "robotType": "Flex", + "apiLevel": "2.20", +} + + +def comment_tip_rack_status(ctx, tip_rack): + """ + Print out the tip status for each row in a tip rack. + Each row (A-H) will print the well statuses for columns 1-12 in a single comment, + with a '🟢' for present tips and a '❌' for missing tips. + """ + range_A_to_H = [chr(i) for i in range(ord("A"), ord("H") + 1)] + range_1_to_12 = range(1, 13) + + ctx.comment(f"Tip rack in {tip_rack.parent}") + + for row in range_A_to_H: + status_line = f"{row}: " + for col in range_1_to_12: + well = f"{row}{col}" + has_tip = tip_rack.wells_by_name()[well].has_tip + status_emoji = "🟢" if has_tip else "❌" + status_line += f"{well} {status_emoji} " + + # Print the full status line for the row + ctx.comment(status_line) + + +def run(protocol): + + trash = protocol.load_trash_bin("A3") # must load trash bin + + partial_tip_rack = protocol.load_labware( + load_name="opentrons_flex_96_tiprack_50ul", + label="Partial Tip Rack", + location="B3", + ) + + # corning_48_wellplate_1.6ml_flat + corning_48 = protocol.load_labware( + load_name="corning_48_wellplate_1.6ml_flat", + label="Corning 48 Wellplate", + location="D2", + ) + + pipette = protocol.load_instrument(instrument_name="flex_8channel_50", mount="right") + + pipette.configure_nozzle_layout( + style=ALL, + start="H1", + end="B1", # Test that end is ignored when style is ALL and on 8.0.0-alpha.6 it is ✅ + tip_racks=[partial_tip_rack], + ) + + pipette.pick_up_tip() + comment_tip_rack_status(protocol, partial_tip_rack) + volume = 20 + + ###### Purpose statement + ### This protocol is made to detect if analysis output ever changes + ### When we try and pipette to wells that do not match the geometry of the nozzles on the pipette + ###### + + # when using 8 channel location is the front-most well in the column of the target labware + pipette.aspirate(volume=volume, location=corning_48["F1"]) + pipette.dispense(volume=volume, location=corning_48["F1"]) + pipette.touch_tip(location=corning_48["F1"]) + pipette.blow_out(location=corning_48["F1"]) + pipette.mix(repetitions=3, volume=volume, location=corning_48["F1"]) + # next line has this error: Invalid source for multichannel transfer: [F1 of Corning 48 Wellplate on slot D2] + # pipette.transfer(volume=volume, source=corning_48["F1"], dest=corning_48["F2"]) + # next line has this error: Invalid source for multichannel transfer: [F2 of Corning 48 Wellplate on slot D2] + # pipette.distribute(volume=20, source=corning_48["F2"], dest=[corning_48["F3"], corning_48["F4"]]) + # next line has this error: + # Invalid source for multichannel transfer: [F6 of Corning 48 Wellplate on slot D2, F7 of Corning 48 Wellplate on slot D2] + # pipette.consolidate(volume=20, source=[corning_48["F6"], corning_48["F7"]], dest=corning_48["F8"]) + + pipette.drop_tip() # so trash bin shows up in the deck map diff --git a/analyses-snapshot-testing/files/protocols/Flex_S_v2_20_96_AllCorners.py b/analyses-snapshot-testing/files/protocols/Flex_S_v2_20_96_AllCorners.py new file mode 100644 index 00000000000..01fc0b45b9b --- /dev/null +++ b/analyses-snapshot-testing/files/protocols/Flex_S_v2_20_96_AllCorners.py @@ -0,0 +1,296 @@ +from opentrons import protocol_api +from opentrons.protocol_api import COLUMN, SINGLE, ROW + +requirements = {"robotType": "Flex", "apiLevel": "2.20"} + + +def run(protocol: protocol_api.ProtocolContext): + pipette = protocol.load_instrument(instrument_name="flex_96channel_1000") + trash = protocol.load_trash_bin("B3") + t1 = protocol.load_labware( + load_name="opentrons_flex_96_tiprack_1000ul", + label="A1 Corner Tiprack 1", + location="B1", + ) + t2 = protocol.load_labware( + load_name="opentrons_flex_96_tiprack_1000ul", + label="D1 Corner Tiprack", + location="C1", + ) + t3 = protocol.load_labware( + load_name="opentrons_flex_96_tiprack_1000ul", + label="A3 Corner Tiprack 1", + location="B2", + ) + t4 = protocol.load_labware( + load_name="opentrons_flex_96_tiprack_1000ul", + label="D3 Corner Tiprack", + location="C2", + ) + t5 = protocol.load_labware( + load_name="opentrons_flex_96_tiprack_1000ul", + label="A3 Corner Tiprack 2", + location="A2", + ) + t6 = protocol.load_labware( + load_name="opentrons_flex_96_tiprack_1000ul", + label="A1 Corner Tiprack 2", + location="D4", + ) + + ### SETUP TIPRACK FUNCTIONS + # These functions serve the purpose of removing tips from a tiprack before it is moved to a corner slot + # This is done to ensure the tiprack is in such a state that it will trigger zero deck extent conflicts + + # Setup T2 + def t2_setup() -> None: + pipette.configure_nozzle_layout( + style=ROW, + start="A1", + tip_racks=[t2], + ) + for i in range(3): + pipette.pick_up_tip() + pipette.drop_tip() + + # Setup T3 + def t3_setup() -> None: + pipette.configure_nozzle_layout(style=COLUMN, start="A1", tip_racks=[t3]) + for i in range(2): + pipette.pick_up_tip() + pipette.drop_tip() + + # Setup T4 + def t4_setup() -> None: + pipette.configure_nozzle_layout( + style=ROW, + start="A1", + tip_racks=[t4], + ) + for i in range(3): + pipette.pick_up_tip() + pipette.drop_tip() + + pipette.configure_nozzle_layout( + style=SINGLE, + start="A1", + tip_racks=[t4], + ) + for i in range(10): + pipette.pick_up_tip() + pipette.drop_tip() + + # Setup T5 + def t5_setup() -> None: + pipette.configure_nozzle_layout( + style=ROW, + start="H1", + tip_racks=[t5], + ) + for i in range(7): + pipette.pick_up_tip() + pipette.drop_tip() + + pipette.configure_nozzle_layout( + style=SINGLE, + start="A1", + tip_racks=[t5], + ) + for i in range(2): + pipette.pick_up_tip() + pipette.drop_tip() + + # Setup T6 + def t6_setup() -> None: + pipette.configure_nozzle_layout( + style=ROW, + start="H1", + tip_racks=[t6], + ) + for i in range(7): + pipette.pick_up_tip() + pipette.drop_tip() + + ### PICKUP TIP FUNCTIONS + # These functions perform pickup tip behavior for a given tiprack + + # Pickup T2 + def t1_pickup() -> None: + pipette.configure_nozzle_layout( + style=SINGLE, + start="A1", + tip_racks=[t1], + ) + for i in range(48): + pipette.pick_up_tip() + pipette.drop_tip() + pipette.configure_nozzle_layout( + style=SINGLE, + start="A12", + tip_racks=[t1], + ) + for i in range(48): + pipette.pick_up_tip() + pipette.drop_tip() + + # Pickup T2 + def t2_pickup() -> None: + pipette.configure_nozzle_layout( + style=SINGLE, + start="A1", + tip_racks=[t2], + ) + for i in range(15): + pipette.pick_up_tip() + pipette.drop_tip() + pipette.configure_nozzle_layout( + style=SINGLE, + start="A12", + tip_racks=[t2], + ) + for i in range(15): + pipette.pick_up_tip() + pipette.drop_tip() + pipette.configure_nozzle_layout( + style=SINGLE, + start="H1", + tip_racks=[t2], + ) + for i in range(15): + pipette.pick_up_tip() + pipette.drop_tip() + pipette.configure_nozzle_layout( + style=SINGLE, + start="H12", + tip_racks=[t2], + ) + for i in range(15): + pipette.pick_up_tip() + pipette.drop_tip() + + # Pickup T3 + def t3_pickup() -> None: + pipette.configure_nozzle_layout( + style=SINGLE, + start="A1", + tip_racks=[t3], + ) + for i in range(40): + pipette.pick_up_tip() + pipette.drop_tip() + pipette.configure_nozzle_layout( + style=SINGLE, + start="A12", + tip_racks=[t3], + ) + for i in range(40): + pipette.pick_up_tip() + pipette.drop_tip() + + # Pickup T4 + def t4_pickup() -> None: + pipette.configure_nozzle_layout( + style=SINGLE, + start="A1", + tip_racks=[t4], + ) + for i in range(10): + pipette.pick_up_tip() + pipette.drop_tip() + pipette.configure_nozzle_layout( + style=SINGLE, + start="A12", + tip_racks=[t4], + ) + for i in range(10): + pipette.pick_up_tip() + pipette.drop_tip() + pipette.configure_nozzle_layout( + style=SINGLE, + start="H1", + tip_racks=[t4], + ) + for i in range(15): + pipette.pick_up_tip() + pipette.drop_tip() + pipette.configure_nozzle_layout( + style=SINGLE, + start="H12", + tip_racks=[t4], + ) + for i in range(15): + pipette.pick_up_tip() + pipette.drop_tip() + + # Pickup T5 + def t5_pickup() -> None: + pipette.configure_nozzle_layout( + style=SINGLE, + start="H1", + tip_racks=[t5], + ) + for i in range(5): + pipette.pick_up_tip() + pipette.drop_tip() + pipette.configure_nozzle_layout( + style=SINGLE, + start="H12", + tip_racks=[t5], + ) + for i in range(5): + pipette.pick_up_tip() + pipette.drop_tip() + + # Pickup T6 + def t6_pickup() -> None: + pipette.configure_nozzle_layout( + style=SINGLE, + start="H1", + tip_racks=[t6], + ) + for i in range(6): + pipette.pick_up_tip() + pipette.drop_tip() + pipette.configure_nozzle_layout( + style=SINGLE, + start="H12", + tip_racks=[t6], + ) + for i in range(6): + pipette.pick_up_tip() + pipette.drop_tip() + + ### Protocol Actions + # Perform Setup of first set of tipracks + protocol.move_labware(t1, "A1", True) + t2_setup() + protocol.move_labware(t2, "D1", True) + t3_setup() + protocol.move_labware(t3, "A3", True) + t4_setup() + protocol.move_labware(t4, "D3", True) + + # Clear out T2 first to make room for T5 + t2_pickup() + protocol.move_labware(t5, "B2", True) + t5_setup() + protocol.move_labware(t5, "C1", True) + + # Clear out T1, T3, and T4 + t1_pickup() + t3_pickup() + protocol.move_labware(t6, "A4", True) + t4_pickup() + protocol.move_labware(t6, "D4", True) + + # Move T3, then move and handle T5 + protocol.move_labware(t3, "D2", True) + protocol.move_labware(t5, "A3", True) + t5_pickup() + + # Move T6 to On-Deck in B2 and setup, then move to A1 and handle + protocol.move_labware(t6, "B2", True) + t6_setup() + protocol.move_labware(t1, "C3", True) + protocol.move_labware(t6, "A1", True) + t6_pickup() diff --git a/analyses-snapshot-testing/files/protocols/Flex_S_v2_20_96_LLD.py b/analyses-snapshot-testing/files/protocols/Flex_S_v2_20_96_LLD.py new file mode 100644 index 00000000000..080fda8a759 --- /dev/null +++ b/analyses-snapshot-testing/files/protocols/Flex_S_v2_20_96_LLD.py @@ -0,0 +1,93 @@ +from opentrons import protocol_api + +# metadata +metadata = { + "protocolName": "2.20 Error Recovery Testing Protocol - 96ch", + "author": "Sara Kowalski", + "description": "Simple Protocol that user can use to Phase 1 Error Recovery options for a 96 channel p1000.", +} + +requirements = { + "robotType": "Flex", + "apiLevel": "2.20", +} + +DRYRUN = "NO" + + +def run(protocol: protocol_api.ProtocolContext): + + # modules/fixtures + trashbin = protocol.load_trash_bin(location="A3") + + # labware + tip_adapter = protocol.load_adapter("opentrons_flex_96_tiprack_adapter", "A2") + tiprack1 = tip_adapter.load_labware("opentrons_flex_96_tiprack_1000ul") + sample_plate = protocol.load_labware("armadillo_96_wellplate_200ul_pcr_full_skirt", "C3") + reservoir = protocol.load_labware("nest_1_reservoir_290ml", "D3") + wet_sample = protocol.load_labware("nest_12_reservoir_15ml", "B3") + + # liquids + water = protocol.define_liquid( + name="Water", + description="water for ER testing", + display_color="#90e0ef", + ) + waterButMoreBlue = protocol.define_liquid( + name="Water but more blue", + description="Water for ER testing", + display_color="#0077b6", + ) + + wet_sample["A1"].load_liquid(liquid=water, volume=800) + wet_sample["A2"].load_liquid(liquid=waterButMoreBlue, volume=800) + + # instruments + p1000 = protocol.load_instrument("flex_96channel_1000", mount="left", tip_racks=[tiprack1]) + + volume = 900 + + ############################## + #####Tip Pick Up Failure###### + ############################## + + protocol.pause("This tests Tip Pick Up Failure (General Error for now)") + protocol.pause("Please remove tip rack from deck. When you're testing recovery, add tiprack back as necessary.") + p1000.pick_up_tip() + + ########################################## + #####Overpressure - While Aspirating###### + ########################################## + + protocol.pause("Overpressure - While Aspirating") + p1000.home() + protocol.pause("Swap with tip(s) that are hot glued shut (you will need to swap the tips for retry recovery options)") + + for i in range(10): + p1000.aspirate(volume, reservoir["A1"].top()) + p1000.dispense(volume, reservoir["A1"].top()) + + #################################### + #####Liquid Presence Detection###### + #################################### + protocol.pause("This tests Liquid Presence Detection - PLEASE MAKE SURE YOU'RE USING 1000UL TIPS OR YOU WILL BREAK THE PIPETTE") + protocol.pause("Make sure reservoir is empty, and have full reservoir on standby to switch out with for recovery") + + p1000.require_liquid_presence(wet_sample["A1"]) + + p1000.aspirate(volume, wet_sample["A1"]) + p1000.dispense(volume, wet_sample["A1"]) + p1000.home() + + ##################################################### + #####Overpressure - While Dispensing###### + ##################################################### + + protocol.pause("Overpressure - While Dispensing") + + p1000.aspirate(volume, reservoir["A1"].top(20)) + protocol.pause("Swap with tip(s) that are hot glued shut (you will need to cut the tips for retry recovery options)") + p1000.dispense(volume, reservoir["A1"].top(20)) + + p1000.return_tip() + p1000.reset_tipracks() diff --git a/analyses-snapshot-testing/files/protocols/Flex_S_v2_20_96_None_COLUMN_HappyPath.py b/analyses-snapshot-testing/files/protocols/Flex_S_v2_20_96_None_COLUMN_HappyPath.py new file mode 100644 index 00000000000..6fec53ee5b3 --- /dev/null +++ b/analyses-snapshot-testing/files/protocols/Flex_S_v2_20_96_None_COLUMN_HappyPath.py @@ -0,0 +1,121 @@ +from opentrons.protocol_api import COLUMN + +metadata = { + "protocolName": "96Channel COLUMN Happy Path", + "description": "96 channel pipette and a COLUMN partial tip configuration.", +} + +requirements = { + "robotType": "Flex", + "apiLevel": "2.20", +} + + +def run(protocol): + + trash = protocol.load_trash_bin("A3") # must load trash bin + + partial_tip_rack = protocol.load_labware( + load_name="opentrons_flex_96_tiprack_1000ul", + label="Partial Tip Rack", + location="B2", + ) + + pipette = protocol.load_instrument(instrument_name="flex_96channel_1000") + + # Which nozzle to use on the pipette + # Think of the nozzles from above like you are looking down on a 96-well plate + # start="A1" Means the West most nozzle column will pickup from the East most column of the tip rack + # start="A12" Means the East most nozzle column will pickup from the West most column of the tip rack + pipette.configure_nozzle_layout( + style=COLUMN, + start="A1", + tip_racks=[partial_tip_rack], + ) + + source_labware = protocol.load_labware( + load_name="nest_96_wellplate_100ul_pcr_full_skirt", + label="Liquid Transfer - Source Labware", + location="C2", + ) + + destination_labware = protocol.load_labware( + load_name="nest_96_wellplate_100ul_pcr_full_skirt", + label="Liquid Transfer - Destination Labware", + location="C3", + ) + + volume = 10 # Default volume for actions that require it + + ############################# + # Pipette do work + + # consolidate does not work with the COLUMN configuration + # consolidate only has a single well as a destination + + # transfer the row + pipette.transfer(volume, source_labware["A1"], destination_labware["A1"]) + + # distribute does not work with the COLUMN configuration + # distribute only has a single well as a source + + pipette.pick_up_tip() + pipette.touch_tip(source_labware["A2"]) + pipette.drop_tip() + pipette.pick_up_tip() + pipette.home() + pipette.drop_tip() + + pipette.pick_up_tip() + well = source_labware["A3"] + # directly from docs http://sandbox.docs.opentrons.com/edge/v2/new_protocol_api.html#opentrons.protocol_api.InstrumentContext.prepare_to_aspirate + pipette.move_to(well.bottom(z=2)) + pipette.mix(10, 10) + pipette.move_to(well.top(z=5)) + pipette.blow_out() + pipette.prepare_to_aspirate() + pipette.move_to(well.bottom(z=2)) + pipette.aspirate(10, well.bottom(z=2)) + pipette.dispense(10) + pipette.drop_tip() + + ############################# + # Change the pipette configuration + + pipette.configure_nozzle_layout( + style=COLUMN, + start="A12", # Which nozzle to start with + tip_racks=[partial_tip_rack], + ) + + ############################# + # Pipette do work + + # consolidate does not work with the COLUMN configuration + # consolidate only has a single well as a destination + + # transfer the row + pipette.transfer(volume, source_labware["A5"], destination_labware["A5"]) + + # distribute does not work with the COLUMN configuration + # distribute only has a single well as a source + + pipette.pick_up_tip() + pipette.touch_tip(source_labware["A6"]) + pipette.drop_tip() + pipette.pick_up_tip() + pipette.home() + pipette.drop_tip() + + pipette.pick_up_tip() + well = source_labware["A7"] + # directly from docs http://sandbox.docs.opentrons.com/edge/v2/new_protocol_api.html#opentrons.protocol_api.InstrumentContext.prepare_to_aspirate + pipette.move_to(well.bottom(z=2)) + pipette.mix(10, 10) + pipette.move_to(well.top(z=5)) + pipette.blow_out() + pipette.prepare_to_aspirate() + pipette.move_to(well.bottom(z=2)) + pipette.aspirate(10, well.bottom(z=2)) + pipette.dispense(10) + pipette.drop_tip() diff --git a/analyses-snapshot-testing/files/protocols/Flex_S_v2_20_96_None_Column3_SINGLE_.py b/analyses-snapshot-testing/files/protocols/Flex_S_v2_20_96_None_Column3_SINGLE_.py new file mode 100644 index 00000000000..e5d1427a477 --- /dev/null +++ b/analyses-snapshot-testing/files/protocols/Flex_S_v2_20_96_None_Column3_SINGLE_.py @@ -0,0 +1,118 @@ +from opentrons import protocol_api +from opentrons.protocol_api import COLUMN, ALL, SINGLE, ROW + +requirements = {"robotType": "Flex", "apiLevel": "2.20"} + + +def run(protocol: protocol_api.ProtocolContext): + pipette = protocol.load_instrument(instrument_name="flex_96channel_1000") + trash = protocol.load_trash_bin("A1") + t1 = protocol.load_labware( + load_name="opentrons_flex_96_tiprack_1000ul", + label="Partial Tip Rack", + location="A2", + ) + t2 = protocol.load_labware( + load_name="opentrons_flex_96_tiprack_1000ul", + label="Partial Tip Rack", + location="B2", + ) + t3 = protocol.load_labware( + load_name="opentrons_flex_96_tiprack_1000ul", + label="Partial Tip Rack", + location="C2", + ) + t4 = protocol.load_labware( + load_name="opentrons_flex_96_tiprack_1000ul", + label="Partial Tip Rack", + location="D2", + ) + + ### Prep tipracks in B2 and D2 by removing 3 columns of tips + pipette.configure_nozzle_layout( + style=COLUMN, + start="A1", + tip_racks=[t2], + ) + for i in range(3): + pipette.pick_up_tip() + pipette.drop_tip() + + pipette.configure_nozzle_layout( + style=COLUMN, + start="A1", + tip_racks=[t4], + ) + for i in range(3): + pipette.pick_up_tip() + pipette.drop_tip() + + ### Relocate tipracks to A3 and C3 for single tip extraction at furthest extant + protocol.move_labware(t2, "A3", True) + protocol.move_labware(t4, "C3", True) + + pipette.configure_nozzle_layout( + style=SINGLE, + start="A1", + tip_racks=[t2, t4], + ) + + for i in range(72 * 2): + pipette.pick_up_tip() + pipette.drop_tip() + + ### Move tipracks out of the way to B1 and C1 + protocol.move_labware(t2, "B1", True) + protocol.move_labware(t4, "C1", True) + + ### Prepare tiprack in A2 by removing 3 columns of tips + pipette.configure_nozzle_layout( + style=COLUMN, + start="A1", + tip_racks=[t1], + ) + for i in range(3): + pipette.pick_up_tip() + pipette.drop_tip() + + ### Prepare tiprack in C2 by removing bottom 3 rows of tips, plus 15 tips (3 leftmost remaining columns) + ### This results in a tiprack of the following layout (matching the requirements for our bottom right extents): + # X X X X X X X X X - - - + # X X X X X X X X X - - - + # X X X X X X X X X - - - + # X X X X X X X X X - - - + # X X X X X X X X X - - - + # - - - - - - - - - - - - + # - - - - - - - - - - - - + # - - - - - - - - - - - - + pipette.configure_nozzle_layout( + style=ROW, + start="A1", + tip_racks=[t3], + ) + for i in range(3): + pipette.pick_up_tip() + pipette.drop_tip() + + pipette.configure_nozzle_layout( + style=SINGLE, + start="A1", + tip_racks=[t3], + ) + for i in range(15): + pipette.pick_up_tip() + pipette.drop_tip() + + ### Relocate tipracks to B3 and D3 on the deck + protocol.move_labware(t1, "B3", True) + protocol.move_labware(t3, "D3", True) + + pipette.configure_nozzle_layout( + style=SINGLE, + start="A1", + tip_racks=[t1, t3], + ) + + for i in range(72 + 45): + pipette.pick_up_tip() + pipette.drop_tip() diff --git a/analyses-snapshot-testing/files/protocols/Flex_S_v2_20_96_None_ROW_HappyPath.py b/analyses-snapshot-testing/files/protocols/Flex_S_v2_20_96_None_ROW_HappyPath.py new file mode 100644 index 00000000000..cf253f04bfe --- /dev/null +++ b/analyses-snapshot-testing/files/protocols/Flex_S_v2_20_96_None_ROW_HappyPath.py @@ -0,0 +1,121 @@ +from opentrons.protocol_api import ROW + +metadata = { + "protocolName": "96Channel ROW Happy Path", + "description": "96 channel pipette and a ROW partial tip configuration.", +} + +requirements = { + "robotType": "Flex", + "apiLevel": "2.20", +} + + +def run(protocol): + + trash = protocol.load_trash_bin("A3") # must load trash bin + + partial_tip_rack = protocol.load_labware( + load_name="opentrons_flex_96_tiprack_1000ul", + label="Partial Tip Rack", + location="B1", + ) + + pipette = protocol.load_instrument(instrument_name="flex_96channel_1000") + + # Which nozzle to use on the pipette + # Think of the nozzles from above like you are looking down on a 96-well plate + # start="A1" Means the North most nozzle row will pickup from the South most row of the tip rack + # start="H1" Means the South most nozzle row will pickup from the North most row of the tip rack + pipette.configure_nozzle_layout( + style=ROW, + start="A1", + tip_racks=[partial_tip_rack], + ) + + source_labware = protocol.load_labware( + load_name="nest_96_wellplate_100ul_pcr_full_skirt", + label="Liquid Transfer - Source Labware", + location="C2", + ) + + destination_labware = protocol.load_labware( + load_name="nest_96_wellplate_100ul_pcr_full_skirt", + label="Liquid Transfer - Destination Labware", + location="C3", + ) + + volume = 10 # Default volume for actions that require it + + ############################# + # Pipette do work + + # consolidate is does not work with the ROW configuration + # consolidate only has a single well as a destination + + # transfer the row + pipette.transfer(volume, source_labware["A1"], destination_labware["A1"]) + + # distribute does not work with the ROW configuration + # distribute only has a single well as a source + + pipette.pick_up_tip() + pipette.touch_tip(source_labware["B1"]) + pipette.drop_tip() + pipette.pick_up_tip() + pipette.home() + pipette.drop_tip() + + pipette.pick_up_tip() + well = source_labware["D1"] + # directly from docs http://sandbox.docs.opentrons.com/edge/v2/new_protocol_api.html#opentrons.protocol_api.InstrumentContext.prepare_to_aspirate + pipette.move_to(well.bottom(z=2)) + pipette.mix(10, 10) + pipette.move_to(well.top(z=5)) + pipette.blow_out() + pipette.prepare_to_aspirate() + pipette.move_to(well.bottom(z=2)) + pipette.aspirate(10, well.bottom(z=2)) + pipette.dispense(10) + pipette.drop_tip() + + ############################# + # Change the pipette configuration + + pipette.configure_nozzle_layout( + style=ROW, + start="H1", # Which nozzle to start with + tip_racks=[partial_tip_rack], + ) + + ############################# + # Pipette do work + + # consolidate is does not work with the ROW configuration + # consolidate only has a single well as a destination + + # transfer the row + pipette.transfer(volume, source_labware["E1"], destination_labware["E1"]) + + # distribute does not work with the ROW configuration + # distribute only has a single well as a source + + pipette.pick_up_tip() + pipette.touch_tip(source_labware["F1"]) + pipette.drop_tip() + pipette.pick_up_tip() + pipette.home() + pipette.drop_tip() + + pipette.pick_up_tip() + well = source_labware["G1"] + # directly from docs http://sandbox.docs.opentrons.com/edge/v2/new_protocol_api.html#opentrons.protocol_api.InstrumentContext.prepare_to_aspirate + pipette.move_to(well.bottom(z=2)) + pipette.mix(10, 10) + pipette.move_to(well.top(z=5)) + pipette.blow_out() + pipette.prepare_to_aspirate() + pipette.move_to(well.bottom(z=2)) + pipette.aspirate(10, well.bottom(z=2)) + pipette.dispense(10) + pipette.drop_tip() diff --git a/analyses-snapshot-testing/files/protocols/Flex_S_v2_20_96_None_SINGLE_4Corners50ul.py b/analyses-snapshot-testing/files/protocols/Flex_S_v2_20_96_None_SINGLE_4Corners50ul.py new file mode 100644 index 00000000000..1ac96b7a7ac --- /dev/null +++ b/analyses-snapshot-testing/files/protocols/Flex_S_v2_20_96_None_SINGLE_4Corners50ul.py @@ -0,0 +1,66 @@ +from opentrons.protocol_api import SINGLE + +metadata = { + "protocolName": "96Channel SINGLE Pickup on all 4 corners 2 pickups", + "description": "96 2 tips picked up on all 4 corners of the tip rack", +} + +requirements = { + "robotType": "Flex", + "apiLevel": "2.20", +} + + +def comment_tip_rack_status(ctx, tip_rack): + """ + Print out the tip status for each row in a tip rack. + Each row (A-H) will print the well statuses for columns 1-12 in a single comment, + with a '🟢' for present tips and a '❌' for missing tips. + """ + range_A_to_H = [chr(i) for i in range(ord("A"), ord("H") + 1)] + range_1_to_12 = range(1, 13) + + ctx.comment(f"Tip rack in {tip_rack.parent}") + + for row in range_A_to_H: + status_line = f"{row}: " + for col in range_1_to_12: + well = f"{row}{col}" + has_tip = tip_rack.wells_by_name()[well].has_tip + status_emoji = "🟢" if has_tip else "❌" + status_line += f"{well} {status_emoji} " + + # Print the full status line for the row + ctx.comment(status_line) + + +def run(protocol): + + trash = protocol.load_trash_bin("A3") # must load trash bin + + four_corners = ["A1", "A12", "H1", "H12"] + + partial_tip_rack = protocol.load_labware( + load_name="opentrons_flex_96_tiprack_50ul", + label="Partial Tip Rack", + location="C2", + ) + + pipette = protocol.load_instrument(instrument_name="flex_96channel_1000") + + for corner in four_corners: + + pipette.configure_nozzle_layout( + style=SINGLE, + start=corner, + tip_racks=[partial_tip_rack], + ) + + pipette.pick_up_tip() + comment_tip_rack_status(protocol, partial_tip_rack) + protocol.pause("How was the pickup of first tip?") + pipette.drop_tip() + pipette.pick_up_tip() + comment_tip_rack_status(protocol, partial_tip_rack) + protocol.pause("How was the pickup of second tip?") + pipette.drop_tip() diff --git a/analyses-snapshot-testing/files/protocols/Flex_S_v2_20_96_None_SINGLE_HappyPathNorthSide.py b/analyses-snapshot-testing/files/protocols/Flex_S_v2_20_96_None_SINGLE_HappyPathNorthSide.py new file mode 100644 index 00000000000..ba26d34802d --- /dev/null +++ b/analyses-snapshot-testing/files/protocols/Flex_S_v2_20_96_None_SINGLE_HappyPathNorthSide.py @@ -0,0 +1,143 @@ +from opentrons.protocol_api import SINGLE + +metadata = { + "protocolName": "96Channel SINGLE Happy Path H1 or H12", + "description": "Tip Rack North Clearance for the 96 channel pipette and a SINGLE partial tip configuration.", +} + +requirements = { + "robotType": "Flex", + "apiLevel": "2.20", +} + + +def run(protocol): + + trash = protocol.load_trash_bin("A3") # must load trash bin + + partial_tip_rack = protocol.load_labware( + load_name="opentrons_flex_96_tiprack_1000ul", + label="Partial Tip Rack", + location="D2", + ) + + pipette = protocol.load_instrument(instrument_name="flex_96channel_1000") + + # Which nozzle to use on the pipette + # Think of the nozzles from above like you are looking down on a 96-well plate + # start="A1" Means the NW nozzle will pickup from the SE corner of the tip rack + # start="A12" Means the SW nozzle will pickup from the NE corner of the tip rack + # start="H1" Means the NE nozzle will pickup from the SW corner of the tip rack + # start="H12" Means the SE nozzle will pickup from the NW corner of the tip rack + pipette.configure_nozzle_layout( + style=SINGLE, + start="H1", # Which nozzle to start with + tip_racks=[partial_tip_rack], + ) + + source_labware_C1 = protocol.load_labware( + load_name="nest_96_wellplate_100ul_pcr_full_skirt", + label="Liquid Transfer - Source Labware", + location="C1", + ) + + destination_labware_C2 = protocol.load_labware( + load_name="nest_96_wellplate_100ul_pcr_full_skirt", + label="Liquid Transfer - Destination Labware", + location="C2", + ) + + volume = 10 # Default volume for actions that require it + + ############################# + # Pipette do work + pipette.consolidate( + [volume, volume], + [source_labware_C1["A3"], source_labware_C1["A4"]], + destination_labware_C2["A3"], + ) + + pipette.transfer(volume, source_labware_C1["A6"], source_labware_C1["A6"]) + + pipette.distribute( + 5, + source_labware_C1["A7"], + [destination_labware_C2["A7"], destination_labware_C2["A8"]], + ) + + pipette.pick_up_tip() + pipette.touch_tip(source_labware_C1["B1"]) + pipette.drop_tip() + pipette.pick_up_tip() + pipette.home() + pipette.drop_tip() + + pipette.pick_up_tip() + well = source_labware_C1["D1"] + # directly from docs http://sandbox.docs.opentrons.com/edge/v2/new_protocol_api.html#opentrons.protocol_api.InstrumentContext.prepare_to_aspirate + pipette.move_to(well.bottom(z=2)) + pipette.mix(10, 10) + pipette.move_to(well.top(z=5)) + pipette.blow_out() + pipette.prepare_to_aspirate() + pipette.move_to(well.bottom(z=2)) + pipette.aspirate(10, well.bottom(z=2)) + pipette.dispense(10) + pipette.drop_tip() + + ############################# + # Change the pipette configuration + + pipette.configure_nozzle_layout( + style=SINGLE, + start="H12", # Which nozzle to start with + tip_racks=[partial_tip_rack], + ) + + source_labware_C3 = protocol.load_labware( + load_name="nest_96_wellplate_100ul_pcr_full_skirt", + label="C3 Source Labware", + location="C3", + ) + + destination_labware_B2 = protocol.load_labware( + load_name="nest_96_wellplate_100ul_pcr_full_skirt", + label="B2 Destination Labware", + location="B2", + ) + + ############################# + # Pipette do work + pipette.consolidate( + [volume, volume], + [source_labware_C3["A3"], source_labware_C3["A4"]], + destination_labware_B2["A3"], + ) + + pipette.transfer(volume, source_labware_C3["A6"], destination_labware_B2["A6"]) + + pipette.distribute( + 5, + source_labware_C3["A7"], + [destination_labware_B2["A7"], destination_labware_B2["A8"]], + ) + + pipette.pick_up_tip() + pipette.touch_tip(source_labware_C3["B1"]) + pipette.drop_tip() + pipette.pick_up_tip() + pipette.home() + pipette.drop_tip() + + pipette.pick_up_tip() + well = source_labware_C3["D1"] + # directly from docs http://sandbox.docs.opentrons.com/edge/v2/new_protocol_api.html#opentrons.protocol_api.InstrumentContext.prepare_to_aspirate + pipette.move_to(well.bottom(z=2)) + pipette.mix(10, 10) + pipette.move_to(well.top(z=5)) + pipette.blow_out() + pipette.prepare_to_aspirate() + pipette.move_to(well.bottom(z=2)) + pipette.aspirate(10, well.bottom(z=2)) + pipette.dispense(10) + pipette.drop_tip() diff --git a/analyses-snapshot-testing/files/protocols/Flex_S_v2_20_96_None_SINGLE_HappyPathSouthSide.py b/analyses-snapshot-testing/files/protocols/Flex_S_v2_20_96_None_SINGLE_HappyPathSouthSide.py new file mode 100644 index 00000000000..e050a0e4558 --- /dev/null +++ b/analyses-snapshot-testing/files/protocols/Flex_S_v2_20_96_None_SINGLE_HappyPathSouthSide.py @@ -0,0 +1,143 @@ +from opentrons.protocol_api import SINGLE + +metadata = { + "protocolName": "96Channel SINGLE Happy Path A1 or A12", + "description": "Unsafe protocol ❗❗❗❗❗❗❗❗❗❗❗ will collide with tube.", +} + +requirements = { + "robotType": "Flex", + "apiLevel": "2.20", +} + + +def run(protocol): + + trash = protocol.load_trash_bin("A3") # must load trash bin + + partial_tip_rack = protocol.load_labware( + load_name="opentrons_flex_96_tiprack_1000ul", + label="Partial Tip Rack", + location="A2", + ) + + pipette = protocol.load_instrument(instrument_name="flex_96channel_1000") + + # Which nozzle to use on the pipette + # Think of the nozzles from above like you are looking down on a 96-well plate + # start="A1" Means the NW nozzle will pickup from the SE corner of the tip rack + # start="A12" Means the SW nozzle will pickup from the NE corner of the tip rack + # start="H1" Means the NE nozzle will pickup from the SW corner of the tip rack + # start="H12" Means the SE nozzle will pickup from the NW corner of the tip rack + pipette.configure_nozzle_layout( + style=SINGLE, + start="A1", # Which nozzle to start with + tip_racks=[partial_tip_rack], + ) + + source_labware_C1 = protocol.load_labware( + load_name="nest_96_wellplate_100ul_pcr_full_skirt", + label="C1 Source Labware", + location="C1", + ) + + destination_labware_C2 = protocol.load_labware( + load_name="nest_96_wellplate_100ul_pcr_full_skirt", + label="C2 Destination Labware", + location="C2", + ) + + volume = 10 # Default volume for actions that require it + + ############################# + # Pipette do work + pipette.consolidate( + [volume, volume], + [source_labware_C1["A3"], source_labware_C1["A4"]], + destination_labware_C2["A3"], + ) + + pipette.transfer(volume, source_labware_C1["A6"], destination_labware_C2["A6"]) + + pipette.distribute( + 5, + source_labware_C1["A7"], + [destination_labware_C2["A7"], destination_labware_C2["A8"]], + ) + + pipette.pick_up_tip() + pipette.touch_tip(source_labware_C1["B1"]) + pipette.drop_tip() + pipette.pick_up_tip() + pipette.home() + pipette.drop_tip() + + pipette.pick_up_tip() + well = source_labware_C1["D1"] + # directly from docs http://sandbox.docs.opentrons.com/edge/v2/new_protocol_api.html#opentrons.protocol_api.InstrumentContext.prepare_to_aspirate + pipette.move_to(well.bottom(z=2)) + pipette.mix(10, 10) + pipette.move_to(well.top(z=5)) + pipette.blow_out() + pipette.prepare_to_aspirate() + pipette.move_to(well.bottom(z=2)) + pipette.aspirate(10, well.bottom(z=2)) + pipette.dispense(10) + pipette.drop_tip() + + ############################# + # Change the pipette configuration + + pipette.configure_nozzle_layout( + style=SINGLE, + start="A12", # Which nozzle to start with + tip_racks=[partial_tip_rack], + ) + + source_labware_B2 = protocol.load_labware( + load_name="nest_96_wellplate_100ul_pcr_full_skirt", + label="B2 Source Labware", + location="B2", + ) + + destination_labware_C3 = protocol.load_labware( + load_name="nest_96_wellplate_100ul_pcr_full_skirt", + label="C3 Destination Labware", + location="C3", + ) + + ############################# + # Pipette do work + pipette.consolidate( + [volume, volume], + [source_labware_B2["A3"], source_labware_B2["A4"]], + destination_labware_C3["A3"], + ) + + pipette.transfer(volume, source_labware_B2["A6"], destination_labware_C3["A6"]) + + pipette.distribute( + 5, + source_labware_B2["A7"], + [destination_labware_C3["A7"], destination_labware_C3["A8"]], + ) + + pipette.pick_up_tip() + pipette.touch_tip(source_labware_B2["B1"]) + pipette.drop_tip() + pipette.pick_up_tip() + pipette.home() + pipette.drop_tip() + + pipette.pick_up_tip() + well = source_labware_B2["D1"] + # directly from docs http://sandbox.docs.opentrons.com/edge/v2/new_protocol_api.html#opentrons.protocol_api.InstrumentContext.prepare_to_aspirate + pipette.move_to(well.bottom(z=2)) + pipette.mix(10, 10) + pipette.move_to(well.top(z=5)) + pipette.blow_out() + pipette.prepare_to_aspirate() + pipette.move_to(well.bottom(z=2)) + pipette.aspirate(10, well.bottom(z=2)) + pipette.dispense(10) + pipette.drop_tip() diff --git a/analyses-snapshot-testing/files/protocols/Flex_S_v2_20_96_None_SINGLE_TubeRackCollision.py b/analyses-snapshot-testing/files/protocols/Flex_S_v2_20_96_None_SINGLE_TubeRackCollision.py new file mode 100644 index 00000000000..b499a0ef16d --- /dev/null +++ b/analyses-snapshot-testing/files/protocols/Flex_S_v2_20_96_None_SINGLE_TubeRackCollision.py @@ -0,0 +1,68 @@ +from opentrons.protocol_api import SINGLE + +metadata = { + "protocolName": "96Channel SINGLE Pickup tuberack collision", + "description": "Unsafe protocol ❗❗❗❗❗❗❗❗❗❗❗ will collide with tube.", +} + +requirements = { + "robotType": "Flex", + "apiLevel": "2.20", +} + + +def comment_tip_rack_status(ctx, tip_rack): + """ + Print out the tip status for each row in a tip rack. + Each row (A-H) will print the well statuses for columns 1-12 in a single comment, + with a '🟢' for present tips and a '❌' for missing tips. + """ + range_A_to_H = [chr(i) for i in range(ord("A"), ord("H") + 1)] + range_1_to_12 = range(1, 13) + + ctx.comment(f"Tip rack in {tip_rack.parent}") + + for row in range_A_to_H: + status_line = f"{row}: " + for col in range_1_to_12: + well = f"{row}{col}" + has_tip = tip_rack.wells_by_name()[well].has_tip + status_emoji = "🟢" if has_tip else "❌" + status_line += f"{well} {status_emoji} " + + # Print the full status line for the row + ctx.comment(status_line) + + +def run(protocol): + + trash = protocol.load_trash_bin("A3") # must load trash bin + + partial_tip_rack = protocol.load_labware( + load_name="opentrons_flex_96_tiprack_50ul", + label="Partial Tip Rack", + location="B2", + ) + + # tubes in column 1 and 2 are taller than the tubes in 3 and 4 + tube_rack = protocol.load_labware( + load_name="opentrons_10_tuberack_falcon_4x50ml_6x15ml_conical", + label="Tube Rack", + location="D2", + ) + + pipette = protocol.load_instrument(instrument_name="flex_96channel_1000") + + pipette.configure_nozzle_layout( + style=SINGLE, + start="H12", + tip_racks=[partial_tip_rack], + ) + + pipette.pick_up_tip() + comment_tip_rack_status(protocol, partial_tip_rack) + # tubes in column 1 and 2 are taller than the tubes in 3 and 4 + # I would expect that with 50ul tips + # the pipette would collide with the tubes in column 1 and 2 + pipette.aspirate(30, tube_rack["B3"].bottom()) + pipette.drop_tip() diff --git a/analyses-snapshot-testing/files/protocols/Flex_S_v2_20_96_Reservoir.py b/analyses-snapshot-testing/files/protocols/Flex_S_v2_20_96_Reservoir.py new file mode 100644 index 00000000000..399c0008d10 --- /dev/null +++ b/analyses-snapshot-testing/files/protocols/Flex_S_v2_20_96_Reservoir.py @@ -0,0 +1,91 @@ +from opentrons.protocol_api import SINGLE + +metadata = { + "protocolName": "96Channel Partial Tip to single well labware", + "description": "How does the 96 channel pipette behave with a partial tip rack and a single well labware?", +} + +requirements = { + "robotType": "Flex", + "apiLevel": "2.20", +} + + +def comment_tip_rack_status(ctx, tip_rack): + """ + Print out the tip status for each row in a tip rack. + Each row (A-H) will print the well statuses for columns 1-12 in a single comment, + with a '🟢' for present tips and a '❌' for missing tips. + """ + range_A_to_H = [chr(i) for i in range(ord("A"), ord("H") + 1)] + range_1_to_12 = range(1, 13) + + ctx.comment(f"Tip rack in {tip_rack.parent}") + + for row in range_A_to_H: + status_line = f"{row}: " + for col in range_1_to_12: + well = f"{row}{col}" + has_tip = tip_rack.wells_by_name()[well].has_tip + status_emoji = "🟢" if has_tip else "❌" + status_line += f"{well} {status_emoji} " + + # Print the full status line for the row + ctx.comment(status_line) + + +def aspirate_to_reservoir_test(ctx, labware): + location = labware.wells()[0] + ctx.comment(f"Aspirating from {labware.parent} {location}") + ctx.aspirate(20, location) + ctx.pause("Where did I aspirate from?") + + +def run(protocol): + + trash = protocol.load_trash_bin("A3") # must load trash bin + + partial_tip_rack = protocol.load_labware( + load_name="opentrons_flex_96_tiprack_200ul", + label="Partial Tip Rack", + location="B2", + ) + + # agilent_1_reservoir_290ml + agilent_290 = protocol.load_labware( + load_name="agilent_1_reservoir_290ml", + label="Agilent 290mL", + location="D1", + ) + + # axygen_1_reservoir_90ml + axygen_90 = protocol.load_labware( + load_name="axygen_1_reservoir_90ml", + label="Axygen 90mL", + location="D2", + ) + + # nest_1_reservoir_195ml + nest_195 = protocol.load_labware( + load_name="nest_1_reservoir_195ml", + label="Nest 195mL", + location="D3", + ) + + pipette = protocol.load_instrument(instrument_name="flex_96channel_1000") + + pipette.configure_nozzle_layout( + style=SINGLE, + start="H1", + tip_racks=[partial_tip_rack], + ) + + pipette.pick_up_tip() + comment_tip_rack_status(protocol, partial_tip_rack) + aspirate_to_reservoir_test(protocol, agilent_290) + + pipette.configure_nozzle_layout( + style=COLUMN, + start="A1", + tip_racks=[partial_tip_rack], + ) diff --git a/analyses-snapshot-testing/files/protocols/Flex_S_v2_20_P50_LPD.py b/analyses-snapshot-testing/files/protocols/Flex_S_v2_20_P50_LPD.py new file mode 100644 index 00000000000..c2038880a03 --- /dev/null +++ b/analyses-snapshot-testing/files/protocols/Flex_S_v2_20_P50_LPD.py @@ -0,0 +1,122 @@ +import random +from typing import Set +from opentrons import protocol_api + +# metadata +metadata = { + "protocolName": "Wet test for LPD", + "author": "Josh McVey", + "description": "http://sandbox.docs.opentrons.com/edge/v2/pipettes/loading.html#liquid-presence-detection", +} + +requirements = { + "robotType": "Flex", + "apiLevel": "2.20", +} + + +def load_liquid_in_all_wells(labware, liquid) -> None: + for well in labware.wells(): + well.load_liquid(liquid=liquid, volume=well.max_volume) + + +def run(protocol: protocol_api.ProtocolContext): + + # modules/fixtures + trashbin = protocol.load_trash_bin(location="A3") + + # labware + tiprack1 = protocol.load_labware("opentrons_flex_96_tiprack_1000ul", "A2") + tiprack2 = protocol.load_labware("opentrons_flex_96_tiprack_50ul", "B2") + sample_plate = protocol.load_labware("armadillo_96_wellplate_200ul_pcr_full_skirt", "C3") + reservoir = protocol.load_labware("nest_1_reservoir_290ml", "D3") + wet_sample = protocol.load_labware("nest_12_reservoir_15ml", "B3") + + # liquids + waterButMoreBlue = protocol.define_liquid( + name="H20", + description="Test this wet!!!", + display_color="#0077b6", + ) + + load_liquid_in_all_wells(wet_sample, waterButMoreBlue) + + # instruments + p50 = protocol.load_instrument("flex_1channel_50", mount="right", tip_racks=[tiprack2], liquid_presence_detection=True) + volume = 50 + + pipette = p50 + + # Wet A1 to sample plate A1 + # should be successful + well = "A1" + pipette.pick_up_tip() + pipette.aspirate(volume, wet_sample.well(well)) + pipette.dispense(volume, sample_plate.well(well)) + pipette.drop_tip() + + # reuse a tip with liquid_presence_detection=True + # we do NOT get an error if we reuse a tip + # but it is not recommended + well = "A2" + pipette.pick_up_tip() + pipette.aspirate(volume, wet_sample.well(well)) + pipette.dispense(volume, sample_plate.well(well)) + + well = "A3" + pipette.aspirate(volume, wet_sample.well(well)) + pipette.dispense(volume, sample_plate.well(well)) + pipette.drop_tip() + + # disable liquid presence detection on the pipette + pipette.liquid_presence_detection = False + # dry aspirate to prove it is off + protocol.comment(f"Reservoir in {reservoir.parent} is to have NO liquid") + pipette.pick_up_tip() + # dry aspirate to prove it is off + pipette.aspirate(volume, reservoir["A1"]) + pipette.blow_out(trashbin) # make sure tip is empty then use for next step + protocol.comment(f"Current volume in pipette: {pipette.current_volume}") # prints 0 + # detect liquid presence + # we expect this to move the pipette to well A1 of the reservoir + # and then return False during the run + # but will always return true in the simulation (analysis) + # ❗❗❗❗❗❗ + # currently the next line is throwing an error: + # Error 4000 GENERAL_ERROR (ProtocolCommandFailedError): TipNotEmptyError: + # This operation requires a tip with no liquid in it. + # https://opentrons.atlassian.net/browse/RQA-3171 + pipette.prepare_to_aspirate() # This removes the error + is_liquid_in_reservoir = pipette.detect_liquid_presence(reservoir["A1"]) + protocol.comment(f"Is there liquid in the reservoir? {is_liquid_in_reservoir}") + if not protocol.is_simulating(): + if is_liquid_in_reservoir: + protocol.comment("🐛🐛🐛🐛🐛 False + for liquid") + pipette.drop_tip() + # ❗❗❗❗❗❗ + + # now we turn back on liquid presence detection + # with the property + pipette.liquid_presence_detection = True + pipette.pick_up_tip() + # the next line should throw an error and pause the protocol + # resolve and continue + protocol.comment(f"We expect an error on the next line") + pipette.aspirate(volume, reservoir["A1"]) + + if pipette.has_tip: + pipette.drop_tip() + + # pipette.liquid_presence_detection = True + # and we try to use + # pipette.detect_liquid_presence + # no error is thrown regardless of the presence of liquid + + pipette.pick_up_tip() + protocol.comment(f"Reservoir in {reservoir.parent} is to have NO liquid") + pipette.detect_liquid_presence(reservoir["A1"]) + is_liquid_in_reservoir = pipette.detect_liquid_presence(reservoir["A1"]) + protocol.comment(f"Is there liquid in the reservoir? {is_liquid_in_reservoir}") + if not protocol.is_simulating(): + if is_liquid_in_reservoir: + protocol.comment("🐛🐛🐛🐛🐛 False + for liquid") diff --git a/analyses-snapshot-testing/files/protocols/Flex_S_v2_20_P50_LPD_wet_tip_scenarios.py b/analyses-snapshot-testing/files/protocols/Flex_S_v2_20_P50_LPD_wet_tip_scenarios.py new file mode 100644 index 00000000000..059d4278001 --- /dev/null +++ b/analyses-snapshot-testing/files/protocols/Flex_S_v2_20_P50_LPD_wet_tip_scenarios.py @@ -0,0 +1,169 @@ +import random +from typing import Set +from opentrons import protocol_api + +# metadata +metadata = { + "protocolName": "LPD with wet tip scenarios", + "author": "Josh McVey", + "description": "http://sandbox.docs.opentrons.com/edge/v2/pipettes/loading.html#liquid-presence-detection", +} + +requirements = { + "robotType": "Flex", + "apiLevel": "2.20", +} + + +def load_liquid_in_all_wells(labware, liquid) -> None: + for well in labware.wells(): + well.load_liquid(liquid=liquid, volume=well.max_volume) + + +def run(protocol: protocol_api.ProtocolContext): + + # modules/fixtures + trashbin = protocol.load_trash_bin(location="A3") + + # labware + tiprack1 = protocol.load_labware("opentrons_flex_96_tiprack_1000ul", "A2") + tiprack2 = protocol.load_labware("opentrons_flex_96_tiprack_50ul", "B2") + sample_plate = protocol.load_labware("armadillo_96_wellplate_200ul_pcr_full_skirt", "C3") + reservoir = protocol.load_labware("nest_1_reservoir_290ml", "D3") + wet_sample = protocol.load_labware("nest_12_reservoir_15ml", "B3") + + # liquids + waterButMoreBlue = protocol.define_liquid( + name="H20", + description="Test this wet!!!", + display_color="#0077b6", + ) + + wet_sample.well("A1").load_liquid(liquid=waterButMoreBlue, volume=200) + wet_sample.well("A2").load_liquid(liquid=waterButMoreBlue, volume=200) + wet_sample.well("A3").load_liquid(liquid=waterButMoreBlue, volume=200) + + # instruments + p50 = protocol.load_instrument("flex_1channel_50", mount="right", tip_racks=[tiprack2], liquid_presence_detection=True) + volume = 50 + + pipette = p50 + total_volume = 30 + + pipette.pick_up_tip() + protocol.comment("touch_tip") + pipette.touch_tip(wet_sample.well("A1")) + protocol.comment("air_gap") + pipette.air_gap(volume=20) + protocol.comment("blow_out with no arguments") + pipette.blow_out() + pipette.drop_tip() + + protocol.comment(f"reuse=True") + pipette.transfer( + volume=10, + source=[wet_sample.well("A1"), wet_sample.well("A2"), wet_sample.well("A3")], + dest=sample_plate.well("A2"), + reuse=True, + ) + + # example_1 = "During mixing, all aspirates on repetitions > 1 LPD with wet tip" + # protocol.comment(f"{example_1} 🔽🔽🔽🔽🔽🔽🔽") + # pipette.pick_up_tip() + # pipette.mix(repetitions=3, volume=20, location=wet_sample.well("A1")) + # pipette.drop_tip() + # protocol.comment(f"{example_1} 🔼🔼🔼🔼🔼🔼🔼") + + # example_2 = "Consolidate default, reuse=true, new_tip once or never;second and subsequent aspirates LPD with wet tip" + # protocol.comment(f"{example_2} 🔽🔽🔽🔽🔽🔽🔽") + # protocol.comment(f"default tip use") + # pipette.consolidate( + # volume=total_volume, + # source=[wet_sample.well("A1"), wet_sample.well("A2"), wet_sample.well("A3")], + # dest=sample_plate.well("A1"), + # ) + # protocol.comment(f"reuse=True") + # pipette.consolidate( + # volume=total_volume, + # source=[wet_sample.well("A1"), wet_sample.well("A2"), wet_sample.well("A3")], + # dest=sample_plate.well("A2"), + # reuse=True, + # ) + # protocol.comment(f"new_tip='once'") + # pipette.consolidate( + # volume=total_volume, + # source=[wet_sample.well("A1"), wet_sample.well("A2"), wet_sample.well("A3")], + # dest=sample_plate.well("A3"), + # new_tip="once", + # ) + # protocol.comment(f"new_tip='never'") + # pipette.pick_up_tip() + # pipette.consolidate( + # volume=total_volume, + # source=[wet_sample.well("A1"), wet_sample.well("A2"), wet_sample.well("A3")], + # dest=sample_plate.well("A4"), + # new_tip="never", + # ) + # pipette.drop_tip() + # protocol.comment(f"{example_2} 🔼🔼🔼🔼🔼🔼🔼") + + # example_3 = "Consolidate mix_before or mix_after, during mixing, all aspirates on repetitions > 1 LPD with wet tip" + # protocol.comment(f"{example_3} 🔽🔽🔽🔽🔽🔽🔽") + # pipette.consolidate( + # volume=total_volume, + # source=[wet_sample.well("A1"), wet_sample.well("A2"), wet_sample.well("A3")], + # dest=sample_plate.well("A5"), + # mix_before=(3, 15), + # mix_after=(3, 20), + # ) + # protocol.comment(f"{example_3} 🔼🔼🔼🔼🔼🔼🔼") + + # example_4 = "Distribute default and reuse=true;second and subsequent aspirates LPD with wet tip" + # protocol.comment(f"{example_4} 🔽🔽🔽🔽🔽🔽🔽") + # pipette.distribute( + # volume=total_volume, + # source=sample_plate.well("A2"), + # dest=[sample_plate.well("A1"), sample_plate.well("A3")], + # reuse=True, + # ) + # protocol.comment(f"{example_4} 🔼🔼🔼🔼🔼🔼🔼") + + # example_5 = "Distribute mix=true, During mixing, all aspirates on repetitions > 1 LPD with wet tip" + # protocol.comment(f"{example_5} 🔽🔽🔽🔽🔽🔽🔽") + # pipette.distribute( + # volume=total_volume, + # source=sample_plate.well("A2"), + # dest=[sample_plate.well("A1"), sample_plate.well("A3")], + # mix=True, + + # # reuse the tip for a second transfer + # # no error + # # we must say in docs do not do this + # protocol.comment("LPD no error thrown on simple command tip reuse 🔽🔽🔽🔽🔽🔽🔽") + # well = "A2" + # pipette.pick_up_tip() + # pipette.aspirate(volume, wet_sample.well(well)) + # pipette.dispense(volume, sample_plate.well(well)) + + # well = "A3" + # pipette.aspirate(volume, wet_sample.well(well)) + # pipette.dispense(volume, sample_plate.well(well)) + # pipette.drop_tip() + # protocol.comment("LPD no error thrown on simple command tip reuse 🔼🔼🔼🔼🔼🔼🔼") + + # # Again no error is thrown + # # but we must say in docs do not do this + # protocol.comment("LPD no error thrown on blowout + prepare_to_aspirate 🔽🔽🔽🔽🔽🔽🔽") + # pipette.pick_up_tip() + # pipette.aspirate(volume=20, location=reservoir["A1"]) + # pipette.blow_out(trashbin) # make sure tip is empty then use for next step + # protocol.comment(f"Current volume in pipette: {pipette.current_volume}") # prints 0 + # # pipette.prepare_to_aspirate() removes the error from line 93 + # # but this should NOT be done!!! + # # Error 4000 GENERAL_ERROR (ProtocolCommandFailedError): TipNotEmptyError: + # # This operation requires a tip with no liquid in it. + # pipette.prepare_to_aspirate() + # is_liquid_in_reservoir = pipette.detect_liquid_presence(reservoir["A1"]) + # protocol.comment(f"Is there liquid in the reservoir? {is_liquid_in_reservoir}") + # pipette.drop_tip() + # protocol.comment("LPD no error thrown on blowout + prepare_to_aspirate 🔼🔼🔼🔼🔼🔼🔼") diff --git a/analyses-snapshot-testing/files/protocols/Flex_S_v2_20_P50_touch_tip_directly.py b/analyses-snapshot-testing/files/protocols/Flex_S_v2_20_P50_touch_tip_directly.py new file mode 100644 index 00000000000..ac8a4420650 --- /dev/null +++ b/analyses-snapshot-testing/files/protocols/Flex_S_v2_20_P50_touch_tip_directly.py @@ -0,0 +1,66 @@ +import random +from typing import Set +from opentrons import protocol_api + +# metadata +metadata = { + "protocolName": "Flex touch tip first", + "author": "Josh McVey", + "description": "touch tip first", +} + +requirements = { + "robotType": "Flex", + "apiLevel": "2.20", +} + + +def load_liquid_in_all_wells(labware, liquid) -> None: + for well in labware.wells(): + well.load_liquid(liquid=liquid, volume=well.max_volume) + + +def run(protocol: protocol_api.ProtocolContext): + + # modules/fixtures + trashbin = protocol.load_trash_bin(location="A3") + + # labware + tiprack1 = protocol.load_labware("opentrons_flex_96_tiprack_1000ul", "A2") + tiprack2 = protocol.load_labware("opentrons_flex_96_tiprack_50ul", "B2") + sample_plate = protocol.load_labware("armadillo_96_wellplate_200ul_pcr_full_skirt", "C3") + reservoir = protocol.load_labware("nest_1_reservoir_290ml", "D3") + wet_sample = protocol.load_labware("nest_12_reservoir_15ml", "B3") + + # liquids + waterButMoreBlue = protocol.define_liquid( + name="H20", + description="Test this wet!!!", + display_color="#0077b6", + ) + + wet_sample.well("A1").load_liquid(liquid=waterButMoreBlue, volume=200) + wet_sample.well("A2").load_liquid(liquid=waterButMoreBlue, volume=200) + wet_sample.well("A3").load_liquid(liquid=waterButMoreBlue, volume=200) + + # instruments + p50 = protocol.load_instrument("flex_1channel_50", mount="right", tip_racks=[tiprack2], liquid_presence_detection=True) + volume = 50 + + pipette = p50 + total_volume = 30 + + pipette.pick_up_tip() + # don't do an aspirate before the touch_tip + # pipette.aspirate(volume=total_volume, location=wet_sample.well("A1")) + protocol.comment("touch_tip") + # no matter if you aspirate before or not, + # the touch_tip is not shown in the app preview run + pipette.touch_tip(location=wet_sample.well("A1")) + protocol.comment("air_gap") + # if you uncomment the air_gap an error is thrown + # I should be at the wet_sample.well("A1") but it says I am at the tiprack + # pipette.air_gap(volume=20) + protocol.comment("blow_out with no arguments") + pipette.blow_out() + pipette.drop_tip() diff --git a/analyses-snapshot-testing/files/protocols/Flex_S_v2_20_P8X1000_P50_LLD.py b/analyses-snapshot-testing/files/protocols/Flex_S_v2_20_P8X1000_P50_LLD.py new file mode 100644 index 00000000000..1550f3313d5 --- /dev/null +++ b/analyses-snapshot-testing/files/protocols/Flex_S_v2_20_P8X1000_P50_LLD.py @@ -0,0 +1,106 @@ +from opentrons import protocol_api + +# metadata +metadata = { + "protocolName": "2.20 Error Recovery Testing Protocol - Modified", + "author": "Sara Kowalski", + "description": "Simple Protocol that user can use to Phase 1 Error Recovery options for single and multi channel pipettes. NOTE: YOU WILL NEED A MODIFIED PIPETTE (NO SHROUD), and changed order of operations to reduce impact of dispense ER failure", +} + +requirements = { + "robotType": "Flex", + "apiLevel": "2.20", +} + +DRYRUN = "NO" + + +def run(protocol: protocol_api.ProtocolContext): + + # modules/fixtures + trashbin = protocol.load_trash_bin(location="A3") + + # labware + tiprack1 = protocol.load_labware("opentrons_flex_96_tiprack_1000ul", "A2") + tiprack2 = protocol.load_labware("opentrons_flex_96_tiprack_50ul", "B2") + sample_plate = protocol.load_labware("armadillo_96_wellplate_200ul_pcr_full_skirt", "C3") + reservoir = protocol.load_labware("nest_1_reservoir_290ml", "D3") + wet_sample = protocol.load_labware("nest_12_reservoir_15ml", "B3") + + # liquids + water = protocol.define_liquid( + name="Water", + description="water for ER testing", + display_color="#90e0ef", + ) + waterButMoreBlue = protocol.define_liquid( + name="Water but more blue", + description="Water for ER testing", + display_color="#0077b6", + ) + + wet_sample["A1"].load_liquid(liquid=water, volume=800) + wet_sample["A2"].load_liquid(liquid=waterButMoreBlue, volume=800) + + # instruments + p1000 = protocol.load_instrument( + "flex_8channel_1000", mount="left", tip_racks=[tiprack1] + ) ## will need a modified pipette that doesn't have the ejector(?) + p50 = protocol.load_instrument( + "flex_1channel_50", mount="right", tip_racks=[tiprack2] + ) ## will need a modified pipette that doesn't have the ejector(?) + + pipette_list = [p1000, p50] + volume = 900 + + for pipette in pipette_list: + if pipette == p50: + volume = 50 + + ############################## + #####Tip Pick Up Failure###### + ############################## + + protocol.pause("This tests Tip Pick Up Failure (General Error for now)") + protocol.pause("Please remove tip rack from deck. When you're testing recovery, add tiprack back as necessary.") + pipette.pick_up_tip() + + ########################################## + #####Overpressure - While Aspirating###### + ########################################## + + protocol.pause("Overpressure - While Aspirating") + pipette.home() + protocol.pause( + "Use p50UL tips - Swap with tip(s) that are hot glued shut (you will need to swap the tips for retry recovery options)" + ) + + for i in range(10): + pipette.aspirate(volume, reservoir["A1"].top()) + pipette.dispense(volume, reservoir["A1"].top()) + + #################################### + #####Liquid Presence Detection###### + #################################### + protocol.pause("This tests Liquid Presence Detection - PLEASE MAKE SURE YOU'RE USING 1000UL TIPS OR YOU WILL BREAK THE PIPETTE") + protocol.pause("Make sure reservoir is empty, and have full reservoir on standby to switch out with for recovery") + + pipette.require_liquid_presence(wet_sample["A1"]) + + pipette.aspirate(volume, wet_sample["A1"]) + pipette.dispense(volume, wet_sample["A1"]) + pipette.home() + + ##################################################### + #####Overpressure - While Dispensing###### + ##################################################### + + protocol.pause("Overpressure - While Dispensing") + + pipette.aspirate(volume, reservoir["A1"].top(20)) + protocol.pause("Swap with tip(s) that are hot glued shut (you will need to cut the tips for retry recovery options)") + pipette.dispense(volume, reservoir["A1"].top(20)) + + pipette.move_to(trashbin) + protocol.pause("You will have to manually remove tips if you're using a modified pipette") + pipette.drop_tip(trashbin) diff --git a/analyses-snapshot-testing/files/protocols/Flex_X_v2_20_96_None_Overrides_TooTallLabware.py b/analyses-snapshot-testing/files/protocols/Flex_X_v2_20_96_None_Overrides_TooTallLabware.py new file mode 100644 index 00000000000..d717c497655 --- /dev/null +++ b/analyses-snapshot-testing/files/protocols/Flex_X_v2_20_96_None_Overrides_TooTallLabware.py @@ -0,0 +1,504 @@ +from dataclasses import dataclass +from typing import Optional +from opentrons.protocol_api import SINGLE, COLUMN, PARTIAL_COLUMN, ROW + +metadata = { + "protocolName": "Too tall labware on pickup tip", + "description": "oooo", +} + +requirements = { + "robotType": "Flex", + "apiLevel": "2.20", +} + + +@dataclass +class PartialTipConfig: + key: str + description: str + startingTip: str + startingNozzle: str + apiTipConfig: str + apiStart: str + apiEnd: Optional[str] + + +# flex_96channel_1000 SINGLE + +ninety_six_single_top_left = PartialTipConfig( + key="ninety_six_single_top_left", + description="96 single picking up top left of tiprack", + startingTip="A1", + startingNozzle="H12", + apiTipConfig=SINGLE, + apiStart="H12", + apiEnd=None, +) + +ninety_six_single_top_right = PartialTipConfig( + key="ninety_six_single_top_right", + description="96 single picking up top right of tiprack", + startingTip="A12", + startingNozzle="H1", + apiTipConfig=SINGLE, + apiStart="H1", + apiEnd=None, +) + +ninety_six_single_bottom_left = PartialTipConfig( + key="ninety_six_single_bottom_left", + description="96 single picking up bottom left of tiprack", + startingTip="H1", + startingNozzle="A12", + apiTipConfig=SINGLE, + apiStart="A12", + apiEnd=None, +) + +ninety_six_single_bottom_right = PartialTipConfig( + key="ninety_six_single_bottom_right", + description="96 single picking up bottom right of tiprack", + startingTip="H12", + startingNozzle="A1", + apiTipConfig=SINGLE, + apiStart="A1", + apiEnd=None, +) + +# flex_96channel_1000 COLUMN + +ninety_six_column_left = PartialTipConfig( + key="ninety_six_column_left", + description="96 column picking up left column of tiprack", + startingTip="Column 1", + startingNozzle="Column 12", + apiTipConfig=COLUMN, + apiStart="A12", + apiEnd=None, +) + + +ninety_six_column_right = PartialTipConfig( + key="ninety_six_column_right", + description="96 column picking up right column of tiprack", + startingTip="Row 12", + startingNozzle="Row 1", + apiTipConfig=COLUMN, + apiStart="A1", + apiEnd=None, +) + +# flex_96channel_1000 ROW + +ninety_six_row_top = PartialTipConfig( + key="ninety_six_row_top", + description="96 row picking up top row of tiprack", + startingTip="Row A", + startingNozzle="Row H", + apiTipConfig=ROW, + apiStart="H1", + apiEnd=None, +) + +ninety_six_row_bottom = PartialTipConfig( + key="ninety_six_row_bottom", + description="96 row picking up bottom row of tiprack", + startingTip="Row H", + startingNozzle="Row A", + apiTipConfig=ROW, + apiStart="A1", + apiEnd=None, +) + +# pipette = protocol.load_instrument(instrument_name="flex_8channel_50", mount="right") +# works for all 8 channel pipettes +eight_single_top = PartialTipConfig( + key="eight_single_top", + description="8 channel single picking up from the top of the tiprack", + startingTip="A1", + startingNozzle="H1", + apiTipConfig=SINGLE, + apiStart="H1", + apiEnd=None, +) + +eight_single_bottom = PartialTipConfig( + key="eight_single_bottom", + description="8 channel single picking up from the bottom of the tiprack", + startingTip="H1", + startingNozzle="A1", + apiTipConfig=SINGLE, + apiStart="A1", + apiEnd=None, +) + + +eight_partial_top_2_tips = PartialTipConfig( + key="eight_partial_top_2_tips", + description="8 partial bottom 2 tips", + startingTip="H1", + startingNozzle="B1", + apiTipConfig=PARTIAL_COLUMN, + apiStart="H1", + apiEnd="B1", +) + +eight_partial_top_3_tips = PartialTipConfig( + key="eight_partial_top_3_tips", + description="8 partial bottom 3 tips", + startingTip="H1", + startingNozzle="C1", + apiTipConfig=PARTIAL_COLUMN, + apiStart="H1", + apiEnd="C1", +) +eight_partial_top_4_tips = PartialTipConfig( + key="eight_partial_top_4", + description="8 partial bottom 4 tips", + startingTip="H1", + startingNozzle="D1", + apiTipConfig=PARTIAL_COLUMN, + apiStart="H1", + apiEnd="D1", +) +eight_partial_top_5_tips = PartialTipConfig( + key="eight_partial_top_5", + description="8 partial bottom 5 tips", + startingTip="H1", + startingNozzle="E1", + apiTipConfig=PARTIAL_COLUMN, + apiStart="H1", + apiEnd="E1", +) +eight_partial_top_6_tips = PartialTipConfig( + key="eight_partial_top_6", + description="8 partial bottom 6 tips", + startingTip="H1", + startingNozzle="F1", + apiTipConfig=PARTIAL_COLUMN, + apiStart="H1", + apiEnd="F1", +) + +eight_partial_top_7_tips = PartialTipConfig( + key="eight_partial_top_7", + description="8 partial bottom 7 tips", + startingTip="H1", + startingNozzle="G1", + apiTipConfig=PARTIAL_COLUMN, + apiStart="H1", + apiEnd="G1", +) + +all_partial_configs = [ + ninety_six_single_top_left, + ninety_six_single_top_right, + ninety_six_single_bottom_left, + ninety_six_single_bottom_right, + ninety_six_column_left, + ninety_six_column_right, + ninety_six_row_top, + ninety_six_row_bottom, + eight_single_top, + eight_single_bottom, + eight_partial_top_2_tips, + eight_partial_top_3_tips, + eight_partial_top_4_tips, + eight_partial_top_5_tips, + eight_partial_top_6_tips, + eight_partial_top_7_tips, +] + + +def find_partial_tip_config(key: str) -> Optional[PartialTipConfig]: + for config in all_partial_configs: + if config.key == key: + return config + raise ValueError(f"Could not find partial tip config with key {key}") + + +@dataclass +class TestCase: + key: str + description: str + pipette_config_key: str + collision_slot: Optional[str] = None + tip_rack_slot: Optional[str] = None + movement: Optional[str] = None + source_slot: Optional[str] = None + source_well: Optional[str] = None + destination_slot: Optional[str] = None + destination_well: Optional[str] = None + + +north = TestCase( + key="north", + description="North too tall labware on pickup tip", + pipette_config_key="ninety_six_single_top_left", + collision_slot="B2", +) + +north_west = TestCase( + key="north_west", + description="NW too tall labware on pickup tip", + pipette_config_key="ninety_six_single_top_left", + collision_slot="B1", +) + +west = TestCase( + key="west", + description="west too tall labware on pickup tip", + pipette_config_key="ninety_six_single_top_left", + collision_slot="C1", +) + +south_west = TestCase( + key="south_west", + description="west too tall labware on pickup tip", + pipette_config_key="ninety_six_single_bottom_left", + collision_slot="D1", +) + +south = TestCase( + key="south", + description="west too tall labware on pickup tip", + pipette_config_key="ninety_six_single_bottom_left", + collision_slot="D2", +) + +south_east = TestCase( + key="south_east", + description="west too tall labware on pickup tip", + pipette_config_key="ninety_six_single_bottom_right", + collision_slot="D3", +) +east = TestCase( + key="east", + description="west too tall labware on pickup tip", + pipette_config_key="ninety_six_single_bottom_right", + collision_slot="C3", +) + +east_column = TestCase( + key="east_column", + description="west too tall labware on pickup tip", + pipette_config_key="ninety_six_column_left", + collision_slot="C1", +) +west_column = TestCase( + key="west_column", + description="west too tall labware on pickup tip", + pipette_config_key="ninety_six_column_right", + collision_slot="C3", +) + +north_row = TestCase( + key="north_row", + description="north row too tall labware on pickup tip", + pipette_config_key="ninety_six_row_top", + collision_slot="B2", +) + +south_row = TestCase( + key="south_row", + description="south row too tall labware on pickup tip", + pipette_config_key="ninety_six_row_bottom", + collision_slot="D2", +) + +top_edge = TestCase(key="top_edge", description="top edge of robot", pipette_config_key="ninety_six_single_top_left", tip_rack_slot="A1") + +bottom_left_edge = TestCase( + key="bottom_left_edge", description="bottom left edge of robot", pipette_config_key="ninety_six_single_bottom_left", tip_rack_slot="D1" +) + +bottom_right_edge = TestCase( + key="bottom_right_edge", + description="bottom right edge of robot", + pipette_config_key="ninety_six_single_bottom_right", + tip_rack_slot="D3", +) + +c3_right_edge = TestCase( + key="c3_right_edge", description="right edge of c2", pipette_config_key="ninety_six_single_bottom_right", tip_rack_slot="C3" +) + +transfer_destination_collision = TestCase( + key="transfer_destination_collision", + description="transfer north", + pipette_config_key="ninety_six_single_top_left", + tip_rack_slot="B2", + source_slot="D2", + source_well="A1", + destination_slot="D3", + destination_well="A1", + movement="transfer", + collision_slot="C3", +) + +transfer_source_collision = TestCase( + key="transfer_source_collision", + description="transfer north", + pipette_config_key="ninety_six_single_top_left", + tip_rack_slot="B2", + source_slot="D2", + source_well="A1", + destination_slot="D3", + destination_well="A1", + movement="transfer", + collision_slot="C1", +) + +mix_collision = TestCase( + key="mix_collision", + description="mix north", + pipette_config_key="ninety_six_single_top_left", + tip_rack_slot="B2", + source_slot="D2", + source_well="A1", + movement="mix", + collision_slot="C1", +) + +consolidate_source_collision = TestCase( + key="consolidate_source_collision", + description="consolidate north", + pipette_config_key="ninety_six_single_top_left", + tip_rack_slot="B2", + source_slot="D2", + source_well="A1", + destination_slot="D3", + destination_well="A1", + movement="consolidate", + collision_slot="C1", +) + +consolidate_destination_collision = TestCase( + key="consolidate_destination_collision", + description="consolidate north", + pipette_config_key="ninety_six_single_top_left", + tip_rack_slot="B2", + source_slot="D2", + source_well="A1", + destination_slot="D3", + destination_well="A1", + movement="consolidate", + collision_slot="C3", +) + +distribute_source_collision = TestCase( + key="distribute_source_collision", + description="distribute north", + pipette_config_key="ninety_six_single_top_left", + tip_rack_slot="B2", + source_slot="D2", + source_well="A1", + destination_slot="D3", + destination_well="A1", + movement="distribute", + collision_slot="C1", +) + +distribute_destination_collision = TestCase( + key="distribute_destination_collision", + description="distribute north", + pipette_config_key="ninety_six_single_top_left", + tip_rack_slot="B2", + source_slot="D2", + source_well="A1", + destination_slot="D3", + destination_well="A1", + movement="distribute", + collision_slot="C3", +) + +# all have been tested manually and throw an error as expected JTM 20240814 +test_cases = [ + transfer_source_collision, + transfer_destination_collision, + c3_right_edge, + north, + north_west, + west, + south_west, + south, + south_east, + east, + east_column, + west_column, + north_row, + south_row, + top_edge, + bottom_left_edge, + bottom_left_edge, + bottom_right_edge, + mix_collision, + consolidate_source_collision, + consolidate_destination_collision, + distribute_source_collision, + distribute_destination_collision, +] + + +def get_test_case(key: str) -> Optional[TestCase]: + for test_case in test_cases: + if test_case.key == key: + return test_case + raise ValueError(f"Could not find test case with key {key}") + + +def run(ctx): + tall_labware_loadname = "opentrons_10_tuberack_falcon_4x50ml_6x15ml_conical" + test_case = get_test_case(key) + + if test_case.tip_rack_slot and test_case.tip_rack_slot != "C2": + tip_rack = ctx.load_labware("opentrons_96_tiprack_1000ul", test_case.tip_rack_slot) + else: + tip_rack = ctx.load_labware("opentrons_96_tiprack_1000ul", "C2") + + pipette_config = find_partial_tip_config(test_case.pipette_config_key) + + pipette = ctx.load_instrument("flex_96channel_1000") + + pipette.configure_nozzle_layout(pipette_config.apiTipConfig, pipette_config.apiStart, tip_racks=[tip_rack]) + + if test_case.collision_slot: + ctx.load_labware(tall_labware_loadname, test_case.collision_slot) + + target_labware_loadname = "nest_96_wellplate_100ul_pcr_full_skirt" + if test_case.source_slot: + source = ctx.load_labware(target_labware_loadname, test_case.source_slot) + + if test_case.destination_slot: + destination = ctx.load_labware(target_labware_loadname, test_case.destination_slot) + + if not test_case.movement: + None # No movement simply pickup tip from the tip rack + pipette.pick_up_tip() + elif test_case.movement == "transfer": + trash = ctx.load_trash_bin("A3") + pipette.transfer(10, source[test_case.source_well], destination[test_case.destination_well]) + elif test_case.movement == "mix": + trash = ctx.load_trash_bin("A3") + well = source[test_case.source_well] + pipette.pick_up_tip() + pipette.move_to(well.bottom(z=2)) + pipette.mix(10, 10) + pipette.move_to(well.top(z=5)) + pipette.blow_out() + pipette.drop_tip() + elif test_case.movement == "consolidate": + trash = ctx.load_trash_bin("A3") + pipette.consolidate( + [10, 10], + [source[test_case.source_well], source[test_case.source_well]], + destination[test_case.destination_well], + ) + elif test_case.movement == "distribute": + trash = ctx.load_trash_bin("A3") + pipette.distribute( + 20, + source[test_case.source_well], + [destination[test_case.destination_well], destination[test_case.destination_well]], + ) diff --git a/analyses-snapshot-testing/files/protocols/Flex_X_v2_20_96_and_8_Overrides_InvalidConfigs.py b/analyses-snapshot-testing/files/protocols/Flex_X_v2_20_96_and_8_Overrides_InvalidConfigs.py new file mode 100644 index 00000000000..9d275c2db84 --- /dev/null +++ b/analyses-snapshot-testing/files/protocols/Flex_X_v2_20_96_and_8_Overrides_InvalidConfigs.py @@ -0,0 +1,185 @@ +from dataclasses import dataclass +from typing import Optional +from opentrons.protocol_api import PARTIAL_COLUMN + +# inspired by https://opentrons.atlassian.net/browse/PLAT-457 + +metadata = { + "protocolName": "Invalid tip configs that should error", + "description": "oooo", +} + +requirements = { + "robotType": "Flex", + "apiLevel": "2.20", +} + + +@dataclass +class PartialTipConfig: + key: str + pipette_load_name: str + description: str + starting_tip: str + starting_nozzle: str + api_tip_config: str + api_start: str + api_end: Optional[str] = None + + +# Want to see +"Partial column configuration is only supported on 8-Channel pipettes" +ninety_six_partial_column_1 = PartialTipConfig( + key="ninety_six_partial_column_1", + pipette_load_name="flex_96channel_1000", + description="96 2 tip pick up top left of tiprack", + starting_tip="A1", + starting_nozzle="H12", + api_tip_config=PARTIAL_COLUMN, + api_start="H12", + api_end="G12", +) + +# https://opentrons.atlassian.net/browse/PLAT-457 +ninety_six_partial_column_2 = PartialTipConfig( + key="ninety_six_partial_column_2", + pipette_load_name="flex_96channel_1000", + description="Full row", + starting_tip="A1", + starting_nozzle="H12", + api_tip_config=PARTIAL_COLUMN, + api_start="H1", + api_end="A1", +) + +ninety_six_partial_column_3 = PartialTipConfig( + key="ninety_six_partial_column_3", + pipette_load_name="flex_96channel_1000", + description="Full Row", + starting_tip="A1", + starting_nozzle="H12", + api_tip_config=PARTIAL_COLUMN, + api_start="H1", + api_end="H12", +) + +# We do not allow PARTIAL_COLUMN to start on the bottom of the tip rack +# Want to see +# "IncompatibleNozzleConfiguration: Attempted Nozzle Configuration does not match any approved map layout for the current pipette." +eight_partial_column_bottom_left = PartialTipConfig( + key="eight_partial_column_bottom_left", + pipette_load_name="flex_8channel_1000", + description="8 channel 2 tip pick up bottom left of tiprack", + starting_tip="H1", + starting_nozzle="A1", + api_tip_config=PARTIAL_COLUMN, + api_start="A1", + api_end="B1", +) + + +# Want to see +# Error 4000 GENERAL_ERROR (ProtocolCommandFailedError): IncompatibleNozzleConfiguration: No entry for front right nozzle 'G12' in pipette +eight_partial_column_bottom_right = PartialTipConfig( + key="eight_partial_column_bottom_right", + pipette_load_name="flex_8channel_1000", + description="8 channel 2 tip pick up bottom left of tiprack", + starting_tip="H12", + starting_nozzle="A1", + api_tip_config=PARTIAL_COLUMN, + api_start="H1", # for partial column only H1 + api_end="G12", # the author thinks this is to specify the ending tip and wants to start at bottom right for 2 tips +) + + +# Partial column configurations require the 'end' parameter. +eight_partial_column_no_end = PartialTipConfig( + key="eight_partial_column_no_end", + pipette_load_name="flex_8channel_1000", + description="8 channel PARTIAL_COLUMN with no end", + starting_tip="H1", + starting_nozzle="A1", + api_tip_config=PARTIAL_COLUMN, + api_start="H1", + # api_end="B1", sets the end to None +) + +# If you call return_tip() while using partial tip pickup, the API will raise an error. +# Error 4000 GENERAL_ERROR (UnexpectedProtocolError): Cannot return tip to a tiprack while the pipette is configured for partial tip. +return_tip_error = PartialTipConfig( + key="return_tip_error", + pipette_load_name="flex_8channel_1000", + description="8 channel 2 tip pick up top left of tiprack", + starting_tip="A1", + starting_nozzle="H1", + api_tip_config=PARTIAL_COLUMN, + api_start="H1", + api_end="G1", # valid 2 tip +) + + +# pipette.drop_tip(tiprack["B1"]) # drops tip in rack location A1 +drop_tip_with_location = PartialTipConfig( + key="drop_tip_with_location", + pipette_load_name="flex_8channel_1000", + description="8 channel 2 tip pick up top left of tiprack", + starting_tip="A1", + starting_nozzle="H1", + api_tip_config=PARTIAL_COLUMN, + api_start="H1", + api_end="G1", # valid 2 tip +) + +all_partial_configs = [ + ninety_six_partial_column_1, + ninety_six_partial_column_2, + ninety_six_partial_column_3, + eight_partial_column_bottom_left, + eight_partial_column_bottom_right, + eight_partial_column_no_end, + return_tip_error, + drop_tip_with_location, +] + + +def find_partial_tip_config(key: str) -> Optional[PartialTipConfig]: + for config in all_partial_configs: + if config.key == key: + return config + raise ValueError(f"Could not find partial tip config with key {key}") + + +def comment_column_has_tip(ctx, tip_rack, column): + range_A_to_H = [chr(i) for i in range(ord("A"), ord("H") + 1)] + wells = [f"{row}{column}" for row in range_A_to_H] + for well in wells: + ctx.comment(f"Tip rack in {tip_rack.parent}, well {well} has tip: {tip_rack.wells_by_name()[well].has_tip}") + + +def run(ctx): + tip_rack = ctx.load_labware("opentrons_flex_96_tiprack_1000ul", "B2") + + pipette_config = find_partial_tip_config(key) + + pipette = ctx.load_instrument(pipette_config.pipette_load_name, "left") + + pipette.configure_nozzle_layout( + style=pipette_config.api_tip_config, start=pipette_config.api_start, end=pipette_config.api_end, tip_racks=[tip_rack] + ) + + target_labware_loadname = "nest_96_wellplate_100ul_pcr_full_skirt" + source = ctx.load_labware(target_labware_loadname, "D2") + destination = ctx.load_labware(target_labware_loadname, "D3") + + trash = ctx.load_trash_bin("A3") + if key == "return_tip_error": + pipette.pick_up_tip() + # this test picks up 2 tips + comment_column_has_tip(ctx, tip_rack, 1) + pipette.return_tip() # this should raise an error + elif key == "drop_tip_with_location": + pipette.pick_up_tip() + comment_column_has_tip(ctx, tip_rack, 1) + pipette.drop_tip(tip_rack["B1"]) # this should raise an error + else: + pipette.transfer(10, source["A1"], destination["A1"]) diff --git a/analyses-snapshot-testing/files/protocols/OT2_S_v2_20_8_None_PARTIAL_COLUMN_HappyPathMixedTipRacks.py b/analyses-snapshot-testing/files/protocols/OT2_S_v2_20_8_None_PARTIAL_COLUMN_HappyPathMixedTipRacks.py new file mode 100644 index 00000000000..784667691d4 --- /dev/null +++ b/analyses-snapshot-testing/files/protocols/OT2_S_v2_20_8_None_PARTIAL_COLUMN_HappyPathMixedTipRacks.py @@ -0,0 +1,111 @@ +from opentrons import protocol_api +from opentrons.protocol_api import PARTIAL_COLUMN + +metadata = { + "protocolName": "Partial Tip with Partial Column and Single Smoke", + "description": "OT-2 protocol with 1ch and 8ch pipette partial/single tip configurations. Mixing tipracks and using separate tipracks. ", +} + +requirements = { + "robotType": "OT-2", + "apiLevel": "2.20", +} + + +def run(protocol: protocol_api.ProtocolContext): + + # DECK SETUP AND LABWARE + partial_tiprack_1 = protocol.load_labware("opentrons_96_tiprack_300ul", "7") + partial_tiprack_2 = protocol.load_labware("opentrons_96_tiprack_300ul", "8") + sample_plate = protocol.load_labware("opentrons_96_wellplate_200ul_pcr_full_skirt", "2") + reservoir_12 = protocol.load_labware("nest_12_reservoir_15ml", "1") + reservoir_1 = protocol.load_labware("nest_1_reservoir_290ml", "3") + + p300_multi = protocol.load_instrument("p300_multi_gen2", mount="left", tip_racks=[partial_tiprack_1]) + p300_single = protocol.load_instrument("p300_single_gen2", mount="right", tip_racks=[partial_tiprack_2]) + + p300_multi.configure_nozzle_layout(style=PARTIAL_COLUMN, start="H1", end="D1", tip_racks=[partial_tiprack_1]) + p300_multi.pick_up_tip() + p300_multi.mix(3, 75, sample_plate["E1"]) + p300_multi.mix(3, 200, reservoir_12["A1"]) + p300_multi.mix(3, 200, reservoir_1["A1"]) + p300_multi.drop_tip() + + p300_multi.transfer( + volume=150, + source=sample_plate["E1"], ##NOTE TO SELF THINK ABOUT THIS THE OFFSET SHOULD BE + dest=sample_plate["E12"], + new_tip="once", + ) + + p300_multi.configure_nozzle_layout(style=PARTIAL_COLUMN, start="H1", end="E1", tip_racks=[partial_tiprack_1]) + p300_multi.distribute( + volume=300, + source=reservoir_12["A12"], + dest=[reservoir_12["A11"], reservoir_12["A10"], reservoir_12["A9"], reservoir_12["A8"], reservoir_12["A7"], reservoir_12["A6"]], + ) + + p300_multi.configure_nozzle_layout(style=PARTIAL_COLUMN, start="H1", end="F1", tip_racks=[partial_tiprack_1]) + p300_multi.consolidate( + volume=25, + source=[ + reservoir_12["A1"], + reservoir_12["A2"], + reservoir_12["A3"], + reservoir_12["A4"], + reservoir_12["A5"], + reservoir_12["A6"], + ], + dest=reservoir_1["A1"], + ) + + p300_multi.pick_up_tip() + p300_multi.touch_tip(reservoir_12["A7"]) + p300_multi.drop_tip() + p300_multi.pick_up_tip() + p300_multi.home() + p300_multi.drop_tip() + + p300_multi.pick_up_tip() + well = reservoir_12["A7"] + # directly from docs http://sandbox.docs.opentrons.com/edge/v2/new_protocol_api.html#opentrons.protocol_api.InstrumentContext.prepare_to_aspirate + p300_multi.move_to(well.bottom(z=2)) + p300_multi.mix(10, 10) + p300_multi.move_to(well.top(z=5)) + p300_multi.blow_out() + p300_multi.prepare_to_aspirate() + p300_multi.move_to(well.bottom(z=2)) + p300_multi.aspirate(10, well.bottom(z=2)) + p300_multi.dispense(10) + p300_multi.drop_tip() + + p300_single.transfer(volume=25, source=sample_plate["A1"], dest=sample_plate["A12"], new_tip="once") + p300_single.distribute( + volume=300, + source=reservoir_12["A1"], + dest=[reservoir_12["A2"], reservoir_12["A3"], reservoir_12["A4"], reservoir_12["A5"], reservoir_12["A6"], reservoir_12["A7"]], + ) + + p300_single.consolidate( + volume=25, + source=[ + reservoir_12["A6"], + reservoir_12["A7"], + reservoir_12["A8"], + reservoir_12["A9"], + reservoir_12["A10"], + reservoir_12["A11"], + reservoir_12["A12"], + ], + dest=reservoir_1["A1"], + ) + + try: + while partial_tiprack_1 != None: + for well in sample_plate.wells(): + p300_single.pick_up_tip(partial_tiprack_1) + p300_single.aspirate(10, well) + p300_single.dispense(10, well) + p300_single.drop_tip() + except: + p300_single.home() diff --git a/analyses-snapshot-testing/files/protocols/OT2_S_v2_20_8_None_SINGLE_HappyPath.py b/analyses-snapshot-testing/files/protocols/OT2_S_v2_20_8_None_SINGLE_HappyPath.py new file mode 100644 index 00000000000..1adf454421c --- /dev/null +++ b/analyses-snapshot-testing/files/protocols/OT2_S_v2_20_8_None_SINGLE_HappyPath.py @@ -0,0 +1,135 @@ +from opentrons.protocol_api import SINGLE + +metadata = { + "protocolName": "OT2 8 Channel SINGLE Happy Path A1 and H1", + "description": "OT2 8 Channel pipette and a SINGLE partial tip configuration.", +} + +requirements = { + "robotType": "OT-2", + "apiLevel": "2.20", +} + + +def run(protocol): + + # trash = protocol.load_trash_bin("A3") # must load trash bin + + partial_tip_rack = protocol.load_labware( + load_name="opentrons_96_tiprack_300ul", + label="Partial Tip Rack", + location="8", + ) + + pipette = protocol.load_instrument(instrument_name="p300_multi_gen2", mount="left") + # mount on the right and you will get an error. + + # On the 8-channel SINGLE + # start="A1" Means the North nozzle will pickup from the SW corner of the tip rack + # start="H1" Means the South nozzle will pickup from the NW corner of the tip rack + pipette.configure_nozzle_layout( + style=SINGLE, + start="A1", # Which nozzle + tip_racks=[partial_tip_rack], + ) + + source_labware_2 = protocol.load_labware( + load_name="nest_96_wellplate_100ul_pcr_full_skirt", + label="2 Source Labware", + location="2", + ) + + destination_labware_3 = protocol.load_labware( + load_name="nest_96_wellplate_100ul_pcr_full_skirt", + label="3 Destination Labware", + location="3", + ) + + volume = 10 # Default volume for actions that require it + + ############################# + # Pipette do work + pipette.consolidate( + [volume, volume], + [source_labware_2["A3"], source_labware_2["A4"]], + destination_labware_3["A3"], + ) + + pipette.transfer(volume, source_labware_2["A6"], destination_labware_3["A6"]) + + pipette.distribute( + 5, + source_labware_2["A7"], + [destination_labware_3["A7"], destination_labware_3["A8"]], + ) + + pipette.pick_up_tip() + pipette.touch_tip(source_labware_2["B1"]) + pipette.drop_tip() + pipette.pick_up_tip() + pipette.home() + pipette.drop_tip() + + pipette.pick_up_tip() + well = source_labware_2["D1"] + # directly from docs http://sandbox.docs.opentrons.com/edge/v2/new_protocol_api.html#opentrons.protocol_api.InstrumentContext.prepare_to_aspirate + pipette.move_to(well.bottom(z=2)) + pipette.mix(10, 10) + pipette.move_to(well.top(z=5)) + pipette.blow_out() + pipette.prepare_to_aspirate() + pipette.move_to(well.bottom(z=2)) + pipette.aspirate(10, well.bottom(z=2)) + pipette.dispense(10) + pipette.drop_tip() + + ############################ + # Change the pipette configuration + + pipette.configure_nozzle_layout( + style=SINGLE, + start="H1", # Which nozzle + tip_racks=[partial_tip_rack], + ) + + source_labware_4 = protocol.load_labware( + load_name="nest_96_wellplate_100ul_pcr_full_skirt", + label="4 Source Labware", + location="4", + ) + + ############################# + # Pipette do work + pipette.consolidate( + [volume, volume], + [source_labware_4["A3"], source_labware_4["A4"]], + destination_labware_3["A3"], + ) + + pipette.transfer(volume, source_labware_4["A6"], source_labware_4["A6"]) + + pipette.distribute( + 5, + source_labware_4["A7"], + [destination_labware_3["A7"], destination_labware_3["A8"]], + ) + + pipette.pick_up_tip() + pipette.touch_tip(destination_labware_3["B1"]) + pipette.drop_tip() + pipette.pick_up_tip() + pipette.home() + pipette.drop_tip() + + pipette.pick_up_tip() + well = destination_labware_3["D1"] + # directly from docs http://sandbox.docs.opentrons.com/edge/v2/new_protocol_api.html#opentrons.protocol_api.InstrumentContext.prepare_to_aspirate + pipette.move_to(well.bottom(z=2)) + pipette.mix(10, 10) + pipette.move_to(well.top(z=5)) + pipette.blow_out() + pipette.prepare_to_aspirate() + pipette.move_to(well.bottom(z=2)) + pipette.aspirate(10, well.bottom(z=2)) + pipette.dispense(10) + pipette.drop_tip() diff --git a/analyses-snapshot-testing/files/protocols/OT2_S_v2_20_8_None_SINGLE_TubeRackCollision.py b/analyses-snapshot-testing/files/protocols/OT2_S_v2_20_8_None_SINGLE_TubeRackCollision.py new file mode 100644 index 00000000000..2cf77913071 --- /dev/null +++ b/analyses-snapshot-testing/files/protocols/OT2_S_v2_20_8_None_SINGLE_TubeRackCollision.py @@ -0,0 +1,64 @@ +from opentrons.protocol_api import SINGLE + +metadata = { + "protocolName": "8Channel SINGLE Pickup Tube Rack collision", + "description": "Unsafe protocol ❗❗❗❗❗❗❗❗❗❗❗ will collide with tube.", +} + +requirements = { + "robotType": "OT-2", + "apiLevel": "2.20", +} + + +def comment_tip_rack_status(ctx, tip_rack): + """ + Print out the tip status for each row in a tip rack. + Each row (A-H) will print the well statuses for columns 1-12 in a single comment, + with a '🟢' for present tips and a '❌' for missing tips. + """ + range_A_to_H = [chr(i) for i in range(ord("A"), ord("H") + 1)] + range_1_to_12 = range(1, 13) + + ctx.comment(f"Tip rack in {tip_rack.parent}") + + for row in range_A_to_H: + status_line = f"{row}: " + for col in range_1_to_12: + well = f"{row}{col}" + has_tip = tip_rack.wells_by_name()[well].has_tip + status_emoji = "🟢" if has_tip else "❌" + status_line += f"{well} {status_emoji} " + + # Print the full status line for the row + ctx.comment(status_line) + + +def run(protocol): + + partial_tip_rack = protocol.load_labware( + load_name="opentrons_96_tiprack_300ul", + label="Partial Tip Rack", + location="3", + ) + + tube_rack = protocol.load_labware( + load_name="opentrons_10_tuberack_falcon_4x50ml_6x15ml_conical", + label="Tube Rack", + location="2", + ) + + pipette = protocol.load_instrument(instrument_name="p300_multi_gen2", mount="left") + + pipette.configure_nozzle_layout( + style=SINGLE, + start="H1", + tip_racks=[partial_tip_rack], + ) + + pipette.pick_up_tip() + comment_tip_rack_status(protocol, partial_tip_rack) + # both commands are not physically possible but throw no error + pipette.aspirate(30, tube_rack["A3"].bottom()) + pipette.dispense(30, tube_rack["A4"].bottom()) + pipette.drop_tip() diff --git a/analyses-snapshot-testing/files/protocols/OT2_S_v2_20_P20M_PARTIAL_COLUMN_Overhang.py b/analyses-snapshot-testing/files/protocols/OT2_S_v2_20_P20M_PARTIAL_COLUMN_Overhang.py new file mode 100644 index 00000000000..6e4a3b5b8e5 --- /dev/null +++ b/analyses-snapshot-testing/files/protocols/OT2_S_v2_20_P20M_PARTIAL_COLUMN_Overhang.py @@ -0,0 +1,155 @@ +from opentrons.protocol_api import PARTIAL_COLUMN + +metadata = { + "protocolName": "p20_multi_gen2 PARTIAL_COLUMN Overhang", + "description": "A protocol that demonstrates overhang into a slot with a partial column configuration.", + "author": "Josh McVey", +} + +requirements = { + "robotType": "OT-2", + "apiLevel": "2.20", +} + + +def comment_tip_rack_status(ctx, tip_rack): + """ + Print out the tip status for each row in a tip rack. + Each row (A-H) will print the well statuses for columns 1-12 in a single comment, + with a '🟢' for present tips and a '❌' for missing tips. + """ + range_A_to_H = [chr(i) for i in range(ord("A"), ord("H") + 1)] + range_1_to_12 = range(1, 13) + + ctx.comment(f"Tip rack in {tip_rack.parent}") + + for row in range_A_to_H: + status_line = f"{row}: " + for col in range_1_to_12: + well = f"{row}{col}" + has_tip = tip_rack.wells_by_name()[well].has_tip + status_emoji = "🟢" if has_tip else "❌" + status_line += f"{well} {status_emoji} " + + # Print the full status line for the row + ctx.comment(status_line) + + +def run(protocol): + + partial_tip_rack = protocol.load_labware( + load_name="opentrons_96_tiprack_20ul", + label="Partial Tip Rack", + location="10", + ) + + pipette = protocol.load_instrument(instrument_name="p20_multi_gen2", mount="left") + + pipette.configure_nozzle_layout( + style=PARTIAL_COLUMN, + start="H1", + end="D1", # 5 Tips + tip_racks=[partial_tip_rack], + ) + + source_labware_5 = protocol.load_labware( + load_name="nest_1_reservoir_290ml", + label="Source Reservoir", + location="5", + ) + + destination_labware_2 = protocol.load_labware( + load_name="nest_96_wellplate_100ul_pcr_full_skirt", + label="PCR Plate", + location="2", + ) + + # Known issue in 8.0.0 + # if you target A1 of the labware in 2 + # nozzle H1 - the front-most nozzle will go to A1 + # this means that tips will be out of the slot + # they will over hang into the 5 slot + # no error is raised + # the overhanging tips will collide with the labware in slot 5 + + # If we ever do detect and error for this + # Take all these examples into a negative Overrides test + + volume = 5 + pipette.pick_up_tip() + comment_tip_rack_status(protocol, partial_tip_rack) + # why with P20 do I get: + # MOTION_PLANNING_FAILURE (PartialTipMovementNotAllowedError): Moving to PCR Plate in slot 2 + # with H1 nozzle partial configuration will result in collision with items in deck slot 5. + # because the P20 would actually collide with the labware in slot 5 + # https://opentrons.atlassian.net/browse/RQA-3198 + # bad - 4 tips will overhang into slot 5 + # pipette.aspirate(volume=volume, location=destination_labware_2["A1"]) + # bad - 3 tips will overhang into slot 5 + # pipette.aspirate(volume=volume, location=destination_labware_2["B1"]) + # bad - 2 tips will overhang into slot 5 + # pipette.aspirate(volume=volume, location=destination_labware_2["C1"]) + # bad - 1 tip will overhang into slot 5 + # pipette.aspirate(volume=volume, location=destination_labware_2["D1"]) + # pipette.aspirate(volume=volume, location=destination_labware_2["E1"]) + # pipette.aspirate(volume=volume, location=destination_labware_2["F1"]) + # pipette.aspirate(volume=volume, location=destination_labware_2["G1"]) + # H is the only safe row + pipette.aspirate(volume=volume, location=destination_labware_2["H1"]) + + +# ignore the below for the time being +""" + # this is safe - from a reservoir + # must aspirate before dispense + pipette.aspirate(volume=volume, location=source_labware_5["A1"]) + # bad - bad - 4 tips will overhang into B2 + pipette.dispense(volume=volume, location=destination_labware_2["A1"]) + # this is safe - from a reservoir + # must aspirate before dispense + pipette.aspirate(volume=volume, location=source_labware_5["A1"]) + # bad - bad - 3 tips will overhang into B2 + pipette.dispense(volume=volume, location=destination_labware_2["B2"]) + # this is safe - from a reservoir + # must aspirate before dispense + pipette.aspirate(volume=volume, location=source_labware_5["A1"]) + # bad - bad - 2 tips will overhang into B2 + pipette.dispense(volume=volume, location=destination_labware_2["C3"]) + # this is safe - from a reservoir + # must aspirate before dispense + pipette.aspirate(volume=volume, location=source_labware_5["A1"]) + # bad - bad - 1 tip will overhang into B2 + pipette.dispense(volume=volume, location=destination_labware_2["D4"]) + # this is safe - from a reservoir + # must aspirate before dispense + pipette.aspirate(volume=volume, location=source_labware_5["A1"]) + # this is safe - 0 tips will overhang into B2 + pipette.dispense(volume=volume, location=destination_labware_2["E5"]) + # bad - has overhang into B2 - 4 tips + pipette.touch_tip(location=destination_labware_2["A1"]) + # bad - has overhang into B2 - 4 tips + pipette.blow_out(location=destination_labware_2["A1"]) + # bad - has overhang into B2 - 4 tips + pipette.mix(repetitions=3, volume=volume, location=destination_labware_2["A2"]) + # bad - aspirate and dispense have overhang into B2 + pipette.drop_tip() + pipette.transfer(volume=volume, source=destination_labware_2["A1"], dest=destination_labware_2["A2"]) + # bad - aspirate has 3 tip overhang but not dispense + pipette.transfer(volume=volume, source=destination_labware_2["B1"], dest=destination_labware_2["E1"]) + # bad - aspirate is safe but dispense has 2 tip overhang + pipette.transfer(volume=volume, source=destination_labware_2["E1"], dest=destination_labware_2["C3"]) + # bad - source and destinations have overhang + pipette.distribute(volume=20, source=destination_labware_2["D2"], dest=[destination_labware_2["D3"], destination_labware_2["D4"]]) + # bad - source has overhang but destinations are safe + pipette.distribute(volume=20, source=destination_labware_2["D2"], dest=[destination_labware_2["E3"], destination_labware_2["E4"]]) + # bad - source has no overhang but 1 destination does + pipette.distribute(volume=20, source=destination_labware_2["E6"], dest=[destination_labware_2["A7"], destination_labware_2["E7"]]) + # bad - source has no overhang but 2 destinations do + pipette.distribute(volume=20, source=destination_labware_2["E7"], dest=[destination_labware_2["A8"], destination_labware_2["A9"]]) + # bad - all sources and destination have overhang + pipette.consolidate(volume=volume, source=[destination_labware_2["A9"], destination_labware_2["A10"]], dest=destination_labware_2["A11"]) + # bad - 1 source has overhang but destination is safe + pipette.consolidate(volume=volume, source=[destination_labware_2["A9"], destination_labware_2["E10"]], dest=destination_labware_2["E11"]) + # bad - sources are safe but destination has overhang + pipette.consolidate(volume=volume, source=[destination_labware_2["E9"], destination_labware_2["E10"]], dest=destination_labware_2["A12"]) +""" diff --git a/analyses-snapshot-testing/files/protocols/OT2_S_v2_20_P20M_Simple.py b/analyses-snapshot-testing/files/protocols/OT2_S_v2_20_P20M_Simple.py new file mode 100644 index 00000000000..6fcfad51541 --- /dev/null +++ b/analyses-snapshot-testing/files/protocols/OT2_S_v2_20_P20M_Simple.py @@ -0,0 +1,90 @@ +from opentrons.protocol_api import PARTIAL_COLUMN + +metadata = { + "protocolName": "p20_multi_gen2 Simple", + "description": "A protocol that demonstrates safe actions with p20_multi_gen2", + "author": "Josh McVey", +} + +requirements = { + "robotType": "OT-2", + "apiLevel": "2.20", +} + + +def comment_tip_rack_status(ctx, tip_rack): + """ + Print out the tip status for each row in a tip rack. + Each row (A-H) will print the well statuses for columns 1-12 in a single comment, + with a '🟢' for present tips and a '❌' for missing tips. + """ + range_A_to_H = [chr(i) for i in range(ord("A"), ord("H") + 1)] + range_1_to_12 = range(1, 13) + + ctx.comment(f"Tip rack in {tip_rack.parent}") + + for row in range_A_to_H: + status_line = f"{row}: " + for col in range_1_to_12: + well = f"{row}{col}" + has_tip = tip_rack.wells_by_name()[well].has_tip + status_emoji = "🟢" if has_tip else "❌" + status_line += f"{well} {status_emoji} " + + # Print the full status line for the row + ctx.comment(status_line) + + +def run(protocol): + + tip_rack = protocol.load_labware( + load_name="opentrons_96_tiprack_20ul", + label="Partial Tip Rack", + location="10", + ) + + pipette = protocol.load_instrument(instrument_name="p20_multi_gen2", mount="left", tip_racks=[tip_rack]) + + source_labware_5 = protocol.load_labware( + load_name="nest_1_reservoir_290ml", + label="Source Reservoir", + location="5", + ) + + destination_labware_2 = protocol.load_labware( + load_name="nest_96_wellplate_100ul_pcr_full_skirt", + label="PCR Plate", + location="2", + ) + + volume = 10 + pipette.pick_up_tip() + comment_tip_rack_status(protocol, tip_rack) + pipette.aspirate(volume=volume, location=destination_labware_2["H1"]) + pipette.dispense(volume=volume, location=destination_labware_2["H2"]) + for i in range(1, 13): + protocol.comment(f"Touching tip to {destination_labware_2[f'H{i}']}") + pipette.touch_tip(location=destination_labware_2[f"H{i}"]) + + pipette.blow_out(location=destination_labware_2["H1"]) + pipette.mix(repetitions=3, volume=volume, location=destination_labware_2["H1"]) + pipette.drop_tip() + # Note that you cannot target Hn like you could on a partial tip + # Invalid source for multichannel transfer: [H3 of PCR Plate on slot 2] + # pipette.transfer(volume=volume, source=destination_labware_2["H3"], dest=destination_labware_2["H4"]) + # comment_tip_rack_status(protocol, tip_rack) + # Invalid source for multichannel transfer: [H4 of PCR Plate on slot 2] + # pipette.distribute(volume=volume, source=destination_labware_2["H4"], dest=[destination_labware_2["H5"], destination_labware_2["H6"]]) + # comment_tip_rack_status(protocol, tip_rack) + # Invalid source for multichannel transfer: [H7 of PCR Plate on slot 2, H8 of PCR Plate on slot 2] + # pipette.consolidate(volume=volume, source=[destination_labware_2["H7"], destination_labware_2["H8"]], dest=destination_labware_2["H9"]) + # comment_tip_rack_status(protocol, tip_rack) + + # but this works and I am inferring + # when using 8 channel pipette and you are specifying a column, use An + pipette.transfer(volume=volume, source=destination_labware_2["A3"], dest=destination_labware_2["A4"]) + comment_tip_rack_status(protocol, tip_rack) + pipette.distribute(volume=volume, source=destination_labware_2["A4"], dest=[destination_labware_2["A5"], destination_labware_2["A6"]]) + comment_tip_rack_status(protocol, tip_rack) + pipette.consolidate(volume=volume, source=[destination_labware_2["A7"], destination_labware_2["A8"]], dest=destination_labware_2["A9"]) + comment_tip_rack_status(protocol, tip_rack) diff --git a/analyses-snapshot-testing/files/protocols/OT2_S_v2_20_P300M_PARTIAL_COLUMN_Overhang.py b/analyses-snapshot-testing/files/protocols/OT2_S_v2_20_P300M_PARTIAL_COLUMN_Overhang.py new file mode 100644 index 00000000000..489b72abfe5 --- /dev/null +++ b/analyses-snapshot-testing/files/protocols/OT2_S_v2_20_P300M_PARTIAL_COLUMN_Overhang.py @@ -0,0 +1,151 @@ +from opentrons.protocol_api import PARTIAL_COLUMN + +metadata = { + "protocolName": "p300_multi_gen2 PARTIAL_COLUMN Overhang", + "description": "A protocol that demonstrates overhang into a slot with a partial column configuration.", + "author": "Josh McVey", +} + +requirements = { + "robotType": "OT-2", + "apiLevel": "2.20", +} + + +def comment_tip_rack_status(ctx, tip_rack): + """ + Print out the tip status for each row in a tip rack. + Each row (A-H) will print the well statuses for columns 1-12 in a single comment, + with a '🟢' for present tips and a '❌' for missing tips. + """ + range_A_to_H = [chr(i) for i in range(ord("A"), ord("H") + 1)] + range_1_to_12 = range(1, 13) + + ctx.comment(f"Tip rack in {tip_rack.parent}") + + for row in range_A_to_H: + status_line = f"{row}: " + for col in range_1_to_12: + well = f"{row}{col}" + has_tip = tip_rack.wells_by_name()[well].has_tip + status_emoji = "🟢" if has_tip else "❌" + status_line += f"{well} {status_emoji} " + + # Print the full status line for the row + ctx.comment(status_line) + + +def run(protocol): + + partial_tip_rack = protocol.load_labware( + load_name="opentrons_96_tiprack_300ul", + label="Partial Tip Rack", + location="10", + ) + + pipette = protocol.load_instrument(instrument_name="p300_multi_gen2", mount="left") + + pipette.configure_nozzle_layout( + style=PARTIAL_COLUMN, + start="H1", + end="D1", # 5 Tips + tip_racks=[partial_tip_rack], + ) + + source_labware_5 = protocol.load_labware( + load_name="nest_1_reservoir_290ml", + label="Source Reservoir", + location="5", + ) + + destination_labware_2 = protocol.load_labware( + load_name="nest_96_wellplate_100ul_pcr_full_skirt", + label="PCR Plate", + location="2", + ) + + # Known issue in 8.0.0 + # if you target A1 of the labware in 2 + # nozzle H1 - the front-most nozzle will go to A1 + # this means that tips will be out of the slot + # they will over hang into the 5 slot + # no error is raised + # the overhanging tips will collide with the labware in 5 + + # If we ever do detect and error for this + # Take all these examples into a negative Overrides test + + volume = 20 + pipette.pick_up_tip() + comment_tip_rack_status(protocol, partial_tip_rack) + # bad - 4 tips will overhang into slot 5 + pipette.aspirate(volume=volume, location=destination_labware_2["A1"]) + # bad - 3 tips will overhang into slot 5 + pipette.aspirate(volume=volume, location=destination_labware_2["B1"]) + # bad - 2 tips will overhang into slot 5 + pipette.aspirate(volume=volume, location=destination_labware_2["C1"]) + # bad - 1 tip will overhang into slot 5 + pipette.aspirate(volume=volume, location=destination_labware_2["D1"]) + # these should be safe??? + pipette.aspirate(volume=volume, location=destination_labware_2["E1"]) + pipette.aspirate(volume=volume, location=destination_labware_2["F1"]) + pipette.aspirate(volume=volume, location=destination_labware_2["G1"]) + # only one that is safe + pipette.aspirate(volume=volume, location=destination_labware_2["H1"]) + + +# ignore the below for the time being +""" + # this is safe - from a reservoir + # must aspirate before dispense + pipette.aspirate(volume=volume, location=source_labware_5["A1"]) + # bad - bad - 4 tips will overhang into B2 + pipette.dispense(volume=volume, location=destination_labware_2["A1"]) + # this is safe - from a reservoir + # must aspirate before dispense + pipette.aspirate(volume=volume, location=source_labware_5["A1"]) + # bad - bad - 3 tips will overhang into B2 + pipette.dispense(volume=volume, location=destination_labware_2["B2"]) + # this is safe - from a reservoir + # must aspirate before dispense + pipette.aspirate(volume=volume, location=source_labware_5["A1"]) + # bad - bad - 2 tips will overhang into B2 + pipette.dispense(volume=volume, location=destination_labware_2["C3"]) + # this is safe - from a reservoir + # must aspirate before dispense + pipette.aspirate(volume=volume, location=source_labware_5["A1"]) + # bad - bad - 1 tip will overhang into B2 + pipette.dispense(volume=volume, location=destination_labware_2["D4"]) + # this is safe - from a reservoir + # must aspirate before dispense + pipette.aspirate(volume=volume, location=source_labware_5["A1"]) + # this is safe - 0 tips will overhang into B2 + pipette.dispense(volume=volume, location=destination_labware_2["E5"]) + # bad - has overhang into B2 - 4 tips + pipette.touch_tip(location=destination_labware_2["A1"]) + # bad - has overhang into B2 - 4 tips + pipette.blow_out(location=destination_labware_2["A1"]) + # bad - has overhang into B2 - 4 tips + pipette.mix(repetitions=3, volume=volume, location=destination_labware_2["A2"]) + # bad - aspirate and dispense have overhang into B2 + pipette.drop_tip() + pipette.transfer(volume=volume, source=destination_labware_2["A1"], dest=destination_labware_2["A2"]) + # bad - aspirate has 3 tip overhang but not dispense + pipette.transfer(volume=volume, source=destination_labware_2["B1"], dest=destination_labware_2["E1"]) + # bad - aspirate is safe but dispense has 2 tip overhang + pipette.transfer(volume=volume, source=destination_labware_2["E1"], dest=destination_labware_2["C3"]) + # bad - source and destinations have overhang + pipette.distribute(volume=20, source=destination_labware_2["D2"], dest=[destination_labware_2["D3"], destination_labware_2["D4"]]) + # bad - source has overhang but destinations are safe + pipette.distribute(volume=20, source=destination_labware_2["D2"], dest=[destination_labware_2["E3"], destination_labware_2["E4"]]) + # bad - source has no overhang but 1 destination does + pipette.distribute(volume=20, source=destination_labware_2["E6"], dest=[destination_labware_2["A7"], destination_labware_2["E7"]]) + # bad - source has no overhang but 2 destinations do + pipette.distribute(volume=20, source=destination_labware_2["E7"], dest=[destination_labware_2["A8"], destination_labware_2["A9"]]) + # bad - all sources and destination have overhang + pipette.consolidate(volume=volume, source=[destination_labware_2["A9"], destination_labware_2["A10"]], dest=destination_labware_2["A11"]) + # bad - 1 source has overhang but destination is safe + pipette.consolidate(volume=volume, source=[destination_labware_2["A9"], destination_labware_2["E10"]], dest=destination_labware_2["E11"]) + # bad - sources are safe but destination has overhang + pipette.consolidate(volume=volume, source=[destination_labware_2["E9"], destination_labware_2["E10"]], dest=destination_labware_2["A12"]) +""" diff --git a/analyses-snapshot-testing/files/protocols/OT2_S_v2_20_P300M_Simple.py b/analyses-snapshot-testing/files/protocols/OT2_S_v2_20_P300M_Simple.py new file mode 100644 index 00000000000..7728a94a077 --- /dev/null +++ b/analyses-snapshot-testing/files/protocols/OT2_S_v2_20_P300M_Simple.py @@ -0,0 +1,94 @@ +from opentrons.protocol_api import PARTIAL_COLUMN, ALL + +metadata = { + "protocolName": "p20_multi_gen2 Simple", + "description": "A protocol that demonstrates safe actions with p20_multi_gen2", + "author": "Josh McVey", +} + +requirements = { + "robotType": "OT-2", + "apiLevel": "2.20", +} + + +def comment_tip_rack_status(ctx, tip_rack): + """ + Print out the tip status for each row in a tip rack. + Each row (A-H) will print the well statuses for columns 1-12 in a single comment, + with a '🟢' for present tips and a '❌' for missing tips. + """ + range_A_to_H = [chr(i) for i in range(ord("A"), ord("H") + 1)] + range_1_to_12 = range(1, 13) + + ctx.comment(f"Tip rack in {tip_rack.parent}") + + for row in range_A_to_H: + status_line = f"{row}: " + for col in range_1_to_12: + well = f"{row}{col}" + has_tip = tip_rack.wells_by_name()[well].has_tip + status_emoji = "🟢" if has_tip else "❌" + status_line += f"{well} {status_emoji} " + + # Print the full status line for the row + ctx.comment(status_line) + + +def run(protocol): + + tip_rack = protocol.load_labware( + load_name="opentrons_96_tiprack_300ul", + label="Partial Tip Rack", + location="10", + ) + + pipette = protocol.load_instrument(instrument_name="p300_multi_gen2", mount="left", tip_racks=[tip_rack]) + + source_labware_5 = protocol.load_labware( + load_name="nest_1_reservoir_290ml", + label="Source Reservoir", + location="5", + ) + + destination_labware_2 = protocol.load_labware( + load_name="nest_96_wellplate_100ul_pcr_full_skirt", + label="PCR Plate", + location="2", + ) + + volume = 40 + pipette.pick_up_tip() + comment_tip_rack_status(protocol, tip_rack) + pipette.aspirate(volume=volume, location=destination_labware_2["H1"]) + pipette.dispense(volume=volume, location=destination_labware_2["H2"]) + for i in range(1, 13): + protocol.comment(f"Touching tip to {destination_labware_2[f'H{i}']}") + pipette.touch_tip(location=destination_labware_2[f"H{i}"]) + + pipette.blow_out(location=destination_labware_2["H1"]) + pipette.mix(repetitions=3, volume=volume, location=destination_labware_2["H1"]) + pipette.drop_tip() + + range_A_to_H = [chr(i) for i in range(ord("A"), ord("H") + 1)] + column1 = [destination_labware_2[f"{row}1"] for row in range_A_to_H] + column2 = [destination_labware_2[f"{row}2"] for row in range_A_to_H] + protocol.comment(f"Transferring {volume}uL from column 1 to column 2") + pipette.transfer(volume=volume, source=column1, dest=column2) + comment_tip_rack_status(protocol, tip_rack) + + # Note that you cannot target Hn like you could on a partial tip + # when I try to use the well destination of Hn for + # transfer, distribute, or consolidate, I get an error like + # Invalid source for multichannel transfer: [H3 of PCR Plate on slot 2] + # pipette.transfer(volume=volume, source=destination_labware_2["H3"], dest=destination_labware_2["H4"]) + # comment_tip_rack_status(protocol, tip_rack) + + # but this works and I am inferring + # when using 8 channel pipette and you are specifying a column, use An + pipette.transfer(volume=volume, source=destination_labware_2["A3"], dest=destination_labware_2["A4"]) + comment_tip_rack_status(protocol, tip_rack) + pipette.distribute(volume=volume, source=destination_labware_2["A4"], dest=[destination_labware_2["A5"], destination_labware_2["A6"]]) + comment_tip_rack_status(protocol, tip_rack) + pipette.consolidate(volume=volume, source=[destination_labware_2["A7"], destination_labware_2["A8"]], dest=destination_labware_2["A9"]) + comment_tip_rack_status(protocol, tip_rack) diff --git a/analyses-snapshot-testing/files/protocols/OT2_S_v2_20_P50_touch_tip.py b/analyses-snapshot-testing/files/protocols/OT2_S_v2_20_P50_touch_tip.py new file mode 100644 index 00000000000..50f04c1ead2 --- /dev/null +++ b/analyses-snapshot-testing/files/protocols/OT2_S_v2_20_P50_touch_tip.py @@ -0,0 +1,52 @@ +import random +from typing import Set +from opentrons import protocol_api + +# metadata +metadata = { + "protocolName": "touch_tip directly on OT2", + "author": "Josh McVey", + "description": "touch tip on OT2", +} + +requirements = { + "robotType": "OT-2", + "apiLevel": "2.20", +} + + +def load_liquid_in_all_wells(labware, liquid) -> None: + for well in labware.wells(): + well.load_liquid(liquid=liquid, volume=well.max_volume) + + +def run(protocol: protocol_api.ProtocolContext): + + # labware + tiprack2 = protocol.load_labware("opentrons_96_tiprack_20ul", "5") + wet_sample = protocol.load_labware("nest_12_reservoir_15ml", "2") + + # liquids + waterButMoreBlue = protocol.define_liquid( + name="H20", + description="Test this wet!!!", + display_color="#0077b6", + ) + + wet_sample.well("A1").load_liquid(liquid=waterButMoreBlue, volume=200) + wet_sample.well("A2").load_liquid(liquid=waterButMoreBlue, volume=200) + wet_sample.well("A3").load_liquid(liquid=waterButMoreBlue, volume=200) + + # instruments + p20 = protocol.load_instrument("p20_single_gen2", mount="right", tip_racks=[tiprack2]) + + pipette = p20 + + pipette.pick_up_tip() + protocol.comment("touch_tip") + pipette.touch_tip(wet_sample.well("A1")) + protocol.comment("air_gap") + pipette.air_gap(volume=10) + protocol.comment("blow_out with no arguments") + pipette.blow_out() + pipette.drop_tip() diff --git a/analyses-snapshot-testing/files/protocols/OT2_X_v2_20_8_Overrides_InvalidConfigs.py b/analyses-snapshot-testing/files/protocols/OT2_X_v2_20_8_Overrides_InvalidConfigs.py new file mode 100644 index 00000000000..e08cf13eda6 --- /dev/null +++ b/analyses-snapshot-testing/files/protocols/OT2_X_v2_20_8_Overrides_InvalidConfigs.py @@ -0,0 +1,151 @@ +# key = "drop_tip_with_location" +from dataclasses import dataclass +from typing import Optional +from opentrons.protocol_api import PARTIAL_COLUMN + +# inspired by https://opentrons.atlassian.net/browse/PLAT-457 + +metadata = { + "protocolName": "Invalid tip configs that should error", + "description": "oooo", +} + +requirements = { + "robotType": "OT-2", + "apiLevel": "2.20", +} + + +@dataclass +class PartialTipConfig: + key: str + pipette_load_name: str + description: str + starting_tip: str + starting_nozzle: str + api_tip_config: str + api_start: str + api_end: Optional[str] = None + + +# We do not allow PARTIAL_COLUMN to start on the bottom of the tip rack +# Want to see +# "IncompatibleNozzleConfiguration: Attempted Nozzle Configuration does not match any approved map layout for the current pipette." +eight_partial_column_bottom_left = PartialTipConfig( + key="eight_partial_column_bottom_left", + pipette_load_name="p300_multi_gen2", + description="8 channel 2 tip pick up bottom left of tiprack", + starting_tip="H1", + starting_nozzle="A1", + api_tip_config=PARTIAL_COLUMN, + api_start="A1", + api_end="B1", +) + + +# Want to see +# Error 4000 GENERAL_ERROR (ProtocolCommandFailedError): IncompatibleNozzleConfiguration: No entry for front right nozzle 'G12' in pipette +eight_partial_column_bottom_right = PartialTipConfig( + key="eight_partial_column_bottom_right", + pipette_load_name="p20_multi_gen2", + description="8 channel 2 tip pick up bottom left of tiprack", + starting_tip="H12", + starting_nozzle="A1", + api_tip_config=PARTIAL_COLUMN, + api_start="H1", # for partial column only H1 + api_end="G12", # the author thinks this is to specify the ending tip and wants to start at bottom right for 2 tips +) + + +# Partial column configurations require the 'end' parameter. +eight_partial_column_no_end = PartialTipConfig( + key="eight_partial_column_no_end", + pipette_load_name="p20_multi_gen2", + description="8 channel PARTIAL_COLUMN with no end", + starting_tip="H1", + starting_nozzle="A1", + api_tip_config=PARTIAL_COLUMN, + api_start="H1", + # api_end="B1", sets the end to None +) + +# If you call return_tip() while using partial tip pickup, the API will raise an error. +# Error 4000 GENERAL_ERROR (UnexpectedProtocolError): Cannot return tip to a tiprack while the pipette is configured for partial tip. +return_tip_error = PartialTipConfig( + key="return_tip_error", + pipette_load_name="p20_multi_gen2", + description="8 channel 2 tip pick up top left of tiprack", + starting_tip="A1", + starting_nozzle="H1", + api_tip_config=PARTIAL_COLUMN, + api_start="H1", + api_end="G1", # valid 2 tip +) + + +# pipette.drop_tip(tiprack["B1"]) # drops tip in rack location A1 +drop_tip_with_location = PartialTipConfig( + key="drop_tip_with_location", + pipette_load_name="p300_multi_gen2", + description="8 channel 2 tip pick up top left of tiprack", + starting_tip="A1", + starting_nozzle="H1", + api_tip_config=PARTIAL_COLUMN, + api_start="H1", + api_end="G1", # valid 2 tip +) + +all_partial_configs = [ + eight_partial_column_bottom_left, + eight_partial_column_bottom_right, + eight_partial_column_no_end, + return_tip_error, + drop_tip_with_location, +] + + +def find_partial_tip_config(key: str) -> Optional[PartialTipConfig]: + for config in all_partial_configs: + if config.key == key: + return config + raise ValueError(f"Could not find partial tip config with key {key}") + + +def comment_column_has_tip(ctx, tip_rack, column): + range_A_to_H = [chr(i) for i in range(ord("A"), ord("H") + 1)] + wells = [f"{row}{column}" for row in range_A_to_H] + for well in wells: + ctx.comment(f"Tip rack in {tip_rack.parent}, well {well} has tip: {tip_rack.wells_by_name()[well].has_tip}") + + +def run(ctx): + + tip_rack_20 = ctx.load_labware("opentrons_96_tiprack_20ul", "1") + tip_rack_300 = ctx.load_labware("opentrons_96_tiprack_300ul", "2") + + pipette_config = find_partial_tip_config(key) + + pipette = ctx.load_instrument(pipette_config.pipette_load_name, "left") + + tip_rack = tip_rack_20 + if pipette_config.pipette_load_name.__contains__("300"): + tip_rack = tip_rack_300 + pipette.configure_nozzle_layout( + style=pipette_config.api_tip_config, start=pipette_config.api_start, end=pipette_config.api_end, tip_racks=[tip_rack] + ) + + target_labware_loadname = "nest_96_wellplate_100ul_pcr_full_skirt" + source = ctx.load_labware(target_labware_loadname, "4") + destination = ctx.load_labware(target_labware_loadname, "5") + + if key == "return_tip_error": + pipette.pick_up_tip() + # this test picks up 2 tips + comment_column_has_tip(ctx, tip_rack, 1) + pipette.return_tip() # this should raise an error + elif key == "drop_tip_with_location": + pipette.pick_up_tip() + comment_column_has_tip(ctx, tip_rack, 1) + pipette.drop_tip(tip_rack["A1"]) # this should raise an error + else: + pipette.transfer(10, source["A1"], destination["A1"]) diff --git a/analyses-snapshot-testing/files/templates/basic_flex_rtp_v1.1.py b/analyses-snapshot-testing/files/templates/basic_flex_rtp_v1.1.py new file mode 100644 index 00000000000..9a35d06e0c4 --- /dev/null +++ b/analyses-snapshot-testing/files/templates/basic_flex_rtp_v1.1.py @@ -0,0 +1,522 @@ +from dataclasses import dataclass +from typing import Any, Optional, Union +from opentrons.protocol_api import SINGLE, COLUMN, PARTIAL_COLUMN, ROW, ALL + +metadata = { + "protocolName": "Basic flex RTP template", +} + +requirements = { + "robotType": "Flex", + "apiLevel": "2.20", +} + +####### RTP DEFINITIONS ####### +# NozzleConfigurationType is from opentrons.hardware_control.nozzle_manager import NozzleConfigurationType +# do not want to import that as that interface or location might change +# type is not in shared-data +# cannot do the below +# ApiTipConfigType = Union[SINGLE, COLUMN, PARTIAL_COLUMN, ROW] + + +@dataclass +class PartialTipConfig: + """Dataclass to hold a partial tip configuration descriptively.""" + + key: str + description: str + starting_tip: str + starting_nozzle: str + api_tip_config: Any + api_start: str + api_end: Optional[str] + + def __str__(self): + return ( + f"🔑 Key: {self.key} | 📝 Description: {self.description} | " + f"💉 Starting Tip: {self.starting_tip} | 🔧 Starting Nozzle: {self.starting_nozzle} | " + f"📜 API Tip Config: {self.api_tip_config} | 🚀 API Start: {self.api_start} | " + f"🛑 API End: {self.api_end if self.api_end else 'None'}" + ) + + +#### Define all viable partial tip configurations. + +# flex_96channel_1000 SINGLE +# names and descriptions describe where relative to the tiprack the pipette will pick up tips + +ninety_six_single_back_left = PartialTipConfig( + key="ninety_six_single_back_left", + description="96 single picking up back left of tiprack", + starting_tip="A1", + starting_nozzle="H12", + api_tip_config=SINGLE, + api_start="H12", + api_end=None, +) + +ninety_six_single_back_right = PartialTipConfig( + key="ninety_six_single_back_right", + description="96 single picking up back right of tiprack", + starting_tip="A12", + starting_nozzle="H1", + api_tip_config=SINGLE, + api_start="H1", + api_end=None, +) + +ninety_six_single_front_left = PartialTipConfig( + key="ninety_six_single_front_left", + description="96 single picking up front left of tiprack", + starting_tip="H1", + starting_nozzle="A12", + api_tip_config=SINGLE, + api_start="A12", + api_end=None, +) + +ninety_six_single_front_right = PartialTipConfig( + key="ninety_six_single_front_right", + description="96 single picking up front right of tiprack", + starting_tip="H12", + starting_nozzle="A1", + api_tip_config=SINGLE, + api_start="A1", + api_end=None, +) + +# flex_96channel_1000 COLUMN + +ninety_six_column_left = PartialTipConfig( + key="ninety_six_column_left", + description="96 column picking up left column of tiprack", + starting_tip="Column 1", + starting_nozzle="Column 12", + api_tip_config=COLUMN, + api_start="A12", + api_end=None, +) + + +ninety_six_column_right = PartialTipConfig( + key="ninety_six_column_right", + description="96 column picking up right column of tiprack", + starting_tip="Row 12", + starting_nozzle="Row 1", + api_tip_config=COLUMN, + api_start="A1", + api_end=None, +) + +# flex_96channel_1000 ROW + +ninety_six_row_back = PartialTipConfig( + key="ninety_six_row_back", + description="96 row picking up back row of tiprack", + starting_tip="Row A", + starting_nozzle="Row H", + api_tip_config=ROW, + api_start="H1", + api_end=None, +) + +ninety_six_row_front = PartialTipConfig( + key="ninety_six_row_front", + description="96 row picking up front row of tiprack", + starting_tip="Row H", + starting_nozzle="Row A", + api_tip_config=ROW, + api_start="A1", + api_end=None, +) + +# 8 channel SINGLE +eight_single = PartialTipConfig( + key="eight_single", + description="8 channel single picking up from the back left of the tiprack", + starting_tip="A1", + starting_nozzle="H1", + api_tip_config=SINGLE, + api_start="H1", + api_end=None, +) + +# PARTIAL_COLUMN +eight_partial_back_7_tips = PartialTipConfig( + key="eight_partial_back_7_tips", + description="8 channel picking up 7 tips", + starting_tip="H1", + starting_nozzle="B1", + api_tip_config=PARTIAL_COLUMN, + api_start="H1", + api_end="B1", +) + +eight_partial_back_6_tips = PartialTipConfig( + key="eight_partial_back_6_tips", + description="8 channel picking up 6 tips", + starting_tip="H1", + starting_nozzle="C1", + api_tip_config=PARTIAL_COLUMN, + api_start="H1", + api_end="C1", +) +eight_partial_back_5_tips = PartialTipConfig( + key="eight_partial_back_5_tips", + description="8 channel picking up 5 tips", + starting_tip="H1", + starting_nozzle="D1", + api_tip_config=PARTIAL_COLUMN, + api_start="H1", + api_end="D1", +) +eight_partial_back_4_tips = PartialTipConfig( + key="eight_partial_back_4_tips", + description="8 channel picking up 4 tips", + starting_tip="H1", + starting_nozzle="E1", + api_tip_config=PARTIAL_COLUMN, + api_start="H1", + api_end="E1", +) +eight_partial_back_3_tips = PartialTipConfig( + key="eight_partial_back_3_tips", + description="8 channel picking up 3 tips", + starting_tip="H1", + starting_nozzle="F1", + api_tip_config=PARTIAL_COLUMN, + api_start="H1", + api_end="F1", +) + +eight_partial_back_2_tips = PartialTipConfig( + key="eight_partial_back_2_tips", + description="8 channel picking up 2 tips", + starting_tip="H1", + starting_nozzle="G1", + api_tip_config=PARTIAL_COLUMN, + api_start="H1", + api_end="G1", +) + +no_tip_config = PartialTipConfig( + key="no_tip_config", + description="Will discard and not set a partial tip config", + starting_tip="", + starting_nozzle="", + api_tip_config=ALL, + api_start="", + api_end="", +) + +# make a list of all the partial tip configurations + +all_partial_configs = [ + ninety_six_single_back_left, + ninety_six_single_back_right, + ninety_six_single_front_left, + ninety_six_single_front_right, + ninety_six_column_left, + ninety_six_column_right, + ninety_six_row_back, + ninety_six_row_front, + eight_single, + eight_partial_back_2_tips, + eight_partial_back_3_tips, + eight_partial_back_4_tips, + eight_partial_back_5_tips, + eight_partial_back_6_tips, + eight_partial_back_7_tips, + no_tip_config, +] + + +def find_partial_tip_config(key: str) -> Optional[PartialTipConfig]: + """Find a partial tip config by key.""" + for config in all_partial_configs: + if config.key == key: + return config + raise ValueError(f"Could not find partial tip config with key {key}") + + +reservoir_choices = [ + { + "display_name": "Agilent Reservoir 290 mL", + "value": "agilent_1_reservoir_290ml", + }, + { + "display_name": "Axygen Reservoir 90 mL", + "value": "axygen_1_reservoir_90ml", + }, + { + "display_name": "nest_12_reservoir_15ml", + "value": "nest_12_reservoir_15ml", + }, + { + "display_name": "Nest Reservoir 195 mL", + "value": "nest_1_reservoir_195ml", + }, + { + "display_name": "Nest Reservoir 290 mL", + "value": "nest_1_reservoir_290ml", + }, + { + "display_name": "usa..._12_reservoir_22ml", + "value": "usascientific_12_reservoir_22ml", + }, +] + +position_choices = [ + {"display_name": "A1", "value": "A1"}, + {"display_name": "A2", "value": "A2"}, + {"display_name": "A3", "value": "A3"}, + {"display_name": "B1", "value": "B1"}, + {"display_name": "B2", "value": "B2"}, + {"display_name": "B3", "value": "B3"}, + {"display_name": "C1", "value": "C1"}, + {"display_name": "C2", "value": "C2"}, + {"display_name": "C3", "value": "C3"}, + {"display_name": "D1", "value": "D1"}, + {"display_name": "D2", "value": "D2"}, + {"display_name": "D3", "value": "D3"}, +] + + +def add_parameters(parameters): + parameters.add_str( + display_name="Partial Tip Configuration", + variable_name="partial_tip_config_key", + default="ninety_six_single_back_left", + description="Partial tip configurations described by pickup nozzle and tip count", + choices=[ # value of each choice maps to the key of the partial tip config dataclass we defined + {"display_name": "96 SINGLE nozzle H12", "value": "ninety_six_single_back_left"}, + {"display_name": "96 SINGLE nozzle H1", "value": "ninety_six_single_back_right"}, + {"display_name": "96 SINGLE nozzle A12", "value": "ninety_six_single_front_left"}, + {"display_name": "96 SINGLE nozzle A1", "value": "ninety_six_single_front_right"}, + {"display_name": "96 COLUMN 1", "value": "ninety_six_column_left"}, + {"display_name": "96 COLUMN 12", "value": "ninety_six_column_right"}, + {"display_name": "96 ROW A", "value": "ninety_six_row_back"}, + {"display_name": "96 ROW H", "value": "ninety_six_row_front"}, + {"display_name": "8 SINGLE", "value": "eight_single"}, + {"display_name": "8 PARTIAL 2 tips", "value": "eight_partial_back_2_tips"}, + {"display_name": "8 PARTIAL 3 tips", "value": "eight_partial_back_3_tips"}, + {"display_name": "8 PARTIAL 4 tips", "value": "eight_partial_back_4_tips"}, + {"display_name": "8 PARTIAL 5 tips", "value": "eight_partial_back_5_tips"}, + {"display_name": "8 PARTIAL 6 tips", "value": "eight_partial_back_6_tips"}, + {"display_name": "8 PARTIAL 7 tips", "value": "eight_partial_back_7_tips"}, + {"display_name": "No Partial tip config", "value": "no_tip_config"}, + ], + ) + + parameters.add_str( + display_name="Pipette", + variable_name="pipette_load_name", + choices=[ + { + "display_name": "50µl single channel", + "value": "flex_1channel_50", + }, + { + "display_name": "1000µl single channel", + "value": "flex_1channel_1000", + }, + { + "display_name": "50µl 8 channel", + "value": "flex_8channel_50", + }, + { + "display_name": "1000µl 8 channel", + "value": "flex_8channel_1000", + }, + { + "display_name": "96-Channel Pipette", + "value": "flex_96channel_1000", + }, + ], + default="flex_96channel_1000", + description="Select the pipette type", + ) + + parameters.add_str( + display_name="Tip Rack", + variable_name="tiprack_load_name", + choices=[ + { + "display_name": "1000µl Filter Tip Rack", + "value": "opentrons_flex_96_filtertiprack_1000ul", + }, + { + "display_name": "1000µl Standard Tip Rack", + "value": "opentrons_flex_96_tiprack_1000ul", + }, + { + "display_name": "200µl Standard Tip Rack", + "value": "opentrons_flex_96_tiprack_200ul", + }, + { + "display_name": "200µl Filter Tip Rack", + "value": "opentrons_flex_96_filtertiprack_200ul", + }, + { + "display_name": "50µl Filter Tip Rack", + "value": "opentrons_flex_96_filtertiprack_50ul", + }, + { + "display_name": "50µl Standard Tip Rack", + "value": "opentrons_flex_96_tiprack_50ul", + }, + ], + default="opentrons_flex_96_tiprack_1000ul", + description="Select the tip rack type", + ) + + parameters.add_str( + display_name="Pipette Mount", + variable_name="pipette_mount", + choices=[ + {"display_name": "left", "value": "left"}, + {"display_name": "right", "value": "right"}, + ], + default="left", + description="Select the pipette mount.", + ) + + parameters.add_str( + display_name="Reservoir A", + variable_name="reservoir_a_load_name", + choices=reservoir_choices, + default="nest_1_reservoir_290ml", + description="Select the reservoir type", + ) + + parameters.add_str( + display_name="Reservoir B", + variable_name="reservoir_b_load_name", + choices=reservoir_choices, + default="nest_1_reservoir_290ml", + description="Select the reservoir type", + ) + + parameters.add_str( + display_name="Tiprack Position", + variable_name="tiprack_position", + default="B2", + description="Select the position of the tiprack", + choices=position_choices, + ) + + parameters.add_str( + display_name="Reservoir A Position", + variable_name="reservoir_a_position", + default="C1", + description="Select the position of reservoir A", + choices=position_choices, + ) + + parameters.add_str( + display_name="Reservoir B Position", + variable_name="reservoir_b_position", + default="D1", + description="Select the position of reservoir B", + choices=position_choices, + ) + + +####### END RTP DEFINITIONS ####### + + +def set_configure_nozzle_layout(ctx, pipette, tipracks, tip_config): + """Convenience function to set the nozzle layout of a pipette + with the given tip config we have mapped to a RTP.""" + ctx.comment(f"Setting nozzle layout for {pipette}") + ctx.comment(f"Tip config: {tip_config}") + if tip_config.api_end: + pipette.configure_nozzle_layout( + style=tip_config.api_tip_config, start=tip_config.api_start, end=tip_config.api_end, tip_racks=tipracks + ) + else: + pipette.configure_nozzle_layout(style=tip_config.api_tip_config, start=tip_config.api_start, tip_racks=tipracks) + + +def comment_tip_rack_status(ctx, tip_rack): + """ + Print out the tip status for each row in a tip rack. + Each row (A-H) will print the well statuses for columns 1-12 in a single comment, + with a '🟢' for present tips and a '❌' for missing tips. + """ + range_A_to_H = [chr(i) for i in range(ord("A"), ord("H") + 1)] + range_1_to_12 = range(1, 13) + + ctx.comment(f"Tip rack in {tip_rack.parent}") + + for row in range_A_to_H: + status_line = f"{row}: " + for col in range_1_to_12: + well = f"{row}{col}" + has_tip = tip_rack.wells_by_name()[well].has_tip + status_emoji = "🟢" if has_tip else "❌" + status_line += f"{well} {status_emoji} " + + # Print the full status line for the row + ctx.comment(status_line) + + +def run(ctx): + trash = ctx.load_trash_bin("A3") # must load trash bin + # get the key from the parameters + tip_config = find_partial_tip_config(ctx.params.partial_tip_config_key) + pipette_load_name = ctx.params.pipette_load_name + tiprack_load_name = ctx.params.tiprack_load_name + tip_rack_position = ctx.params.tiprack_position + pipette_mount = ctx.params.pipette_mount + reservoir_a_load_name = ctx.params.reservoir_a_load_name + reservoir_b_load_name = ctx.params.reservoir_b_load_name + reservoir_a_position = ctx.params.reservoir_a_position + reservoir_b_position = ctx.params.reservoir_b_position + # print out the tip config + ctx.comment(f"Running with {tip_config}") + ctx.comment(f"Using pipette {pipette_load_name}") + ctx.comment(f"Using tip rack {tiprack_load_name}") + ctx.comment(f"Using pipette mount {pipette_mount}") + ctx.comment(f"Using reservoir A {reservoir_a_load_name}") + ctx.comment(f"Using reservoir B {reservoir_b_load_name}") + ctx.comment(f"Using reservoir A position {reservoir_a_position}") + ctx.comment(f"Using reservoir B position {reservoir_b_position}") + # load the labware + reservoir_a = ctx.load_labware(reservoir_a_load_name, reservoir_a_position) + reservoir_b = ctx.load_labware(reservoir_b_load_name, reservoir_b_position) + # example code on Flex for a pipette + # comment shows we picked up the tips we expected + if tip_config.key == "no_tip_config" and pipette_load_name == "flex_96channel_1000": + tip_rack = ctx.load_labware(tiprack_load_name, tip_rack_position, adapter="opentrons_flex_96_tiprack_adapter") + else: + tip_rack = ctx.load_labware(tiprack_load_name, tip_rack_position) + pipette = ctx.load_instrument(pipette_load_name, pipette_mount) + # use this convenience function to set the nozzle layout + set_configure_nozzle_layout(ctx=ctx, pipette=pipette, tipracks=[tip_rack], tip_config=tip_config) + + def how_much_to_pipette(tiprack_load_name): + if "50" in tiprack_load_name: + return 20 + else: + return 100 + + volume = how_much_to_pipette(tiprack_load_name) + + pipette.pick_up_tip() + comment_tip_rack_status(ctx=ctx, tip_rack=tip_rack) + ctx.comment("aspirate from reservoir A") + pipette.aspirate(volume=volume, location=reservoir_a.wells()[0]) + ctx.comment("dispense to reservoir B") + pipette.dispense(volume=volume, location=reservoir_b.wells()[0]) + ctx.comment("mixing in reservoir B") + pipette.mix(repetitions=3, volume=volume / 2) + ctx.comment("Aspirate from reservoir A") + pipette.aspirate(volume=volume, location=reservoir_a.wells()[0]) + ctx.comment("Blow out in reservoir A") + pipette.blow_out() + ctx.comment("Aspirate from reservoir B") + pipette.aspirate(volume=volume, location=reservoir_b.wells()[0]) + ctx.comment("air_gap with no argument in reservoir B") + pipette.air_gap() + pipette.drop_tip() diff --git a/analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[09676b9f7e][Flex_X_v2_20_96_None_Overrides_TooTallLabware_Override_south_west].json b/analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[09676b9f7e][Flex_X_v2_20_96_None_Overrides_TooTallLabware_Override_south_west].json new file mode 100644 index 00000000000..2ca289680ef --- /dev/null +++ b/analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[09676b9f7e][Flex_X_v2_20_96_None_Overrides_TooTallLabware_Override_south_west].json @@ -0,0 +1,1500 @@ +{ + "commands": [ + { + "commandType": "home", + "completedAt": "TIMESTAMP", + "createdAt": "TIMESTAMP", + "id": "UUID", + "key": "50c7ae73a4e3f7129874f39dfb514803", + "notes": [], + "params": {}, + "result": {}, + "startedAt": "TIMESTAMP", + "status": "succeeded" + }, + { + "commandType": "loadLabware", + "completedAt": "TIMESTAMP", + "createdAt": "TIMESTAMP", + "id": "UUID", + "key": "73d9d4d55ae8466f3a793ceb70545fa5", + "notes": [], + "params": { + "loadName": "opentrons_96_tiprack_1000ul", + "location": { + "slotName": "C2" + }, + "namespace": "opentrons", + "version": 1 + }, + "result": { + "definition": { + "allowedRoles": [], + "brand": { + "brand": "Opentrons", + "brandId": [], + "links": [ + "https://shop.opentrons.com/collections/opentrons-tips/products/opentrons-1000ul-tips" + ] + }, + "cornerOffsetFromSlot": { + "x": 0, + "y": 0, + "z": 0 + }, + "dimensions": { + "xDimension": 127.76, + "yDimension": 85.48, + "zDimension": 97.47 + }, + "gripperOffsets": {}, + "groups": [ + { + "metadata": {}, + "wells": [ + "A1", + "A10", + "A11", + "A12", + "A2", + "A3", + "A4", + "A5", + "A6", + "A7", + "A8", + "A9", + "B1", + "B10", + "B11", + "B12", + "B2", + "B3", + "B4", + "B5", + "B6", + "B7", + "B8", + "B9", + "C1", + "C10", + "C11", + "C12", + "C2", + "C3", + "C4", + "C5", + "C6", + "C7", + "C8", + "C9", + "D1", + "D10", + "D11", + "D12", + "D2", + "D3", + "D4", + "D5", + "D6", + "D7", + "D8", + "D9", + "E1", + "E10", + "E11", + "E12", + "E2", + "E3", + "E4", + "E5", + "E6", + "E7", + "E8", + "E9", + "F1", + "F10", + "F11", 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When you're testing recovery, add tiprack back as necessary." + }, + "result": {}, + "startedAt": "TIMESTAMP", + "status": "succeeded" + }, + { + "commandType": "pickUpTip", + "completedAt": "TIMESTAMP", + "createdAt": "TIMESTAMP", + "id": "UUID", + "key": "748924f7bc1bc2293181fde240dd2497", + "notes": [], + "params": { + "labwareId": "UUID", + "pipetteId": "UUID", + "wellLocation": { + "offset": { + "x": 0.0, + "y": 0.0, + "z": 0.0 + }, + "origin": "top" + }, + "wellName": "A1" + }, + "result": { + "position": { + "x": 178.38, + "y": 395.38, + "z": 99.0 + }, + "tipDiameter": 5.47, + "tipLength": 85.92999999999999, + "tipVolume": 1000.0 + }, + "startedAt": "TIMESTAMP", + "status": "succeeded" + }, + { + "commandType": "waitForResume", + "completedAt": "TIMESTAMP", + "createdAt": "TIMESTAMP", + "id": "UUID", + "key": "b9df600eccab4fa173cf714a9e113bac", + "notes": [], + "params": { + "message": "Overpressure - While Aspirating" + }, + "result": {}, + "startedAt": "TIMESTAMP", + "status": "succeeded" + }, + { + "commandType": "home", + "completedAt": "TIMESTAMP", + "createdAt": "TIMESTAMP", + "id": "UUID", + "key": "7058414b08572e4a67114c649fbc4baf", + "notes": [], + "params": { + "axes": [ + "leftPlunger", + "leftZ" + ] + }, + "result": {}, + "startedAt": "TIMESTAMP", + "status": "succeeded" + }, + { + "commandType": "waitForResume", + "completedAt": "TIMESTAMP", + "createdAt": "TIMESTAMP", + "id": "UUID", + "key": "f8432cddacf8e16c07eba0897f1eb9e4", + "notes": [], + "params": { + "message": "Use p50UL tips - Swap with tip(s) that are hot glued shut (you will need to swap the tips for retry recovery options)" + }, + "result": {}, + "startedAt": "TIMESTAMP", + "status": "succeeded" + }, + { + "commandType": "aspirate", + "completedAt": "TIMESTAMP", + "createdAt": "TIMESTAMP", + "id": "UUID", + "key": "64ac4c89015a5b101b05c9f241d2b01a", + "notes": [], + "params": { + "flowRate": 716.0, + "labwareId": "UUID", + "pipetteId": "UUID", + "volume": 900.0, + "wellLocation": { + 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+ "labwareId": "UUID", + "pipetteId": "UUID", + "volume": 900.0, + "wellLocation": { + "offset": { + "x": 0.0, + "y": 0.0, + "z": 0.0 + }, + "origin": "top" + }, + "wellName": "A1" + }, + "result": { + "position": { + "x": 391.88, + "y": 42.74, + "z": 44.4 + }, + "volume": 900.0 + }, + "startedAt": "TIMESTAMP", + "status": "succeeded" + }, + { + "commandType": "dispense", + "completedAt": "TIMESTAMP", + "createdAt": "TIMESTAMP", + "id": "UUID", + "key": "d5a40428312b4232069455942e7fc4fb", + "notes": [], + "params": { + "flowRate": 716.0, + "labwareId": "UUID", + "pipetteId": "UUID", + "volume": 900.0, + "wellLocation": { + "offset": { + "x": 0.0, + "y": 0.0, + "z": 0.0 + }, + "origin": "top" + }, + "wellName": "A1" + }, + "result": { + "position": { + "x": 391.88, + "y": 42.74, + "z": 44.4 + }, + "volume": 900.0 + }, + "startedAt": "TIMESTAMP", + "status": "succeeded" + }, + { + "commandType": "aspirate", + "completedAt": "TIMESTAMP", + "createdAt": "TIMESTAMP", + "id": "UUID", + "key": "89153d8b32e4685dbc442e6591d02947", + "notes": [], + "params": { + "flowRate": 716.0, + "labwareId": "UUID", + "pipetteId": "UUID", + "volume": 900.0, + "wellLocation": { + "offset": { + "x": 0.0, + "y": 0.0, + "z": 0.0 + }, + "origin": "top" + }, + "wellName": "A1" + }, + "result": { + "position": { + "x": 391.88, + "y": 42.74, + "z": 44.4 + }, + "volume": 900.0 + }, + "startedAt": "TIMESTAMP", + "status": "succeeded" + }, + { + "commandType": "dispense", + "completedAt": "TIMESTAMP", + "createdAt": "TIMESTAMP", + "id": "UUID", + "key": "a5b8fd811d0ef18cc2dfd021bd49f205", + "notes": [], + "params": { + "flowRate": 716.0, + "labwareId": "UUID", + "pipetteId": "UUID", + "volume": 900.0, + "wellLocation": { + "offset": { + "x": 0.0, + "y": 0.0, + "z": 0.0 + }, + "origin": "top" + }, + "wellName": "A1" + }, + "result": { + "position": { + "x": 391.88, + "y": 42.74, + "z": 44.4 + }, + "volume": 900.0 + }, + "startedAt": "TIMESTAMP", + "status": "succeeded" + }, + { + "commandType": 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900.0 + }, + "startedAt": "TIMESTAMP", + "status": "succeeded" + }, + { + "commandType": "aspirate", + "completedAt": "TIMESTAMP", + "createdAt": "TIMESTAMP", + "id": "UUID", + "key": "bedb30145351546caecd4fde02041d3e", + "notes": [], + "params": { + "flowRate": 716.0, + "labwareId": "UUID", + "pipetteId": "UUID", + "volume": 900.0, + "wellLocation": { + "offset": { + "x": 0.0, + "y": 0.0, + "z": 0.0 + }, + "origin": "top" + }, + "wellName": "A1" + }, + "result": { + "position": { + "x": 391.88, + "y": 42.74, + "z": 44.4 + }, + "volume": 900.0 + }, + "startedAt": "TIMESTAMP", + "status": "succeeded" + }, + { + "commandType": "dispense", + "completedAt": "TIMESTAMP", + "createdAt": "TIMESTAMP", + "id": "UUID", + "key": "14184571a28f9a7cbced653653a5e4c8", + "notes": [], + "params": { + "flowRate": 716.0, + "labwareId": "UUID", + "pipetteId": "UUID", + "volume": 900.0, + "wellLocation": { + "offset": { + "x": 0.0, + "y": 0.0, + "z": 0.0 + }, + "origin": "top" + }, + "wellName": "A1" + }, 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+ "x": 0.0, + "y": 0.0, + "z": 0.0 + }, + "origin": "top" + }, + "wellName": "A1" + }, + "result": { + "position": { + "x": 391.88, + "y": 42.74, + "z": 44.4 + }, + "volume": 900.0 + }, + "startedAt": "TIMESTAMP", + "status": "succeeded" + }, + { + "commandType": "aspirate", + "completedAt": "TIMESTAMP", + "createdAt": "TIMESTAMP", + "id": "UUID", + "key": "2eb6e6298939a64ca99771710a0f796c", + "notes": [], + "params": { + "flowRate": 716.0, + "labwareId": "UUID", + "pipetteId": "UUID", + "volume": 900.0, + "wellLocation": { + "offset": { + "x": 0.0, + "y": 0.0, + "z": 0.0 + }, + "origin": "top" + }, + "wellName": "A1" + }, + "result": { + "position": { + "x": 391.88, + "y": 42.74, + "z": 44.4 + }, + "volume": 900.0 + }, + "startedAt": "TIMESTAMP", + "status": "succeeded" + }, + { + "commandType": "dispense", + "completedAt": "TIMESTAMP", + "createdAt": "TIMESTAMP", + "id": "UUID", + "key": "09e6b07abc76b0f47eca5bde4a073fc8", + "notes": [], + "params": { + "flowRate": 716.0, + "labwareId": "UUID", + "pipetteId": "UUID", + "volume": 900.0, + "wellLocation": { + "offset": { + "x": 0.0, + "y": 0.0, + "z": 0.0 + }, + "origin": "top" + }, + "wellName": "A1" + }, + "result": { + "position": { + "x": 391.88, + "y": 42.74, + "z": 44.4 + }, + "volume": 900.0 + }, + "startedAt": "TIMESTAMP", + "status": "succeeded" + }, + { + "commandType": "aspirate", + "completedAt": "TIMESTAMP", + "createdAt": "TIMESTAMP", + "id": "UUID", + "key": "f77abbc6fccb00d97c44105e4d0dc8c5", + "notes": [], + "params": { + "flowRate": 716.0, + "labwareId": "UUID", + "pipetteId": "UUID", + "volume": 900.0, + "wellLocation": { + "offset": { + "x": 0.0, + "y": 0.0, + "z": 0.0 + }, + "origin": "top" + }, + "wellName": "A1" + }, + "result": { + "position": { + "x": 391.88, + "y": 42.74, + "z": 44.4 + }, + "volume": 900.0 + }, + "startedAt": "TIMESTAMP", + "status": "succeeded" + }, + { + "commandType": "dispense", + "completedAt": "TIMESTAMP", + "createdAt": "TIMESTAMP", + "id": "UUID", + "key": "cf010ab2b5036733a0536650b665ef0d", + "notes": [], + "params": { + "flowRate": 716.0, + "labwareId": "UUID", + "pipetteId": "UUID", + "volume": 900.0, + "wellLocation": { + "offset": { + "x": 0.0, + "y": 0.0, + "z": 0.0 + }, + "origin": "top" + }, + "wellName": "A1" + }, + "result": { + "position": { + "x": 391.88, + "y": 42.74, + "z": 44.4 + }, + "volume": 900.0 + }, + "startedAt": "TIMESTAMP", + "status": "succeeded" + }, + { + "commandType": "aspirate", + "completedAt": "TIMESTAMP", + "createdAt": "TIMESTAMP", + "id": "UUID", + "key": "7201cbd6da4b3a1f9f9a46b87e7f0406", + "notes": [], + "params": { + "flowRate": 716.0, + "labwareId": "UUID", + "pipetteId": "UUID", + "volume": 900.0, + "wellLocation": { + "offset": { + "x": 0.0, + "y": 0.0, + "z": 0.0 + }, + "origin": "top" + }, + "wellName": "A1" + }, + "result": { + "position": { + "x": 391.88, + "y": 42.74, + "z": 44.4 + }, + "volume": 900.0 + }, + "startedAt": "TIMESTAMP", + "status": "succeeded" + }, + { + "commandType": "dispense", + "completedAt": "TIMESTAMP", + "createdAt": "TIMESTAMP", + "id": "UUID", + "key": "2ede2f094fbeec343eed731eef8194e7", + "notes": [], + "params": { + "flowRate": 716.0, + "labwareId": "UUID", + "pipetteId": "UUID", + "volume": 900.0, + "wellLocation": { + "offset": { + "x": 0.0, + "y": 0.0, + "z": 0.0 + }, + "origin": "top" + }, + "wellName": "A1" + }, + "result": { + "position": { + "x": 391.88, + "y": 42.74, + "z": 44.4 + }, + "volume": 900.0 + }, + "startedAt": "TIMESTAMP", + "status": "succeeded" + }, + { + "commandType": "aspirate", + "completedAt": "TIMESTAMP", + "createdAt": "TIMESTAMP", + "id": "UUID", + "key": "9d8af9e55efc49019e13e9deb41f8931", + "notes": [], + "params": { + "flowRate": 716.0, + "labwareId": "UUID", + "pipetteId": "UUID", + "volume": 900.0, + "wellLocation": { + "offset": { + "x": 0.0, + "y": 0.0, + "z": 0.0 + }, + "origin": "top" + }, + "wellName": "A1" + }, + "result": { + "position": { + "x": 391.88, + "y": 42.74, + "z": 44.4 + }, + "volume": 900.0 + }, + "startedAt": "TIMESTAMP", + "status": "succeeded" + }, + { + "commandType": "dispense", + "completedAt": "TIMESTAMP", + "createdAt": "TIMESTAMP", + "id": "UUID", + "key": "99f5375c033353b7601cae5b9aa65ac0", + "notes": [], + "params": { + "flowRate": 716.0, + "labwareId": "UUID", + "pipetteId": "UUID", + "volume": 900.0, + "wellLocation": { + "offset": { + "x": 0.0, + "y": 0.0, + "z": 0.0 + }, + "origin": "top" + }, + "wellName": "A1" + }, + "result": { + "position": { + "x": 391.88, + "y": 42.74, + "z": 44.4 + }, + "volume": 900.0 + }, + "startedAt": "TIMESTAMP", + "status": "succeeded" + }, + { + "commandType": "waitForResume", + "completedAt": "TIMESTAMP", + "createdAt": "TIMESTAMP", + "id": "UUID", + "key": "8c2e09cbe90d48fa924fb8cc51ab6f2e", + "notes": [], + "params": { + "message": "This tests Liquid Presence Detection - PLEASE MAKE SURE YOU'RE USING 1000UL TIPS OR YOU WILL BREAK THE PIPETTE" + }, + "result": {}, + "startedAt": "TIMESTAMP", + "status": "succeeded" + }, + { + "commandType": "waitForResume", + "completedAt": "TIMESTAMP", + "createdAt": "TIMESTAMP", + "id": "UUID", + "key": "113ace5134dc05770bbbc9f25616e4d2", + "notes": [], + "params": { + "message": "Make sure reservoir is empty, and have full reservoir on standby to switch out with for recovery" + }, + "result": {}, + "startedAt": "TIMESTAMP", + "status": "succeeded" + }, + { + "commandType": "liquidProbe", + "completedAt": "TIMESTAMP", + "createdAt": "TIMESTAMP", + "id": "UUID", + "key": "1c5720bacb264e3da2b314e18b3591c5", + "notes": [], + "params": { + "labwareId": "UUID", + "pipetteId": "UUID", + "wellLocation": { + "offset": { + "x": 0.0, + "y": 0.0, + "z": 2.0 + }, + "origin": "top" + }, + "wellName": "A1" + }, + "result": { + "position": { + "x": 342.38, + "y": 256.78, + "z": 33.4 + }, + "z_position": 0.0 + }, + "startedAt": "TIMESTAMP", + "status": "succeeded" + }, + { + "commandType": "aspirate", + "completedAt": "TIMESTAMP", + "createdAt": "TIMESTAMP", + "id": "UUID", + "key": "e0bbd11eb919a3804d1d23771f645a8d", + "notes": [], + "params": { + "flowRate": 716.0, + "labwareId": "UUID", + "pipetteId": "UUID", + "volume": 900.0, + "wellLocation": { + "offset": { + "x": 0.0, + "y": 0.0, + "z": -25.85 + }, + "origin": "top" + }, + "wellName": "A1" + }, + "result": { + "position": { + "x": 342.38, + "y": 256.78, + "z": 5.55 + }, + "volume": 900.0 + }, + "startedAt": "TIMESTAMP", + "status": "succeeded" + }, + { + "commandType": "dispense", + "completedAt": "TIMESTAMP", + "createdAt": "TIMESTAMP", + "id": "UUID", + "key": "b66c39dd7f7222e62b5c25ef63dc4eaa", + "notes": [], + "params": { + "flowRate": 716.0, + "labwareId": "UUID", + "pipetteId": "UUID", + "volume": 900.0, + "wellLocation": { + "offset": { + "x": 0.0, + "y": 0.0, + "z": -25.85 + }, + "origin": "top" + }, + "wellName": "A1" + }, + "result": { + "position": { + "x": 342.38, + "y": 256.78, + "z": 5.55 + }, + "volume": 900.0 + }, + "startedAt": "TIMESTAMP", + "status": "succeeded" + }, + { + "commandType": "home", + "completedAt": "TIMESTAMP", + "createdAt": "TIMESTAMP", + "id": "UUID", + "key": "1f47f37d8e4b3aea8bbea66e7014ab27", + "notes": [], + "params": { + "axes": [ + "leftPlunger", + "leftZ" + ] + }, + "result": {}, + "startedAt": "TIMESTAMP", + "status": "succeeded" + }, + { + "commandType": "waitForResume", + "completedAt": "TIMESTAMP", + "createdAt": "TIMESTAMP", + "id": "UUID", + "key": "0f904e31fcd8dcc7ac6778e30cb61bb8", + "notes": [], + "params": { + "message": "Overpressure - While Dispensing" + }, + "result": {}, + "startedAt": "TIMESTAMP", + "status": "succeeded" + }, + { + "commandType": "aspirate", + "completedAt": "TIMESTAMP", + "createdAt": "TIMESTAMP", + "id": "UUID", + "key": "f04ecdcd9f9b5219d1cf73c37e540d9f", + "notes": [], + "params": { + "flowRate": 716.0, + "labwareId": "UUID", + "pipetteId": "UUID", + "volume": 900.0, + "wellLocation": { + "offset": { + "x": 0.0, + "y": 0.0, + "z": 19.999999999999993 + }, + "origin": "top" + }, + "wellName": "A1" + }, + "result": { + "position": { + "x": 391.88, + "y": 42.74, + "z": 64.39999999999999 + }, + "volume": 900.0 + }, + "startedAt": "TIMESTAMP", + "status": "succeeded" + }, + { + "commandType": "waitForResume", + "completedAt": "TIMESTAMP", + "createdAt": "TIMESTAMP", + "id": "UUID", + "key": "690df57327aeb3c16ca4ad85203d1ec5", + "notes": [], + "params": { + "message": "Swap with tip(s) that are hot glued shut (you will need to cut the tips for retry recovery options)" + }, + "result": {}, + "startedAt": "TIMESTAMP", + "status": "succeeded" + }, + { + "commandType": "dispense", + "completedAt": "TIMESTAMP", + "createdAt": "TIMESTAMP", + "id": "UUID", + "key": "631e9e0a8230489d6abb8665f0f13463", + "notes": [], + "params": { + "flowRate": 716.0, + "labwareId": "UUID", + "pipetteId": "UUID", + "volume": 900.0, + "wellLocation": { + "offset": { + "x": 0.0, + "y": 0.0, + "z": 19.999999999999993 + }, + "origin": "top" + }, + "wellName": "A1" + }, + "result": { + "position": { + "x": 391.88, + "y": 42.74, + "z": 64.39999999999999 + }, + "volume": 900.0 + }, + "startedAt": "TIMESTAMP", + "status": "succeeded" + }, + { + "commandType": "moveToAddressableAreaForDropTip", + "completedAt": "TIMESTAMP", + "createdAt": "TIMESTAMP", + "id": "UUID", + "key": "0e801e389ac14f125f5ef5db2eae3d08", + "notes": [], + "params": { + "addressableAreaName": "movableTrashA3", + "alternateDropLocation": false, + "forceDirect": false, + "ignoreTipConfiguration": true, + "offset": { + "x": 0.0, + "y": 0.0, + "z": 0.0 + }, + "pipetteId": "UUID" + }, + "result": { + "position": { + "x": 434.25, + "y": 364.0, + "z": 40.0 + } + }, + "startedAt": "TIMESTAMP", + "status": "succeeded" + }, + { + "commandType": "waitForResume", + "completedAt": "TIMESTAMP", + "createdAt": "TIMESTAMP", + "id": "UUID", + "key": "20b6b0a1dd75709308db2b292ec03992", + "notes": [], + "params": { + "message": "You will have to manually remove tips if you're using a modified pipette" + }, + "result": {}, + "startedAt": "TIMESTAMP", + "status": "succeeded" + }, + { + "commandType": "moveToAddressableAreaForDropTip", + "completedAt": "TIMESTAMP", + "createdAt": "TIMESTAMP", + "id": "UUID", + "key": "d7fecbae31209f6f04a2ee350e584c46", + "notes": [], + "params": { + "addressableAreaName": "movableTrashA3", + "alternateDropLocation": false, + "forceDirect": false, + "ignoreTipConfiguration": true, + "offset": { + "x": 0.0, + "y": 0.0, + "z": 0.0 + }, + "pipetteId": "UUID" + }, + "result": { + "position": { + "x": 434.25, + "y": 364.0, + "z": 40.0 + } + }, + "startedAt": "TIMESTAMP", + "status": "succeeded" + }, + { + "commandType": "dropTipInPlace", + "completedAt": "TIMESTAMP", + "createdAt": "TIMESTAMP", + "id": "UUID", + "key": "c4e9dc65f4db718d38cf627ad786ac83", + "notes": [], + "params": { + "pipetteId": "UUID" + }, + "result": {}, + "startedAt": "TIMESTAMP", + "status": "succeeded" + }, + { + "commandType": "waitForResume", + "completedAt": "TIMESTAMP", + "createdAt": "TIMESTAMP", + "id": "UUID", + "key": "65bf172b33169e051174a2d2c6ff08f9", + "notes": [], + "params": { + "message": "This tests Tip Pick Up Failure (General Error for now)" + }, + "result": {}, + "startedAt": "TIMESTAMP", + "status": "succeeded" + }, + { + "commandType": "waitForResume", + "completedAt": "TIMESTAMP", + "createdAt": "TIMESTAMP", + "id": "UUID", + "key": "eddba592c53196f06dd465abd040ab57", + "notes": [], + "params": { + "message": "Please remove tip rack from deck. When you're testing recovery, add tiprack back as necessary." + }, + "result": {}, + "startedAt": "TIMESTAMP", + "status": "succeeded" + }, + { + "commandType": "pickUpTip", + "completedAt": "TIMESTAMP", + "createdAt": "TIMESTAMP", + "id": "UUID", + "key": "d3fb46eb1e9183a7897d150cc1ef5898", + "notes": [], + "params": { + "labwareId": "UUID", + "pipetteId": "UUID", + "wellLocation": { + "offset": { + "x": 0.0, + "y": 0.0, + "z": 0.0 + }, + "origin": "top" + }, + "wellName": "A1" + }, + "result": { + "position": { + "x": 178.38, + "y": 288.38, + "z": 99.0 + }, + "tipDiameter": 5.58, + "tipLength": 47.81, + "tipVolume": 50.0 + }, + "startedAt": "TIMESTAMP", + "status": "succeeded" + }, + { + "commandType": "waitForResume", + "completedAt": "TIMESTAMP", + "createdAt": "TIMESTAMP", + "id": "UUID", + "key": "5019b8a5d55914c4a86174b01c40d297", + "notes": [], + "params": { + "message": "Overpressure - While Aspirating" + }, + "result": {}, + "startedAt": "TIMESTAMP", + "status": "succeeded" + }, + { + "commandType": "home", + "completedAt": "TIMESTAMP", + "createdAt": "TIMESTAMP", + "id": "UUID", + "key": "7aafe07a40a3c427dee717cc84c6e303", + "notes": [], + "params": { + "axes": [ + "rightPlunger", + "rightZ" + ] + }, + "result": {}, + "startedAt": "TIMESTAMP", + "status": "succeeded" + }, + { + "commandType": "waitForResume", + "completedAt": "TIMESTAMP", + "createdAt": "TIMESTAMP", + "id": "UUID", + "key": "2630be2e9b808711cf5ff3c5d69815df", + "notes": [], + "params": { + "message": "Use p50UL tips - Swap with tip(s) that are hot glued shut (you will need to swap the tips for retry recovery options)" + }, + "result": {}, + "startedAt": "TIMESTAMP", + "status": "succeeded" + }, + { + "commandType": "aspirate", + "completedAt": "TIMESTAMP", + "createdAt": "TIMESTAMP", + "id": "UUID", + "key": "2492d664f9c55efed5652b1cbcf9fdde", + "notes": [], + "params": { + "flowRate": 35.0, + "labwareId": "UUID", + "pipetteId": "UUID", + "volume": 50.0, + "wellLocation": { + "offset": { + "x": 0.0, + "y": 0.0, + "z": 0.0 + }, + "origin": "top" + }, + "wellName": "A1" + }, + "result": { + "position": { + "x": 391.88, + "y": 42.74, + "z": 44.4 + }, + "volume": 50.0 + }, + "startedAt": "TIMESTAMP", + "status": "succeeded" + }, + { + "commandType": "dispense", + "completedAt": "TIMESTAMP", + "createdAt": "TIMESTAMP", + "id": "UUID", + "key": "b2d6eb28bc88f476044b1e7e4d6b4107", + "notes": [], + "params": { + "flowRate": 57.0, + "labwareId": "UUID", + "pipetteId": "UUID", + "volume": 50.0, + "wellLocation": { + "offset": { + "x": 0.0, + "y": 0.0, + "z": 0.0 + }, + "origin": "top" + }, + "wellName": "A1" + }, + "result": { + "position": { + "x": 391.88, + "y": 42.74, + "z": 44.4 + }, + "volume": 50.0 + }, + "startedAt": "TIMESTAMP", + "status": "succeeded" + }, + { + "commandType": "aspirate", + "completedAt": "TIMESTAMP", + "createdAt": "TIMESTAMP", + "id": "UUID", + "key": "737fbfd381fa1576044bb4666a4c9483", + "notes": [], + "params": { + "flowRate": 35.0, + "labwareId": "UUID", + "pipetteId": "UUID", + "volume": 50.0, + "wellLocation": { + "offset": { + "x": 0.0, + "y": 0.0, + "z": 0.0 + }, + "origin": "top" + }, + "wellName": "A1" + }, + "result": { + "position": { + "x": 391.88, + "y": 42.74, + "z": 44.4 + }, + "volume": 50.0 + }, + "startedAt": "TIMESTAMP", + "status": "succeeded" + }, + { + "commandType": "dispense", + "completedAt": "TIMESTAMP", + "createdAt": "TIMESTAMP", + "id": "UUID", + "key": "e45f68ed478fc9f9825f00ff31fcde46", + "notes": [], + "params": { + "flowRate": 57.0, + "labwareId": "UUID", + "pipetteId": "UUID", + "volume": 50.0, + "wellLocation": { + "offset": { + "x": 0.0, + "y": 0.0, + "z": 0.0 + }, + "origin": "top" + }, + "wellName": "A1" + }, + "result": { + "position": { + "x": 391.88, + "y": 42.74, + "z": 44.4 + }, + "volume": 50.0 + }, + "startedAt": "TIMESTAMP", + "status": "succeeded" + }, + { + "commandType": "aspirate", + "completedAt": "TIMESTAMP", + "createdAt": "TIMESTAMP", + "id": "UUID", + "key": "9dead7e7447f7a0dbdb9b2145d28c692", + "notes": [], + "params": { + "flowRate": 35.0, + "labwareId": "UUID", + "pipetteId": "UUID", + "volume": 50.0, + "wellLocation": { + "offset": { + "x": 0.0, + "y": 0.0, + "z": 0.0 + }, + "origin": "top" + }, + "wellName": "A1" + }, + "result": { + "position": { + "x": 391.88, + "y": 42.74, + "z": 44.4 + }, + "volume": 50.0 + }, + "startedAt": "TIMESTAMP", + "status": "succeeded" + }, + { + "commandType": "dispense", + "completedAt": "TIMESTAMP", + "createdAt": "TIMESTAMP", + "id": "UUID", + "key": "f154f5a1679179fabd7a55e8e26d0992", + "notes": [], + "params": { + "flowRate": 57.0, + "labwareId": "UUID", + "pipetteId": "UUID", + "volume": 50.0, + "wellLocation": { + "offset": { + "x": 0.0, + "y": 0.0, + "z": 0.0 + }, + "origin": "top" + }, + "wellName": "A1" + }, + "result": { + "position": { + "x": 391.88, + "y": 42.74, + "z": 44.4 + }, + "volume": 50.0 + }, + "startedAt": "TIMESTAMP", + "status": "succeeded" + }, + { + "commandType": "aspirate", + "completedAt": "TIMESTAMP", + "createdAt": "TIMESTAMP", + "id": "UUID", + "key": "e20d2093cb882e562bdf5bc427646443", + "notes": [], + "params": { + "flowRate": 35.0, + "labwareId": "UUID", + "pipetteId": "UUID", + "volume": 50.0, + "wellLocation": { + "offset": { + "x": 0.0, + "y": 0.0, + "z": 0.0 + }, + "origin": "top" + }, + "wellName": "A1" + }, + "result": { + "position": { + "x": 391.88, + "y": 42.74, + "z": 44.4 + }, + "volume": 50.0 + }, + "startedAt": "TIMESTAMP", + "status": "succeeded" + }, + { + "commandType": "dispense", + "completedAt": "TIMESTAMP", + "createdAt": "TIMESTAMP", + "id": "UUID", + "key": "b0a14d30a958196db673fa5ac8eae550", + "notes": [], + "params": { + "flowRate": 57.0, + "labwareId": "UUID", + "pipetteId": "UUID", + "volume": 50.0, + "wellLocation": { + "offset": { + "x": 0.0, + "y": 0.0, + "z": 0.0 + }, + "origin": "top" + }, + "wellName": "A1" + }, + "result": { + "position": { + "x": 391.88, + "y": 42.74, + "z": 44.4 + }, + "volume": 50.0 + }, + "startedAt": "TIMESTAMP", + "status": "succeeded" + }, + { + "commandType": "aspirate", + "completedAt": "TIMESTAMP", + "createdAt": "TIMESTAMP", + "id": "UUID", + "key": "dcba87cf3be1f8600a2dea25b0a83274", + "notes": [], + "params": { + "flowRate": 35.0, + "labwareId": "UUID", + "pipetteId": "UUID", + "volume": 50.0, + "wellLocation": { + "offset": { + "x": 0.0, + "y": 0.0, + "z": 0.0 + }, + "origin": "top" + }, + "wellName": "A1" + }, + "result": { + "position": { + "x": 391.88, + "y": 42.74, + "z": 44.4 + }, + "volume": 50.0 + }, + "startedAt": "TIMESTAMP", + "status": "succeeded" + }, + { + "commandType": "dispense", + "completedAt": "TIMESTAMP", + "createdAt": "TIMESTAMP", + "id": "UUID", + "key": "c9c41ee06959a54f1aab7a8c5119912b", + "notes": [], + "params": { + "flowRate": 57.0, + "labwareId": "UUID", + "pipetteId": "UUID", + "volume": 50.0, + "wellLocation": { + "offset": { + "x": 0.0, + "y": 0.0, + "z": 0.0 + }, + "origin": "top" + }, + "wellName": "A1" + }, + "result": { + "position": { + "x": 391.88, + "y": 42.74, + "z": 44.4 + }, + "volume": 50.0 + }, + "startedAt": "TIMESTAMP", + "status": "succeeded" + }, + { + "commandType": "aspirate", + "completedAt": "TIMESTAMP", + "createdAt": "TIMESTAMP", + "id": "UUID", + "key": "e4c179da374f4f5ba047d341a2aa629e", + "notes": [], + "params": { + "flowRate": 35.0, + "labwareId": "UUID", + "pipetteId": "UUID", + "volume": 50.0, + "wellLocation": { + "offset": { + "x": 0.0, + "y": 0.0, + "z": 0.0 + }, + "origin": "top" + }, + "wellName": "A1" + }, + "result": { + "position": { + "x": 391.88, + "y": 42.74, + "z": 44.4 + }, + "volume": 50.0 + }, + "startedAt": "TIMESTAMP", + "status": "succeeded" + }, + { + "commandType": "dispense", + "completedAt": "TIMESTAMP", + "createdAt": "TIMESTAMP", + "id": "UUID", + "key": "bd6698a069e856a66de54a83992d695f", + "notes": [], + "params": { + "flowRate": 57.0, + "labwareId": "UUID", + "pipetteId": "UUID", + "volume": 50.0, + "wellLocation": { + "offset": { + "x": 0.0, + "y": 0.0, + "z": 0.0 + }, + "origin": "top" + }, + "wellName": "A1" + }, + "result": { + "position": { + "x": 391.88, + "y": 42.74, + "z": 44.4 + }, + "volume": 50.0 + }, + "startedAt": "TIMESTAMP", + "status": "succeeded" + }, + { + "commandType": "aspirate", + "completedAt": "TIMESTAMP", + "createdAt": "TIMESTAMP", + "id": "UUID", + "key": "6d4f1b88b6955d6574e48e31084aeac4", + "notes": [], + "params": { + "flowRate": 35.0, + "labwareId": "UUID", + "pipetteId": "UUID", + "volume": 50.0, + "wellLocation": { + "offset": { + "x": 0.0, + "y": 0.0, + "z": 0.0 + }, + "origin": "top" + }, + "wellName": "A1" + }, + "result": { + "position": { + "x": 391.88, + "y": 42.74, + "z": 44.4 + }, + "volume": 50.0 + }, + "startedAt": "TIMESTAMP", + "status": "succeeded" + }, + { + "commandType": "dispense", + "completedAt": "TIMESTAMP", + "createdAt": "TIMESTAMP", + "id": "UUID", + "key": "147d5fc4adfbe0a46301abaa465df262", + "notes": [], + "params": { + "flowRate": 57.0, + "labwareId": "UUID", + "pipetteId": "UUID", + "volume": 50.0, + "wellLocation": { + "offset": { + "x": 0.0, + "y": 0.0, + "z": 0.0 + }, + "origin": "top" + }, + "wellName": "A1" + }, + "result": { + "position": { + "x": 391.88, + "y": 42.74, + "z": 44.4 + }, + "volume": 50.0 + }, + "startedAt": "TIMESTAMP", + "status": "succeeded" + }, + { + "commandType": "aspirate", + "completedAt": "TIMESTAMP", + "createdAt": "TIMESTAMP", + "id": "UUID", + "key": "b660287ab347393357863827d926402d", + "notes": [], + "params": { + "flowRate": 35.0, + "labwareId": "UUID", + "pipetteId": "UUID", + "volume": 50.0, + "wellLocation": { + "offset": { + "x": 0.0, + "y": 0.0, + "z": 0.0 + }, + "origin": "top" + }, + "wellName": "A1" + }, + "result": { + "position": { + "x": 391.88, + "y": 42.74, + "z": 44.4 + }, + "volume": 50.0 + }, + "startedAt": "TIMESTAMP", + "status": "succeeded" + }, + { + "commandType": "dispense", + "completedAt": "TIMESTAMP", + "createdAt": "TIMESTAMP", + "id": "UUID", + "key": "afaecd2d3f12f463dc0c1596fbec73d8", + "notes": [], + "params": { + "flowRate": 57.0, + "labwareId": "UUID", + "pipetteId": "UUID", + "volume": 50.0, + "wellLocation": { + "offset": { + "x": 0.0, + "y": 0.0, + "z": 0.0 + }, + "origin": "top" + }, + "wellName": "A1" + }, + "result": { + "position": { + "x": 391.88, + "y": 42.74, + "z": 44.4 + }, + "volume": 50.0 + }, + "startedAt": "TIMESTAMP", + "status": "succeeded" + }, + { + "commandType": "aspirate", + "completedAt": "TIMESTAMP", + "createdAt": "TIMESTAMP", + "id": "UUID", + "key": "18a206fcf40b85ef77d65a95eb69b977", + "notes": [], + "params": { + "flowRate": 35.0, + "labwareId": "UUID", + "pipetteId": "UUID", + "volume": 50.0, + "wellLocation": { + "offset": { + "x": 0.0, + "y": 0.0, + "z": 0.0 + }, + "origin": "top" + }, + "wellName": "A1" + }, + "result": { + "position": { + "x": 391.88, + "y": 42.74, + "z": 44.4 + }, + "volume": 50.0 + }, + "startedAt": "TIMESTAMP", + "status": "succeeded" + }, + { + "commandType": "dispense", + "completedAt": "TIMESTAMP", + "createdAt": "TIMESTAMP", + "id": "UUID", + "key": "a66f9c581041537d7c9a0b5b83b2a3bb", + "notes": [], + "params": { + "flowRate": 57.0, + "labwareId": "UUID", + "pipetteId": "UUID", + "volume": 50.0, + "wellLocation": { + "offset": { + "x": 0.0, + "y": 0.0, + "z": 0.0 + }, + "origin": "top" + }, + "wellName": "A1" + }, + "result": { + "position": { + "x": 391.88, + "y": 42.74, + "z": 44.4 + }, + "volume": 50.0 + }, + "startedAt": "TIMESTAMP", + "status": "succeeded" + }, + { + "commandType": "aspirate", + "completedAt": "TIMESTAMP", + "createdAt": "TIMESTAMP", + "id": "UUID", + "key": "ff3ce00c290b4f3a025b51cc08e87e7f", + "notes": [], + "params": { + "flowRate": 35.0, + "labwareId": "UUID", + "pipetteId": "UUID", + "volume": 50.0, + "wellLocation": { + "offset": { + "x": 0.0, + "y": 0.0, + "z": 0.0 + }, + "origin": "top" + }, + "wellName": "A1" + }, + "result": { + "position": { + "x": 391.88, + "y": 42.74, + "z": 44.4 + }, + "volume": 50.0 + }, + "startedAt": "TIMESTAMP", + "status": "succeeded" + }, + { + "commandType": "dispense", + "completedAt": "TIMESTAMP", + "createdAt": "TIMESTAMP", + "id": "UUID", + "key": "0c2b7f9b5117e811de2ca8c708719a4f", + "notes": [], + "params": { + "flowRate": 57.0, + "labwareId": "UUID", + "pipetteId": "UUID", + "volume": 50.0, + "wellLocation": { + "offset": { + "x": 0.0, + "y": 0.0, + "z": 0.0 + }, + "origin": "top" + }, + "wellName": "A1" + }, + "result": { + "position": { + "x": 391.88, + "y": 42.74, + "z": 44.4 + }, + "volume": 50.0 + }, + "startedAt": "TIMESTAMP", + "status": "succeeded" + }, + { + "commandType": "waitForResume", + "completedAt": "TIMESTAMP", + "createdAt": "TIMESTAMP", + "id": "UUID", + "key": "16b3eb79760f3264be5d1d29a9405940", + "notes": [], + "params": { + "message": "This tests Liquid Presence Detection - PLEASE MAKE SURE YOU'RE USING 1000UL TIPS OR YOU WILL BREAK THE PIPETTE" + }, + "result": {}, + "startedAt": "TIMESTAMP", + "status": "succeeded" + }, + { + "commandType": "waitForResume", + "completedAt": "TIMESTAMP", + "createdAt": "TIMESTAMP", + "id": "UUID", + "key": "448d8d14a4ba598c39cedae64f1a7d1d", + "notes": [], + "params": { + "message": "Make sure reservoir is empty, and have full reservoir on standby to switch out with for recovery" + }, + "result": {}, + "startedAt": "TIMESTAMP", + "status": "succeeded" + }, + { + "commandType": "liquidProbe", + "completedAt": "TIMESTAMP", + "createdAt": "TIMESTAMP", + "id": "UUID", + "key": "de2087c49b77fe03a83649111113c157", + "notes": [], + "params": { + "labwareId": "UUID", + "pipetteId": "UUID", + "wellLocation": { + "offset": { + "x": 0.0, + "y": 0.0, + "z": 2.0 + }, + "origin": "top" + }, + "wellName": "A1" + }, + "result": { + "position": { + "x": 342.38, + "y": 256.78, + "z": 33.4 + }, + "z_position": 0.0 + }, + "startedAt": "TIMESTAMP", + "status": "succeeded" + }, + { + "commandType": "aspirate", + "completedAt": "TIMESTAMP", + "createdAt": "TIMESTAMP", + "id": "UUID", + "key": "bcb050e4952ef2d7f7c42dd6838c3c24", + "notes": [], + "params": { + "flowRate": 35.0, + "labwareId": "UUID", + "pipetteId": "UUID", + "volume": 50.0, + "wellLocation": { + "offset": { + "x": 0.0, + "y": 0.0, + "z": -25.85 + }, + "origin": "top" + }, + "wellName": "A1" + }, + "result": { + "position": { + "x": 342.38, + "y": 256.78, + "z": 5.55 + }, + "volume": 50.0 + }, + "startedAt": "TIMESTAMP", + "status": "succeeded" + }, + { + "commandType": "dispense", + "completedAt": "TIMESTAMP", + "createdAt": "TIMESTAMP", + "id": "UUID", + "key": "48dbf180376bece74dd403b1407f9db6", + "notes": [], + "params": { + "flowRate": 57.0, + "labwareId": "UUID", + "pipetteId": "UUID", + "volume": 50.0, + "wellLocation": { + "offset": { + "x": 0.0, + "y": 0.0, + "z": -25.85 + }, + "origin": "top" + }, + "wellName": "A1" + }, + "result": { + "position": { + "x": 342.38, + "y": 256.78, + "z": 5.55 + }, + "volume": 50.0 + }, + "startedAt": "TIMESTAMP", + "status": "succeeded" + }, + { + "commandType": "home", + "completedAt": "TIMESTAMP", + "createdAt": "TIMESTAMP", + "id": "UUID", + "key": "431a83945a647ae1699424f1b19555d4", + "notes": [], + "params": { + "axes": [ + "rightPlunger", + "rightZ" + ] + }, + "result": {}, + "startedAt": "TIMESTAMP", + "status": "succeeded" + }, + { + "commandType": "waitForResume", + "completedAt": "TIMESTAMP", + "createdAt": "TIMESTAMP", + "id": "UUID", + "key": "d291fec87c615fe4446dd14989ec6503", + "notes": [], + "params": { + "message": "Overpressure - While Dispensing" + }, + "result": {}, + "startedAt": "TIMESTAMP", + "status": "succeeded" + }, + { + "commandType": "aspirate", + "completedAt": "TIMESTAMP", + "createdAt": "TIMESTAMP", + "id": "UUID", + "key": "29849adcc3a3cc1c478077d9336f1037", + "notes": [], + "params": { + "flowRate": 35.0, + "labwareId": "UUID", + "pipetteId": "UUID", + "volume": 50.0, + "wellLocation": { + "offset": { + "x": 0.0, + "y": 0.0, + "z": 19.999999999999993 + }, + "origin": "top" + }, + "wellName": "A1" + }, + 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[ + { + "description": "water for ER testing", + "displayColor": "#90e0ef", + "displayName": "Water", + "id": "UUID" + }, + { + "description": "Water for ER testing", + "displayColor": "#0077b6", + "displayName": "Water but more blue", + "id": "UUID" + } + ], + "metadata": { + "author": "Sara Kowalski", + "description": "Simple Protocol that user can use to Phase 1 Error Recovery options for single and multi channel pipettes. NOTE: YOU WILL NEED A MODIFIED PIPETTE (NO SHROUD), and changed order of operations to reduce impact of dispense ER failure", + "protocolName": "2.20 Error Recovery Testing Protocol - Modified" + }, + "modules": [], + "pipettes": [ + { + "id": "UUID", + "mount": "left", + "pipetteName": "p1000_multi_flex" + }, + { + "id": "UUID", + "mount": "right", + "pipetteName": "p50_single_flex" + } + ], + "result": "ok", + "robotType": "OT-3 Standard", + "runTimeParameters": [] +} diff --git a/analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[196ec488f7][Flex_X_v2_20_96_None_Overrides_TooTallLabware_Override_west].json b/analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[196ec488f7][Flex_X_v2_20_96_None_Overrides_TooTallLabware_Override_west].json new file mode 100644 index 00000000000..98709caf300 --- /dev/null +++ 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\"/usr/local/lib/python3.10/site-packages/opentrons/protocol_api/instrument_context.py\", line N, in configure_nozzle_layout\n validated_end = _check_valid_end_nozzle(validated_start, end)\n\n File \"/usr/local/lib/python3.10/site-packages/opentrons/protocol_api/instrument_context.py\", line N, in _check_valid_end_nozzle\n raise ValueError(\"Partial column configurations require the 'end' parameter.\")\n" + }, + "errorType": "PythonException", + "id": "UUID", + "isDefined": false, + "wrappedErrors": [] + } + ] + } + ], + "files": [ + { + "name": "Flex_X_v2_20_96_and_8_Overrides_InvalidConfigs_Override_eight_partial_column_no_end.py", + "role": "main" + } + ], + "labware": [ + { + "definitionUri": "opentrons/opentrons_flex_96_tiprack_1000ul/1", + "id": "UUID", + "loadName": "opentrons_flex_96_tiprack_1000ul", + "location": { + "slotName": "B2" + } + } + ], + "liquids": [], + "metadata": { + "description": "oooo", + "protocolName": "Invalid tip configs that should error" + }, + 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}, + "H6": { + "depth": 59.3, + "diameter": 5.23, + "shape": "circular", + "totalLiquidVolume": 300, + "x": 59.38, + "y": 11.24, + "z": 5.39 + }, + "H7": { + "depth": 59.3, + "diameter": 5.23, + "shape": "circular", + "totalLiquidVolume": 300, + "x": 68.38, + "y": 11.24, + "z": 5.39 + }, + "H8": { + "depth": 59.3, + "diameter": 5.23, + "shape": "circular", + "totalLiquidVolume": 300, + "x": 77.38, + "y": 11.24, + "z": 5.39 + }, + "H9": { + "depth": 59.3, + "diameter": 5.23, + "shape": "circular", + "totalLiquidVolume": 300, + "x": 86.38, + "y": 11.24, + "z": 5.39 + } + } + }, + "labwareId": "UUID" + }, + "startedAt": "TIMESTAMP", + "status": "succeeded" + }, + { + "commandType": "loadPipette", + "completedAt": "TIMESTAMP", + "createdAt": "TIMESTAMP", + "id": "UUID", + "key": "54fddab1eb921f6e1d3aa7e96d2ac307", + "notes": [], + "params": { + "liquidPresenceDetection": false, + "mount": "left", + "pipetteName": "p20_multi_gen2", + "tipOverlapNotAfterVersion": "v3" + }, + "result": { + "pipetteId": "UUID" + }, + "startedAt": "TIMESTAMP", + "status": "succeeded" + } + ], + "config": { + "apiVersion": [ + 2, + 20 + ], + "protocolType": "python" + }, + "createdAt": "TIMESTAMP", + "errors": [ + { + "createdAt": "TIMESTAMP", + "detail": "ValueError [line 134]: Partial column configurations require the 'end' parameter.", + "errorCode": "4000", + "errorInfo": {}, + "errorType": "ExceptionInProtocolError", + "id": "UUID", + "isDefined": false, + "wrappedErrors": [ + { + "createdAt": "TIMESTAMP", + "detail": "ValueError: Partial column configurations require the 'end' parameter.", + "errorCode": "4000", + "errorInfo": { + "args": "(\"Partial column configurations require the 'end' parameter.\",)", + "class": "ValueError", + "traceback": " File \"/usr/local/lib/python3.10/site-packages/opentrons/protocols/execution/execute_python.py\", line N, in exec_run\n exec(\"run(__context)\", new_globs)\n\n File \"\", line N, in \n\n File \"OT2_X_v2_20_8_Overrides_InvalidConfigs_Override_eight_partial_column_no_end.py\", line N, in run\n\n File \"/usr/local/lib/python3.10/site-packages/opentrons/protocols/api_support/util.py\", line N, in _check_version_wrapper\n return decorated_obj(*args, **kwargs)\n\n File \"/usr/local/lib/python3.10/site-packages/opentrons/protocol_api/instrument_context.py\", line N, in configure_nozzle_layout\n validated_end = _check_valid_end_nozzle(validated_start, end)\n\n File \"/usr/local/lib/python3.10/site-packages/opentrons/protocol_api/instrument_context.py\", line N, in _check_valid_end_nozzle\n raise ValueError(\"Partial column configurations require the 'end' parameter.\")\n" + }, + "errorType": "PythonException", + "id": "UUID", + "isDefined": false, + "wrappedErrors": [] + } + ] + } + ], + "files": [ + { + "name": "OT2_X_v2_20_8_Overrides_InvalidConfigs_Override_eight_partial_column_no_end.py", + "role": "main" + } + ], + "labware": [ + { + "definitionUri": 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"pipetteId": "UUID" + }, + "startedAt": "TIMESTAMP", + "status": "succeeded" + } + ], + "config": { + "apiVersion": [ + 2, + 20 + ], + "protocolType": "python" + }, + "createdAt": "TIMESTAMP", + "errors": [ + { + "createdAt": "TIMESTAMP", + "detail": "ValueError [line 167]: Partial column configuration is only supported on 8-Channel pipettes.", + "errorCode": "4000", + "errorInfo": {}, + "errorType": "ExceptionInProtocolError", + "id": "UUID", + "isDefined": false, + "wrappedErrors": [ + { + "createdAt": "TIMESTAMP", + "detail": "ValueError: Partial column configuration is only supported on 8-Channel pipettes.", + "errorCode": "4000", + "errorInfo": { + "args": "('Partial column configuration is only supported on 8-Channel pipettes.',)", + "class": "ValueError", + "traceback": " File \"/usr/local/lib/python3.10/site-packages/opentrons/protocols/execution/execute_python.py\", line N, in exec_run\n exec(\"run(__context)\", new_globs)\n\n File \"\", line N, in \n\n File \"Flex_X_v2_20_96_and_8_Overrides_InvalidConfigs_Override_ninety_six_partial_column_2.py\", line N, in run\n\n File \"/usr/local/lib/python3.10/site-packages/opentrons/protocols/api_support/util.py\", line N, in _check_version_wrapper\n return decorated_obj(*args, **kwargs)\n\n File \"/usr/local/lib/python3.10/site-packages/opentrons/protocol_api/instrument_context.py\", line N, in configure_nozzle_layout\n self._raise_if_configuration_not_supported_by_pipette(style)\n\n File \"/usr/local/lib/python3.10/site-packages/opentrons/protocol_api/instrument_context.py\", line N, in _raise_if_configuration_not_supported_by_pipette\n raise ValueError(\n" + }, + "errorType": "PythonException", + "id": "UUID", + "isDefined": false, + "wrappedErrors": [] + } + ] + } + ], + "files": [ + { + "name": "Flex_X_v2_20_96_and_8_Overrides_InvalidConfigs_Override_ninety_six_partial_column_2.py", + "role": "main" + } + ], + "labware": [ + { + "definitionUri": "opentrons/opentrons_flex_96_tiprack_1000ul/1", + "id": "UUID", + "loadName": "opentrons_flex_96_tiprack_1000ul", + "location": { + "slotName": "B2" + } + } + ], + "liquids": [], + "metadata": { + "description": "oooo", + "protocolName": "Invalid tip configs that should error" + }, + "modules": [], + "pipettes": [ + { + "id": "UUID", + "mount": "left", + "pipetteName": "p1000_96" + } + ], + "result": "not-ok", + "robotType": "OT-3 Standard", + "runTimeParameters": [] +} diff --git a/analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[6122c72996][Flex_X_v2_20_96_and_8_Overrides_InvalidConfigs_Override_ninety_six_partial_column_1].json b/analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[6122c72996][Flex_X_v2_20_96_and_8_Overrides_InvalidConfigs_Override_ninety_six_partial_column_1].json new file mode 100644 index 00000000000..1dcac6e453a --- /dev/null +++ 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300, + "x": 59.38, + "y": 47.24, + "z": 5.39 + }, + "D7": { + "depth": 59.3, + "diameter": 5.23, + "shape": "circular", + "totalLiquidVolume": 300, + "x": 68.38, + "y": 47.24, + "z": 5.39 + }, + "D8": { + "depth": 59.3, + "diameter": 5.23, + "shape": "circular", + "totalLiquidVolume": 300, + "x": 77.38, + "y": 47.24, + "z": 5.39 + }, + "D9": { + "depth": 59.3, + "diameter": 5.23, + "shape": "circular", + "totalLiquidVolume": 300, + "x": 86.38, + "y": 47.24, + "z": 5.39 + }, + "E1": { + "depth": 59.3, + "diameter": 5.23, + "shape": "circular", + "totalLiquidVolume": 300, + "x": 14.38, + "y": 38.24, + "z": 5.39 + }, + "E10": { + "depth": 59.3, + "diameter": 5.23, + "shape": "circular", + "totalLiquidVolume": 300, + "x": 95.38, + "y": 38.24, + "z": 5.39 + }, + "E11": { + "depth": 59.3, + "diameter": 5.23, + "shape": "circular", + "totalLiquidVolume": 300, + "x": 104.38, + "y": 38.24, + "z": 5.39 + }, + "E12": { + "depth": 59.3, + "diameter": 5.23, + "shape": "circular", + "totalLiquidVolume": 300, + "x": 113.38, + "y": 38.24, + "z": 5.39 + }, + "E2": { + "depth": 59.3, + "diameter": 5.23, + "shape": "circular", + "totalLiquidVolume": 300, + "x": 23.38, + "y": 38.24, + "z": 5.39 + }, + "E3": { + "depth": 59.3, + "diameter": 5.23, + "shape": "circular", + "totalLiquidVolume": 300, + "x": 32.38, + "y": 38.24, + "z": 5.39 + }, + "E4": { + "depth": 59.3, + "diameter": 5.23, + "shape": "circular", + "totalLiquidVolume": 300, + "x": 41.38, + "y": 38.24, + "z": 5.39 + }, + "E5": { + "depth": 59.3, + "diameter": 5.23, + "shape": "circular", + "totalLiquidVolume": 300, + "x": 50.38, + "y": 38.24, + "z": 5.39 + }, + "E6": { + "depth": 59.3, + "diameter": 5.23, + "shape": "circular", + "totalLiquidVolume": 300, + "x": 59.38, + "y": 38.24, + "z": 5.39 + }, + "E7": { + "depth": 59.3, + "diameter": 5.23, + "shape": "circular", + "totalLiquidVolume": 300, + "x": 68.38, + "y": 38.24, + "z": 5.39 + }, + "E8": { + "depth": 59.3, + "diameter": 5.23, + "shape": "circular", + "totalLiquidVolume": 300, + "x": 77.38, + "y": 38.24, + "z": 5.39 + }, + "E9": { + "depth": 59.3, + "diameter": 5.23, + "shape": "circular", + "totalLiquidVolume": 300, + "x": 86.38, + "y": 38.24, + "z": 5.39 + }, + "F1": { + "depth": 59.3, + "diameter": 5.23, + "shape": "circular", + "totalLiquidVolume": 300, + "x": 14.38, + "y": 29.24, + "z": 5.39 + }, + "F10": { + "depth": 59.3, + "diameter": 5.23, + "shape": "circular", + "totalLiquidVolume": 300, + "x": 95.38, + "y": 29.24, + "z": 5.39 + }, + "F11": { + "depth": 59.3, + "diameter": 5.23, + "shape": "circular", + "totalLiquidVolume": 300, + "x": 104.38, + "y": 29.24, + "z": 5.39 + }, + "F12": { + "depth": 59.3, + "diameter": 5.23, + "shape": "circular", + "totalLiquidVolume": 300, + "x": 113.38, + "y": 29.24, + "z": 5.39 + }, + "F2": { + "depth": 59.3, + "diameter": 5.23, + "shape": "circular", + "totalLiquidVolume": 300, + "x": 23.38, + "y": 29.24, + "z": 5.39 + }, + "F3": { + "depth": 59.3, + "diameter": 5.23, + "shape": 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"circular", + "totalLiquidVolume": 300, + "x": 14.38, + "y": 20.24, + "z": 5.39 + }, + "G10": { + "depth": 59.3, + "diameter": 5.23, + "shape": "circular", + "totalLiquidVolume": 300, + "x": 95.38, + "y": 20.24, + "z": 5.39 + }, + "G11": { + "depth": 59.3, + "diameter": 5.23, + "shape": "circular", + "totalLiquidVolume": 300, + "x": 104.38, + "y": 20.24, + "z": 5.39 + }, + "G12": { + "depth": 59.3, + "diameter": 5.23, + "shape": "circular", + "totalLiquidVolume": 300, + "x": 113.38, + "y": 20.24, + "z": 5.39 + }, + "G2": { + "depth": 59.3, + "diameter": 5.23, + "shape": "circular", + "totalLiquidVolume": 300, + "x": 23.38, + "y": 20.24, + "z": 5.39 + }, + "G3": { + "depth": 59.3, + "diameter": 5.23, + "shape": "circular", + "totalLiquidVolume": 300, + "x": 32.38, + "y": 20.24, + "z": 5.39 + }, + "G4": { + "depth": 59.3, + "diameter": 5.23, + "shape": "circular", + "totalLiquidVolume": 300, + "x": 41.38, + "y": 20.24, + "z": 5.39 + }, + "G5": { + "depth": 59.3, + "diameter": 5.23, + "shape": "circular", + "totalLiquidVolume": 300, + "x": 50.38, + "y": 20.24, + "z": 5.39 + }, + "G6": { + "depth": 59.3, + "diameter": 5.23, + "shape": "circular", + "totalLiquidVolume": 300, + "x": 59.38, + "y": 20.24, + "z": 5.39 + }, + "G7": { + "depth": 59.3, + "diameter": 5.23, + "shape": "circular", + "totalLiquidVolume": 300, + "x": 68.38, + "y": 20.24, + "z": 5.39 + }, + "G8": { + "depth": 59.3, + "diameter": 5.23, + "shape": "circular", + "totalLiquidVolume": 300, + "x": 77.38, + "y": 20.24, + "z": 5.39 + }, + "G9": { + "depth": 59.3, + "diameter": 5.23, + "shape": "circular", + "totalLiquidVolume": 300, + "x": 86.38, + "y": 20.24, + "z": 5.39 + }, + "H1": { + "depth": 59.3, + "diameter": 5.23, + "shape": "circular", + "totalLiquidVolume": 300, + "x": 14.38, + "y": 11.24, + "z": 5.39 + }, + "H10": { + "depth": 59.3, + "diameter": 5.23, + "shape": "circular", + "totalLiquidVolume": 300, + "x": 95.38, + "y": 11.24, + "z": 5.39 + }, + "H11": { + "depth": 59.3, + "diameter": 5.23, + "shape": "circular", + "totalLiquidVolume": 300, + "x": 104.38, + "y": 11.24, + "z": 5.39 + }, + "H12": { + "depth": 59.3, + "diameter": 5.23, + "shape": "circular", + "totalLiquidVolume": 300, + "x": 113.38, + "y": 11.24, + "z": 5.39 + }, + "H2": { + "depth": 59.3, + "diameter": 5.23, + "shape": "circular", + "totalLiquidVolume": 300, + "x": 23.38, + "y": 11.24, + "z": 5.39 + }, + "H3": { + "depth": 59.3, + "diameter": 5.23, + "shape": "circular", + "totalLiquidVolume": 300, + "x": 32.38, + "y": 11.24, + "z": 5.39 + }, + "H4": { + "depth": 59.3, + "diameter": 5.23, + "shape": "circular", + "totalLiquidVolume": 300, + "x": 41.38, + "y": 11.24, + "z": 5.39 + }, + "H5": { + "depth": 59.3, + "diameter": 5.23, + "shape": "circular", + "totalLiquidVolume": 300, + "x": 50.38, + "y": 11.24, + "z": 5.39 + }, + "H6": { + "depth": 59.3, + "diameter": 5.23, + "shape": "circular", + "totalLiquidVolume": 300, + "x": 59.38, + "y": 11.24, + "z": 5.39 + }, + "H7": { + "depth": 59.3, + "diameter": 5.23, + "shape": "circular", + "totalLiquidVolume": 300, + "x": 68.38, + "y": 11.24, + "z": 5.39 + }, + "H8": { + "depth": 59.3, + "diameter": 5.23, + "shape": "circular", + "totalLiquidVolume": 300, + "x": 77.38, + "y": 11.24, + "z": 5.39 + }, + "H9": { + "depth": 59.3, + "diameter": 5.23, + "shape": "circular", + "totalLiquidVolume": 300, + "x": 86.38, + "y": 11.24, + "z": 5.39 + } + } + }, + "labwareId": "UUID" + }, + "startedAt": "TIMESTAMP", + "status": "succeeded" + }, + { + "commandType": "loadPipette", + "completedAt": "TIMESTAMP", + "createdAt": "TIMESTAMP", + "id": "UUID", + "key": "54fddab1eb921f6e1d3aa7e96d2ac307", + "notes": [], + "params": { + "liquidPresenceDetection": false, + "mount": "left", + "pipetteName": "p20_multi_gen2", + "tipOverlapNotAfterVersion": "v3" + }, + "result": { + "pipetteId": "UUID" + }, + "startedAt": "TIMESTAMP", + "status": "succeeded" + }, + { + "commandType": "configureNozzleLayout", + "completedAt": "TIMESTAMP", + "createdAt": "TIMESTAMP", + "error": { + "createdAt": "TIMESTAMP", + "detail": "No entry for back left nozzle 'G12' in pipette", + "errorCode": "4007", + "errorInfo": {}, + "errorType": "IncompatibleNozzleConfiguration", + "id": "UUID", + "isDefined": false, + "wrappedErrors": [ + { + "createdAt": "TIMESTAMP", + "detail": "KeyError: 'G12'", + "errorCode": "4000", + "errorInfo": { + "args": "('G12',)", + "class": "KeyError", + "traceback": " File \"/usr/local/lib/python3.10/site-packages/opentrons/hardware_control/nozzle_manager.py\", line N, in build\n back_left_row_index, back_left_column_index = _row_col_indices_for_nozzle(\n\n File \"/usr/local/lib/python3.10/site-packages/opentrons/hardware_control/nozzle_manager.py\", line N, in _row_col_indices_for_nozzle\n return _row_or_col_index_for_nozzle(rows, nozzle), _row_or_col_index_for_nozzle(\n\n File \"/usr/local/lib/python3.10/site-packages/opentrons/hardware_control/nozzle_manager.py\", line N, in _row_or_col_index_for_nozzle\n raise KeyError(nozzle)\n" + }, + "errorType": "PythonException", + "id": "UUID", + "isDefined": false, + "wrappedErrors": [] + } + ] + }, + "id": "UUID", + "key": "4b1d27a6f17f312dd76668f0c48ed406", + "notes": [], + "params": { + "configurationParams": { + "backLeftNozzle": "G12", + "frontRightNozzle": "H1", + "primaryNozzle": "H1", + "style": "QUADRANT" + }, + "pipetteId": "UUID" + }, + "startedAt": "TIMESTAMP", + "status": "failed" + } + ], + "config": { + "apiVersion": [ + 2, + 20 + ], + "protocolType": "python" + }, + "createdAt": "TIMESTAMP", + "errors": [ + { + "createdAt": "TIMESTAMP", + "detail": "ProtocolCommandFailedError [line 134]: Error 4000 GENERAL_ERROR (ProtocolCommandFailedError): IncompatibleNozzleConfiguration: No entry for back left nozzle 'G12' in pipette", + "errorCode": "4000", + "errorInfo": {}, + "errorType": "ExceptionInProtocolError", + "id": "UUID", + "isDefined": false, + "wrappedErrors": [ + { + "createdAt": "TIMESTAMP", + "detail": "IncompatibleNozzleConfiguration: No entry for back left nozzle 'G12' in pipette", + "errorCode": "4000", + "errorInfo": {}, + "errorType": "ProtocolCommandFailedError", + "id": "UUID", + "isDefined": false, + "wrappedErrors": [ + { + "createdAt": "TIMESTAMP", + "detail": "No entry for back left nozzle 'G12' in pipette", + "errorCode": "4007", + "errorInfo": {}, + "errorType": "IncompatibleNozzleConfiguration", + "id": "UUID", + "isDefined": false, + "wrappedErrors": [ + { + "createdAt": "TIMESTAMP", + "detail": "KeyError: 'G12'", + "errorCode": "4000", + "errorInfo": { + "args": "('G12',)", + "class": "KeyError", + "traceback": " File \"/usr/local/lib/python3.10/site-packages/opentrons/hardware_control/nozzle_manager.py\", line N, in build\n back_left_row_index, back_left_column_index = _row_col_indices_for_nozzle(\n\n File \"/usr/local/lib/python3.10/site-packages/opentrons/hardware_control/nozzle_manager.py\", line N, in _row_col_indices_for_nozzle\n return _row_or_col_index_for_nozzle(rows, nozzle), _row_or_col_index_for_nozzle(\n\n File \"/usr/local/lib/python3.10/site-packages/opentrons/hardware_control/nozzle_manager.py\", line N, in _row_or_col_index_for_nozzle\n raise KeyError(nozzle)\n" + }, + "errorType": "PythonException", + "id": "UUID", + "isDefined": false, + "wrappedErrors": [] + } + ] + } + ] + } + ] + } + ], + "files": [ + { + "name": "OT2_X_v2_20_8_Overrides_InvalidConfigs_Override_eight_partial_column_bottom_right.py", + "role": "main" + } + ], + "labware": [ + { + "definitionUri": "opentrons/opentrons_96_tiprack_20ul/1", + "id": "UUID", + "loadName": "opentrons_96_tiprack_20ul", + "location": { + "slotName": "1" + } + }, + { + "definitionUri": "opentrons/opentrons_96_tiprack_300ul/1", + "id": "UUID", + "loadName": "opentrons_96_tiprack_300ul", + "location": { + "slotName": "2" + } + } + ], + "liquids": [], + "metadata": { + "description": "oooo", + "protocolName": "Invalid tip configs that should error" + }, + "modules": [], + "pipettes": [ + { + "id": "UUID", + "mount": "left", + "pipetteName": "p20_multi_gen2" + } + ], + "result": "not-ok", + "robotType": "OT-2 Standard", + "runTimeParameters": [] +} diff --git a/analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[a0b755a1a1][Flex_X_v2_20_96_None_Overrides_TooTallLabware_Override_north_west].json b/analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[a0b755a1a1][Flex_X_v2_20_96_None_Overrides_TooTallLabware_Override_north_west].json new file mode 100644 index 00000000000..eca34fc28c3 --- /dev/null +++ b/analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[a0b755a1a1][Flex_X_v2_20_96_None_Overrides_TooTallLabware_Override_north_west].json @@ -0,0 +1,1500 @@ +{ + "commands": [ + { + "commandType": "home", + "completedAt": "TIMESTAMP", + "createdAt": "TIMESTAMP", + "id": "UUID", + "key": "50c7ae73a4e3f7129874f39dfb514803", + "notes": [], + "params": {}, + "result": {}, + "startedAt": "TIMESTAMP", + "status": 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left nozzle 'G12' in pipette", + "errorCode": "4007", + "errorInfo": {}, + "errorType": "IncompatibleNozzleConfiguration", + "id": "UUID", + "isDefined": false, + "wrappedErrors": [ + { + "createdAt": "TIMESTAMP", + "detail": "KeyError: 'G12'", + "errorCode": "4000", + "errorInfo": { + "args": "('G12',)", + "class": "KeyError", + "traceback": " File \"/usr/local/lib/python3.10/site-packages/opentrons/hardware_control/nozzle_manager.py\", line N, in build\n back_left_row_index, back_left_column_index = _row_col_indices_for_nozzle(\n\n File \"/usr/local/lib/python3.10/site-packages/opentrons/hardware_control/nozzle_manager.py\", line N, in _row_col_indices_for_nozzle\n return _row_or_col_index_for_nozzle(rows, nozzle), _row_or_col_index_for_nozzle(\n\n File \"/usr/local/lib/python3.10/site-packages/opentrons/hardware_control/nozzle_manager.py\", line N, in _row_or_col_index_for_nozzle\n raise KeyError(nozzle)\n" + }, + "errorType": "PythonException", + "id": "UUID", + "isDefined": false, + "wrappedErrors": [] + } + ] + }, + "id": "UUID", + "key": "2c37ad797da7df791b57a7843a203e88", + "notes": [], + "params": { + "configurationParams": { + "backLeftNozzle": "G12", + "frontRightNozzle": "H1", + "primaryNozzle": "H1", + "style": "QUADRANT" + }, + "pipetteId": "UUID" + }, + "startedAt": "TIMESTAMP", + "status": "failed" + } + ], + "config": { + "apiVersion": [ + 2, + 20 + ], + "protocolType": "python" + }, + "createdAt": "TIMESTAMP", + "errors": [ + { + "createdAt": "TIMESTAMP", + "detail": "ProtocolCommandFailedError [line 167]: Error 4000 GENERAL_ERROR (ProtocolCommandFailedError): IncompatibleNozzleConfiguration: No entry for back left nozzle 'G12' in pipette", + "errorCode": "4000", + "errorInfo": {}, + "errorType": "ExceptionInProtocolError", + "id": "UUID", + "isDefined": false, + "wrappedErrors": [ + { + "createdAt": "TIMESTAMP", + "detail": "IncompatibleNozzleConfiguration: No entry for back left nozzle 'G12' in pipette", + "errorCode": "4000", + "errorInfo": {}, + "errorType": "ProtocolCommandFailedError", + "id": "UUID", + "isDefined": false, + "wrappedErrors": [ + { + "createdAt": "TIMESTAMP", + "detail": "No entry for back left nozzle 'G12' in pipette", + "errorCode": "4007", + "errorInfo": {}, + "errorType": "IncompatibleNozzleConfiguration", + "id": "UUID", + "isDefined": false, + "wrappedErrors": [ + { + "createdAt": "TIMESTAMP", + "detail": "KeyError: 'G12'", + "errorCode": "4000", + "errorInfo": { + "args": "('G12',)", + "class": "KeyError", + "traceback": " File \"/usr/local/lib/python3.10/site-packages/opentrons/hardware_control/nozzle_manager.py\", line N, in build\n back_left_row_index, back_left_column_index = _row_col_indices_for_nozzle(\n\n File \"/usr/local/lib/python3.10/site-packages/opentrons/hardware_control/nozzle_manager.py\", line N, in _row_col_indices_for_nozzle\n return _row_or_col_index_for_nozzle(rows, nozzle), _row_or_col_index_for_nozzle(\n\n File \"/usr/local/lib/python3.10/site-packages/opentrons/hardware_control/nozzle_manager.py\", line N, in _row_or_col_index_for_nozzle\n raise KeyError(nozzle)\n" + }, + "errorType": "PythonException", + "id": "UUID", + "isDefined": false, + "wrappedErrors": [] + } + ] + } + ] + } + ] + } + ], + "files": [ + { + "name": "Flex_X_v2_20_96_and_8_Overrides_InvalidConfigs_Override_eight_partial_column_bottom_right.py", + "role": "main" + } + ], + "labware": [ + { + "definitionUri": "opentrons/opentrons_flex_96_tiprack_1000ul/1", + "id": "UUID", + "loadName": "opentrons_flex_96_tiprack_1000ul", + "location": { + "slotName": "B2" + } + } + ], + "liquids": [], + "metadata": { + "description": "oooo", + "protocolName": "Invalid tip configs that should error" + }, + "modules": [], + "pipettes": [ + { + "id": "UUID", + "mount": "left", + "pipetteName": "p1000_multi_flex" + } + ], + "result": "not-ok", + "robotType": "OT-3 Standard", + "runTimeParameters": [] +} diff --git a/analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[d2c818bf00][Flex_S_v2_20_P50_LPD].json b/analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[d2c818bf00][Flex_S_v2_20_P50_LPD].json new file mode 100644 index 00000000000..0e914568a92 --- /dev/null +++ b/analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[d2c818bf00][Flex_S_v2_20_P50_LPD].json @@ -0,0 +1,5125 @@ +{ + "commands": [ + { + "commandType": "home", + "completedAt": "TIMESTAMP", + "createdAt": "TIMESTAMP", + "id": "UUID", + "key": "50c7ae73a4e3f7129874f39dfb514803", + "notes": [], + "params": {}, + "result": {}, + "startedAt": "TIMESTAMP", + "status": "succeeded" + }, + { + "commandType": "loadLabware", + "completedAt": "TIMESTAMP", + "createdAt": "TIMESTAMP", + "id": "UUID", + "key": "73d9d4d55ae8466f3a793ceb70545fa5", + "notes": [], + "params": { + "loadName": "opentrons_flex_96_tiprack_1000ul", + "location": { + "slotName": "A2" + }, + "namespace": "opentrons", + "version": 1 + }, + "result": { + "definition": { + "allowedRoles": [], + "brand": { + "brand": "Opentrons", + "brandId": [] + }, + "cornerOffsetFromSlot": { + "x": 0, + "y": 0, + "z": 0 + }, + "dimensions": { + "xDimension": 127.75, + "yDimension": 85.75, + "zDimension": 99 + }, + "gripForce": 16.0, + "gripHeightFromLabwareBottom": 23.9, + "gripperOffsets": {}, + "groups": [ + { + "metadata": {}, + "wells": [ + "A1", + "A10", + "A11", + "A12", + "A2", + "A3", + "A4", + "A5", + "A6", + "A7", + "A8", + "A9", + "B1", + "B10", + "B11", + "B12", + "B2", + "B3", + "B4", + "B5", + "B6", + "B7", + "B8", + "B9", + "C1", + "C10", + "C11", + "C12", + "C2", + "C3", + "C4", + "C5", + "C6", + "C7", + "C8", + "C9", + "D1", + "D10", + "D11", + "D12", + "D2", + "D3", + "D4", + "D5", + "D6", + "D7", + "D8", + "D9", + "E1", + "E10", + "E11", + "E12", + "E2", + "E3", + "E4", + "E5", + "E6", + "E7", + "E8", + "E9", + "F1", + "F10", + 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+ "H4" + ], + [ + "A5", + "B5", + "C5", + "D5", + "E5", + "F5", + "G5", + "H5" + ], + [ + "A6", + "B6", + "C6", + "D6", + "E6", + "F6", + "G6", + "H6" + ], + [ + "A7", + "B7", + "C7", + "D7", + "E7", + "F7", + "G7", + "H7" + ], + [ + "A8", + "B8", + "C8", + "D8", + "E8", + "F8", + "G8", + "H8" + ], + [ + "A9", + "B9", + "C9", + "D9", + "E9", + "F9", + "G9", + "H9" + ] + ], + "parameters": { + "format": "96Standard", + "isMagneticModuleCompatible": false, + "isTiprack": true, + "loadName": "opentrons_flex_96_tiprack_1000ul", + "quirks": [], + "tipLength": 95.6, + "tipOverlap": 10.5 + }, + "schemaVersion": 2, + "stackingOffsetWithLabware": { + "opentrons_flex_96_tiprack_adapter": { + "x": 0, + "y": 0, + "z": 121 + } + }, + "stackingOffsetWithModule": {}, + "version": 1, + "wells": { + "A1": { + "depth": 97.5, + "diameter": 5.47, + "shape": "circular", + "totalLiquidVolume": 1000, + "x": 14.38, + "y": 74.38, + "z": 1.5 + }, + "A10": { + "depth": 97.5, + "diameter": 5.47, + "shape": 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column configuration is only supported on 8-Channel pipettes.", + "errorCode": "4000", + "errorInfo": {}, + "errorType": "ExceptionInProtocolError", + "id": "UUID", + "isDefined": false, + "wrappedErrors": [ + { + "createdAt": "TIMESTAMP", + "detail": "ValueError: Partial column configuration is only supported on 8-Channel pipettes.", + "errorCode": "4000", + "errorInfo": { + "args": "('Partial column configuration is only supported on 8-Channel pipettes.',)", + "class": "ValueError", + "traceback": " File \"/usr/local/lib/python3.10/site-packages/opentrons/protocols/execution/execute_python.py\", line N, in exec_run\n exec(\"run(__context)\", new_globs)\n\n File \"\", line N, in \n\n File \"Flex_X_v2_20_96_and_8_Overrides_InvalidConfigs_Override_ninety_six_partial_column_3.py\", line N, in run\n\n File \"/usr/local/lib/python3.10/site-packages/opentrons/protocols/api_support/util.py\", line N, in _check_version_wrapper\n return decorated_obj(*args, **kwargs)\n\n File 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+ "shape": "circular", + "totalLiquidVolume": 100, + "x": 113.38, + "y": 20.24, + "z": 0.92 + }, + "G2": { + "depth": 14.78, + "diameter": 5.34, + "shape": "circular", + "totalLiquidVolume": 100, + "x": 23.38, + "y": 20.24, + "z": 0.92 + }, + "G3": { + "depth": 14.78, + "diameter": 5.34, + "shape": "circular", + "totalLiquidVolume": 100, + "x": 32.38, + "y": 20.24, + "z": 0.92 + }, + "G4": { + "depth": 14.78, + "diameter": 5.34, + "shape": "circular", + "totalLiquidVolume": 100, + "x": 41.38, + "y": 20.24, + "z": 0.92 + }, + "G5": { + "depth": 14.78, + "diameter": 5.34, + "shape": "circular", + "totalLiquidVolume": 100, + "x": 50.38, + "y": 20.24, + "z": 0.92 + }, + "G6": { + "depth": 14.78, + "diameter": 5.34, + "shape": "circular", + "totalLiquidVolume": 100, + "x": 59.38, + "y": 20.24, + "z": 0.92 + }, + "G7": { + "depth": 14.78, + "diameter": 5.34, + "shape": "circular", + "totalLiquidVolume": 100, + "x": 68.38, + "y": 20.24, + "z": 0.92 + }, + "G8": { + "depth": 14.78, + "diameter": 5.34, + "shape": "circular", + "totalLiquidVolume": 100, + "x": 77.38, + "y": 20.24, + "z": 0.92 + }, + "G9": { + "depth": 14.78, + "diameter": 5.34, + "shape": "circular", + "totalLiquidVolume": 100, + "x": 86.38, + "y": 20.24, + "z": 0.92 + }, + "H1": { + "depth": 14.78, + "diameter": 5.34, + "shape": "circular", + "totalLiquidVolume": 100, + "x": 14.38, + "y": 11.24, + "z": 0.92 + }, + "H10": { + "depth": 14.78, + "diameter": 5.34, + "shape": "circular", + "totalLiquidVolume": 100, + "x": 95.38, + "y": 11.24, + "z": 0.92 + }, + "H11": { + "depth": 14.78, + "diameter": 5.34, + "shape": "circular", + "totalLiquidVolume": 100, + "x": 104.38, + "y": 11.24, + "z": 0.92 + }, + "H12": { + "depth": 14.78, + "diameter": 5.34, + "shape": "circular", + "totalLiquidVolume": 100, + "x": 113.38, + "y": 11.24, + "z": 0.92 + }, + "H2": { + "depth": 14.78, + "diameter": 5.34, + "shape": "circular", + "totalLiquidVolume": 100, + "x": 23.38, + "y": 11.24, + "z": 0.92 + }, + "H3": { + "depth": 14.78, + "diameter": 5.34, + "shape": "circular", + "totalLiquidVolume": 100, + "x": 32.38, + "y": 11.24, + "z": 0.92 + }, + "H4": { + "depth": 14.78, + "diameter": 5.34, + "shape": "circular", + "totalLiquidVolume": 100, + "x": 41.38, + "y": 11.24, + "z": 0.92 + }, + "H5": { + "depth": 14.78, + "diameter": 5.34, + "shape": "circular", + "totalLiquidVolume": 100, + "x": 50.38, + "y": 11.24, + "z": 0.92 + }, + "H6": { + "depth": 14.78, + "diameter": 5.34, + "shape": "circular", + "totalLiquidVolume": 100, + "x": 59.38, + "y": 11.24, + "z": 0.92 + }, + "H7": { + "depth": 14.78, + "diameter": 5.34, + "shape": "circular", + "totalLiquidVolume": 100, + "x": 68.38, + "y": 11.24, + "z": 0.92 + }, + "H8": { + "depth": 14.78, + "diameter": 5.34, + "shape": "circular", + "totalLiquidVolume": 100, + "x": 77.38, + "y": 11.24, + "z": 0.92 + }, + "H9": { + "depth": 14.78, + "diameter": 5.34, + "shape": "circular", + "totalLiquidVolume": 100, + "x": 86.38, + "y": 11.24, + "z": 0.92 + } + } + }, + "labwareId": "UUID" + }, + "startedAt": "TIMESTAMP", + "status": "succeeded" + }, + { + "commandType": "pickUpTip", + "completedAt": "TIMESTAMP", + "createdAt": "TIMESTAMP", + "id": "UUID", + "key": "8de5f9595204f05bd1016cce23cd32b9", + "notes": [], + "params": { + "labwareId": "UUID", + "pipetteId": "UUID", + "wellLocation": { + "offset": { + "x": 0.0, + "y": 0.0, + "z": 0.0 + }, + "origin": "top" + }, + "wellName": "A1" + }, + "result": { + "position": { + "x": 178.38, + "y": 288.24, + "z": 97.47 + }, + "tipDiameter": 7.23, + "tipLength": 77.5, + "tipVolume": 1000.0 + }, + "startedAt": "TIMESTAMP", + "status": "succeeded" + } + ], + "config": { + "apiVersion": [ + 2, + 20 + ], + "protocolType": "python" + }, + "createdAt": "TIMESTAMP", + "errors": [ + { + "createdAt": "TIMESTAMP", + "detail": "PartialTipMovementNotAllowedError [line 501]: Error 2004 MOTION_PLANNING_FAILURE (PartialTipMovementNotAllowedError): Moving to NEST 96 Well Plate 100 µL PCR Full Skirt in slot D2 with H12 nozzle partial configuration will result in collision with items in deck slot C1.", + "errorCode": "4000", + "errorInfo": {}, + "errorType": "ExceptionInProtocolError", + "id": "UUID", + "isDefined": false, + "wrappedErrors": [ + { + "createdAt": "TIMESTAMP", + "detail": "Moving to NEST 96 Well Plate 100 µL PCR Full Skirt in slot D2 with H12 nozzle partial configuration will result in collision with items in deck slot C1.", + "errorCode": "2004", + "errorInfo": {}, + "errorType": "PartialTipMovementNotAllowedError", + "id": "UUID", + "isDefined": false, + "wrappedErrors": [] + } + ] + } + ], + "files": [ + { + "name": "Flex_X_v2_20_96_None_Overrides_TooTallLabware_Override_distribute_source_collision.py", + "role": "main" + } + ], + "labware": [ + { + "definitionUri": "opentrons/opentrons_96_tiprack_1000ul/1", + "id": "UUID", + "loadName": "opentrons_96_tiprack_1000ul", + "location": { + "slotName": "B2" + } + }, + { + "definitionUri": "opentrons/opentrons_10_tuberack_falcon_4x50ml_6x15ml_conical/1", + "id": "UUID", + "loadName": "opentrons_10_tuberack_falcon_4x50ml_6x15ml_conical", + "location": { + "slotName": "C1" + } + }, + { + "definitionUri": "opentrons/nest_96_wellplate_100ul_pcr_full_skirt/2", + "id": "UUID", + "loadName": "nest_96_wellplate_100ul_pcr_full_skirt", + "location": { + "slotName": "D2" + } + }, + { + "definitionUri": "opentrons/nest_96_wellplate_100ul_pcr_full_skirt/2", + "id": "UUID", + "loadName": "nest_96_wellplate_100ul_pcr_full_skirt", + "location": { + "slotName": "D3" + } + } + ], + "liquids": [], + "metadata": { + "description": "oooo", + "protocolName": "Too tall labware on pickup tip" + }, + "modules": [], + "pipettes": [ + { + "id": "UUID", + "mount": "left", + "pipetteName": "p1000_96" + } + ], + "result": "not-ok", + "robotType": "OT-3 Standard", + "runTimeParameters": [] +} From 69049a5bde51d43a1ffa453ae995674c2bb6d33b Mon Sep 17 00:00:00 2001 From: koji Date: Mon, 7 Oct 2024 09:26:28 -0400 Subject: [PATCH 09/27] feat(protocol-designer): use i18n for getBlowoutLocationOptionsForForm (#16422) * feat(protocol-designer): use i18n for getBlowoutLocationOptionsForForm --- .../src/assets/localization/en/shared.json | 2 + .../StepForm/__tests__/utils.test.ts | 59 +++++++++++++++++++ .../Designer/ProtocolSteps/StepForm/utils.ts | 5 +- .../__tests__/ProtocolSteps.test.tsx | 7 +++ 4 files changed, 71 insertions(+), 2 deletions(-) create mode 100644 protocol-designer/src/pages/Designer/ProtocolSteps/StepForm/__tests__/utils.test.ts diff --git a/protocol-designer/src/assets/localization/en/shared.json b/protocol-designer/src/assets/localization/en/shared.json index 92872373624..4da0ce66196 100644 --- a/protocol-designer/src/assets/localization/en/shared.json +++ b/protocol-designer/src/assets/localization/en/shared.json @@ -10,6 +10,7 @@ "confirm": "Confirm", "create_a_protocol": "Create a protocol", "create_new": "Create new", + "destination_well": "Destination Well", "developer_ff": "Developer feature flags", "done": "Done", "edit_existing": "Edit existing protocol", @@ -106,6 +107,7 @@ "shared_sessions": "Share sessions with Opentrons", "shares_name": "This labware has the same load name or display name as {{customOrStandard}}, which is already in this protocol.", "slot_detail": "Slot Detail", + "source_well": "Source Well", "stagingArea": "Staging area", "step_count": "Step {{current}}", "step": "Step {{current}} / {{max}}", diff --git a/protocol-designer/src/pages/Designer/ProtocolSteps/StepForm/__tests__/utils.test.ts b/protocol-designer/src/pages/Designer/ProtocolSteps/StepForm/__tests__/utils.test.ts new file mode 100644 index 00000000000..e95aad5d427 --- /dev/null +++ b/protocol-designer/src/pages/Designer/ProtocolSteps/StepForm/__tests__/utils.test.ts @@ -0,0 +1,59 @@ +import { describe, it, expect } from 'vitest' +import { + SOURCE_WELL_BLOWOUT_DESTINATION, + DEST_WELL_BLOWOUT_DESTINATION, +} from '@opentrons/step-generation' +import { getBlowoutLocationOptionsForForm } from '../utils' + +describe('getBlowoutLocationOptionsForForm', () => { + const destOption = { + name: 'Destination Well', + value: DEST_WELL_BLOWOUT_DESTINATION, + } + const sourceOption = { + name: 'Source Well', + value: SOURCE_WELL_BLOWOUT_DESTINATION, + } + + it('should return destination option for mix stepType', () => { + const result = getBlowoutLocationOptionsForForm({ stepType: 'mix' }) + expect(result).toEqual([destOption]) + }) + + it('should return source and destination options for moveLiquid stepType with single path', () => { + const result = getBlowoutLocationOptionsForForm({ + stepType: 'moveLiquid', + path: 'single', + }) + expect(result).toEqual([sourceOption, destOption]) + }) + + it('should return source option and disabled destination option for moveLiquid stepType with multiDispense path', () => { + const result = getBlowoutLocationOptionsForForm({ + stepType: 'moveLiquid', + path: 'multiDispense', + }) + expect(result).toEqual([sourceOption, { ...destOption, disabled: true }]) + }) + + it('should return disabled source option and destination option for moveLiquid stepType with multiAspirate path', () => { + const result = getBlowoutLocationOptionsForForm({ + stepType: 'moveLiquid', + path: 'multiAspirate', + }) + expect(result).toEqual([{ ...sourceOption, disabled: true }, destOption]) + }) + + it('should return disabled source and destination options for moveLiquid stepType with undefined path', () => { + const result = getBlowoutLocationOptionsForForm({ stepType: 'moveLiquid' }) + expect(result).toEqual([ + { ...sourceOption, disabled: true }, + { ...destOption, disabled: true }, + ]) + }) + + it('should return an empty array for unknown stepType', () => { + const result = getBlowoutLocationOptionsForForm({ stepType: 'comment' }) + expect(result).toEqual([]) + }) +}) diff --git a/protocol-designer/src/pages/Designer/ProtocolSteps/StepForm/utils.ts b/protocol-designer/src/pages/Designer/ProtocolSteps/StepForm/utils.ts index 15a6c6b7ce7..9293b6b6c64 100644 --- a/protocol-designer/src/pages/Designer/ProtocolSteps/StepForm/utils.ts +++ b/protocol-designer/src/pages/Designer/ProtocolSteps/StepForm/utils.ts @@ -11,6 +11,7 @@ import { getDisabledFields, getDefaultsForStepType, } from '../../../../steplist/formLevel' +import { i18n } from '../../../../assets/localization' import { PROFILE_CYCLE } from '../../../../form-types' import type { PipetteEntity } from '@opentrons/step-generation' import type { Options } from '@opentrons/components' @@ -34,11 +35,11 @@ export function getBlowoutLocationOptionsForForm(args: { const { stepType, path } = args // TODO: Ian 2019-02-21 use i18n for names const destOption = { - name: 'Destination Well', + name: i18n.t('shared:destination_well'), value: DEST_WELL_BLOWOUT_DESTINATION, } const sourceOption = { - name: 'Source Well', + name: i18n.t('shared:source_well'), value: SOURCE_WELL_BLOWOUT_DESTINATION, } diff --git a/protocol-designer/src/pages/Designer/ProtocolSteps/__tests__/ProtocolSteps.test.tsx b/protocol-designer/src/pages/Designer/ProtocolSteps/__tests__/ProtocolSteps.test.tsx index 41f6f014227..db393cc693e 100644 --- a/protocol-designer/src/pages/Designer/ProtocolSteps/__tests__/ProtocolSteps.test.tsx +++ b/protocol-designer/src/pages/Designer/ProtocolSteps/__tests__/ProtocolSteps.test.tsx @@ -15,6 +15,13 @@ vi.mock('../../../../ui/steps/selectors') vi.mock('../StepForm') vi.mock('../../DeckSetup') vi.mock('../Timeline') + +vi.mock('../../../../assets/localization', () => ({ + t: vi.fn().mockReturnValue({ + t: (key: string) => key, + }), +})) + const render = () => { return renderWithProviders()[0] } From 9ac510595e85cd126082d0b387f8870d35475720 Mon Sep 17 00:00:00 2001 From: Josh McVey Date: Mon, 7 Oct 2024 09:42:09 -0500 Subject: [PATCH 10/27] chore(release): notes for Internal Release 2.2.0-alpha.0 (#16425) # Overview Internal release notes for Internal Release 2.2.0-alpha.0. Tagging edge in the monorepo and HEADs on "main" branches of dependency repositories if necessary. --- api/release-notes-internal.md | 4 ++++ app-shell/build/release-notes-internal.md | 4 ++++ 2 files changed, 8 insertions(+) diff --git a/api/release-notes-internal.md b/api/release-notes-internal.md index 6ddd85c885b..2d99270edc2 100644 --- a/api/release-notes-internal.md +++ b/api/release-notes-internal.md @@ -2,6 +2,10 @@ For more details about this release, please see the full [technical change log][ [technical change log]: https://github.com/Opentrons/opentrons/releases +## Internal Release 2.2.0-alpha.0 + +This internal release, pulled from the `edge` branch, contains features being developed for 8.2.0. It's for internal testing only. + ## Internal Release 2.0.0-alpha.4 This internal release, pulled from the `edge` branch, contains features being developed for 8.0.0. It's for internal testing only. There are no changes to `buildroot`, `ot3-firmware`, or `oe-core` since the last internal release. diff --git a/app-shell/build/release-notes-internal.md b/app-shell/build/release-notes-internal.md index ce6e62da888..5316ca3ad71 100644 --- a/app-shell/build/release-notes-internal.md +++ b/app-shell/build/release-notes-internal.md @@ -1,6 +1,10 @@ For more details about this release, please see the full [technical changelog][]. [technical change log]: https://github.com/Opentrons/opentrons/releases +## Internal Release 2.2.0-alpha.0 + +This internal release, pulled from the `edge` branch, contains features being developed for 8.2.0. It's for internal testing only. + ## Internal Release 2.0.0-alpha.4 This internal release, pulled from the `edge` branch, contains features being developed for 8.0.0. It's for internal testing only. There are no changes to `buildroot`, `ot3-firmware`, or `oe-core` since the last internal release. From 56cd3614a572cc463281c096e4710f35c4fb145e Mon Sep 17 00:00:00 2001 From: Max Marrone Date: Mon, 7 Oct 2024 11:11:46 -0400 Subject: [PATCH 11/27] feat(robot-server): Wire up global error recovery setting (#16416) ## Overview Closes EXEC-719. ## Changelog * Connect the new `PATCH /errorRecovery/settings` HTTP API so it actually affects run behavior. This closes EXEC-719. * One quirk to my implementation: This will not affect preexisting runs, *unless* you *also* do `PUT /runs/{id}/errorRecoveryPolicy`. In effect, `PUT /runs/{id}/errorRecoveryPolicy` refreshes the run's snapshot of `/errorRecovery/settings`. This is probably confusing; it would be better if `PATCH /errorRecovery/settings` immediately affected the preexisting run, or if `PUT /runs/{id}/errorRecoveryPolicy` did not have that refresh effect. I don't think this matters in practice because this button will be disabled or inaccessible in our UIs while there's an active run. Also fix a couple of nearby, unticketed bugs: * If a client gave us an empty error recovery policy, we were no-opping. Instead, we want to overwrite the current policy with the new empty one. * The logic in `error_recovery_mapping.py` was unintentionally enabling error recovery on OT-2 robots if the policy was specific enough. We want it to always be disabled on OT-2s. --- .../protocol_engine/error_recovery_policy.py | 1 + .../error_recovery/settings/router.py | 4 - .../error_recovery/settings/store.py | 13 +- .../robot_server/runs/dependencies.py | 10 +- .../runs/error_recovery_mapping.py | 121 +++++++---- .../runs/error_recovery_models.py | 49 +++-- .../robot_server/runs/router/base_router.py | 17 +- .../robot_server/runs/run_data_manager.py | 34 ++- .../runs/run_orchestrator_store.py | 8 +- .../error_recovery/settings/test_store.py | 4 +- .../tests/runs/router/test_base_router.py | 8 +- .../tests/runs/test_error_recovery_mapping.py | 6 +- .../tests/runs/test_run_data_manager.py | 199 +++++++++--------- ...tore.py => test_run_orchestrator_store.py} | 12 ++ 14 files changed, 283 insertions(+), 203 deletions(-) rename robot-server/tests/runs/{test_engine_store.py => test_run_orchestrator_store.py} (94%) diff --git a/api/src/opentrons/protocol_engine/error_recovery_policy.py b/api/src/opentrons/protocol_engine/error_recovery_policy.py index f9f39d99f4d..d959651393e 100644 --- a/api/src/opentrons/protocol_engine/error_recovery_policy.py +++ b/api/src/opentrons/protocol_engine/error_recovery_policy.py @@ -40,6 +40,7 @@ class ErrorRecoveryPolicy(Protocol): and return an appropriate `ErrorRecoveryType`. Args: + config: The config of the calling `ProtocolEngine`. failed_command: The command that failed, in its final `status=="failed"` state. defined_error_data: If the command failed with a defined error, details about that error. If the command failed with an undefined error, `None`. diff --git a/robot-server/robot_server/error_recovery/settings/router.py b/robot-server/robot_server/error_recovery/settings/router.py index 1a302b05582..4fdfeee5498 100644 --- a/robot-server/robot_server/error_recovery/settings/router.py +++ b/robot-server/robot_server/error_recovery/settings/router.py @@ -61,10 +61,6 @@ async def _get_current_response( store: ErrorRecoverySettingStore, ) -> PydanticResponse[SimpleBody[ResponseData]]: is_enabled = store.get_is_enabled() - if is_enabled is None: - # todo(mm, 2024-09-30): This defaulting will probably need to move down a layer - # when we connect this setting to `POST /runs`. - is_enabled = True return await PydanticResponse.create( SimpleBody.construct(data=ResponseData.construct(enabled=is_enabled)) ) diff --git a/robot-server/robot_server/error_recovery/settings/store.py b/robot-server/robot_server/error_recovery/settings/store.py index 6cef66aae2e..7bad6b5c77c 100644 --- a/robot-server/robot_server/error_recovery/settings/store.py +++ b/robot-server/robot_server/error_recovery/settings/store.py @@ -10,24 +10,25 @@ from robot_server.persistence.tables import boolean_setting_table, BooleanSettingKey +_ERROR_RECOVERY_ENABLED_DEFAULT = True + + class ErrorRecoverySettingStore: """Persistently stores settings related to error recovery.""" def __init__(self, sql_engine: sqlalchemy.engine.Engine) -> None: self._sql_engine = sql_engine - def get_is_enabled(self) -> bool | None: - """Get the value of the "error recovery enabled" setting. - - `None` is the default, i.e. it's never been explicitly set one way or the other. - """ + def get_is_enabled(self) -> bool: + """Get the value of the "error recovery enabled" setting.""" with self._sql_engine.begin() as transaction: - return transaction.execute( + result: bool | None = transaction.execute( sqlalchemy.select(boolean_setting_table.c.value).where( boolean_setting_table.c.key == BooleanSettingKey.ENABLE_ERROR_RECOVERY ) ).scalar_one_or_none() + return result if result is not None else _ERROR_RECOVERY_ENABLED_DEFAULT def set_is_enabled(self, is_enabled: bool | None) -> None: """Set the value of the "error recovery enabled" setting. diff --git a/robot-server/robot_server/runs/dependencies.py b/robot-server/robot_server/runs/dependencies.py index 146297715a9..60c96d1e5e6 100644 --- a/robot-server/robot_server/runs/dependencies.py +++ b/robot-server/robot_server/runs/dependencies.py @@ -2,6 +2,10 @@ from typing import Annotated from fastapi import Depends, status +from robot_server.error_recovery.settings.store import ( + ErrorRecoverySettingStore, + get_error_recovery_setting_store, +) from robot_server.protocols.dependencies import get_protocol_store from robot_server.protocols.protocol_models import ProtocolKind from robot_server.protocols.protocol_store import ProtocolStore @@ -156,12 +160,16 @@ async def get_run_data_manager( ], run_store: Annotated[RunStore, Depends(get_run_store)], runs_publisher: Annotated[RunsPublisher, Depends(get_runs_publisher)], + error_recovery_setting_store: Annotated[ + ErrorRecoverySettingStore, Depends(get_error_recovery_setting_store) + ], ) -> RunDataManager: """Get a run data manager to keep track of current/historical run data.""" return RunDataManager( - task_runner=task_runner, run_orchestrator_store=run_orchestrator_store, run_store=run_store, + error_recovery_setting_store=error_recovery_setting_store, + task_runner=task_runner, runs_publisher=runs_publisher, ) diff --git a/robot-server/robot_server/runs/error_recovery_mapping.py b/robot-server/robot_server/runs/error_recovery_mapping.py index fb936eddadd..d29ebf4b054 100644 --- a/robot-server/robot_server/runs/error_recovery_mapping.py +++ b/robot-server/robot_server/runs/error_recovery_mapping.py @@ -1,5 +1,4 @@ """Functions used for managing error recovery policy.""" -from typing import Optional from opentrons.protocol_engine.state.config import Config from robot_server.runs.error_recovery_models import ErrorRecoveryRule, ReactionIfMatch from opentrons.protocol_engine.commands.command_unions import ( @@ -14,52 +13,96 @@ def create_error_recovery_policy_from_rules( rules: list[ErrorRecoveryRule], + enabled: bool, ) -> ErrorRecoveryPolicy: - """Given a list of error recovery rules return an error recovery policy.""" + """Map a robot-server error recovery policy to an opentrons.protocol_engine one. - def _policy( + In its HTTP API, robot-server expresses error recovery policies as Pydantic models. + But opentrons.protocol_engine is more general, expressing them as Python callables. + + Args: + rules: The rules in the robot-server error recovery policy. + enabled: Whether error recovery should be enabled at all. + If `False`, `rules` is ignored. + + Returns: + An error recovery policy in `opentrons.protocol_engine` terms. + """ + + def mapped_policy( config: Config, failed_command: Command, - defined_error_data: Optional[CommandDefinedErrorData], + defined_error_data: CommandDefinedErrorData | None, ) -> ErrorRecoveryType: - for rule in rules: - command_type_matches = ( - failed_command.commandType == rule.matchCriteria.command.commandType - ) - error_type_matches = ( - defined_error_data is not None - and defined_error_data.public.errorType - == rule.matchCriteria.command.error.errorType + first_matching_rule = next( + ( + rule + for rule in rules + if _rule_matches_error(rule, failed_command, defined_error_data) + ), + None, + ) + robot_is_flex = config.robot_type == "OT-3 Standard" + error_is_defined = defined_error_data is not None + + if not enabled: + return ErrorRecoveryType.FAIL_RUN + elif not robot_is_flex: + # Although error recovery can theoretically work on OT-2s, we haven't tested + # it, and it's generally scarier because the OT-2 has much less hardware + # feedback. + return ErrorRecoveryType.FAIL_RUN + elif first_matching_rule is not None: + # The input policy explicitly deals this error, so do what it says. + return _map_error_recovery_type(first_matching_rule.ifMatch) + else: + # The input policy doesn't explicitly deal with this error, so the decision + # is our own. + # + # We try to WAIT_FOR_RECOVERY whenever we can, for two reasons: + # + # 1. It matches the frontend's current expectations. + # For example, the frontend expects us to WAIT_FOR_RECOVERY on + # overpressure errors, but it does not send us an error recovery policy + # that explicitly says that; it relies on this default. + # 2. Philosophically, we always want to give the operator a shot at + # recovery, even if we don't know the details of the problem and can't + # guarantee good robot behavior if they keep using it. + # + # We currently FAIL_RUN for undefined errors, with the thinking that they + # are especially likely to have messed something up in Protocol Engine's + # internal state, and that they are especially likely to cause confusing + # behavior. But we might want to change that--see point (2) above. + return ( + ErrorRecoveryType.WAIT_FOR_RECOVERY + if error_is_defined + else ErrorRecoveryType.FAIL_RUN ) - if command_type_matches and error_type_matches: - if rule.ifMatch == ReactionIfMatch.IGNORE_AND_CONTINUE: - return ErrorRecoveryType.IGNORE_AND_CONTINUE - elif rule.ifMatch == ReactionIfMatch.FAIL_RUN: - return ErrorRecoveryType.FAIL_RUN - elif rule.ifMatch == ReactionIfMatch.WAIT_FOR_RECOVERY: - return ErrorRecoveryType.WAIT_FOR_RECOVERY + return mapped_policy - return default_error_recovery_policy(config, failed_command, defined_error_data) - return _policy +def _rule_matches_error( + rule: ErrorRecoveryRule, + failed_command: Command, + defined_error_data: CommandDefinedErrorData | None, +) -> bool: + command_type_matches = ( + failed_command.commandType == rule.matchCriteria.command.commandType + ) + error_type_matches = ( + defined_error_data is not None + and defined_error_data.public.errorType + == rule.matchCriteria.command.error.errorType + ) + return command_type_matches and error_type_matches -def default_error_recovery_policy( - config: Config, - failed_command: Command, - defined_error_data: Optional[CommandDefinedErrorData], -) -> ErrorRecoveryType: - """The `ErrorRecoveryPolicy` to use when none has been set on a run.""" - # Although error recovery can theoretically work on OT-2s, we haven't tested it, - # and it's generally scarier because the OT-2 has much less hardware feedback. - robot_is_flex = config.robot_type == "OT-3 Standard" - # If the error is defined, we're taking that to mean that we should - # WAIT_FOR_RECOVERY. This is not necessarily the right long-term logic--we might - # want to FAIL_RUN on certain defined errors and WAIT_FOR_RECOVERY on certain - # undefined errors--but this is convenient for now. - error_is_defined = defined_error_data is not None - if robot_is_flex and error_is_defined: - return ErrorRecoveryType.WAIT_FOR_RECOVERY - else: - return ErrorRecoveryType.FAIL_RUN +def _map_error_recovery_type(reaction_if_match: ReactionIfMatch) -> ErrorRecoveryType: + match reaction_if_match: + case ReactionIfMatch.IGNORE_AND_CONTINUE: + return ErrorRecoveryType.IGNORE_AND_CONTINUE + case ReactionIfMatch.FAIL_RUN: + return ErrorRecoveryType.FAIL_RUN + case ReactionIfMatch.WAIT_FOR_RECOVERY: + return ErrorRecoveryType.WAIT_FOR_RECOVERY diff --git a/robot-server/robot_server/runs/error_recovery_models.py b/robot-server/robot_server/runs/error_recovery_models.py index 5558c65a8ac..a2990a007cb 100644 --- a/robot-server/robot_server/runs/error_recovery_models.py +++ b/robot-server/robot_server/runs/error_recovery_models.py @@ -4,13 +4,31 @@ from pydantic import BaseModel, Field +# There's a lot of nested classes here. +# Here's an example of a JSON document that this code models: +# { +# "policyRules": [ +# { +# "matchCriteria": { +# "command": { +# "commandType": "foo", +# "error": { +# "errorType": "bar" +# } +# } +# }, +# "ifMatch": "ignoreAndContinue" +# } +# ] +# } + class ReactionIfMatch(Enum): - """The type of the error recovery setting. + """How to handle a given error. - * `"ignoreAndContinue"`: Ignore this error and future errors of the same type. - * `"failRun"`: Errors of this type should fail the run. - * `"waitForRecovery"`: Instances of this error should initiate a recover operation. + * `"ignoreAndContinue"`: Ignore this error and continue with the next command. + * `"failRun"`: Fail the run. + * `"waitForRecovery"`: Enter interactive error recovery mode. """ @@ -19,20 +37,6 @@ class ReactionIfMatch(Enum): WAIT_FOR_RECOVERY = "waitForRecovery" -# There's a lot of nested classes here. This is the JSON schema this code models. -# "ErrorRecoveryRule": { -# "matchCriteria": { -# "command": { -# "commandType": "foo", -# "error": { -# "errorType": "bar" -# } -# } -# }, -# "ifMatch": "baz" -# } - - class ErrorMatcher(BaseModel): """The error type that this rule applies to.""" @@ -67,7 +71,7 @@ class ErrorRecoveryRule(BaseModel): ) ifMatch: ReactionIfMatch = Field( ..., - description="The specific recovery setting that will be in use if the type parameters match.", + description="How to handle errors matched by this rule.", ) @@ -76,6 +80,9 @@ class ErrorRecoveryPolicy(BaseModel): policyRules: List[ErrorRecoveryRule] = Field( ..., - description="A list or error recovery rules to apply for a run's recovery management." - "The rules are evaluated first-to-last. The first exact match will dectate recovery management.", + description=( + "A list of error recovery rules to apply for a run's recovery management." + " The rules are evaluated first-to-last." + " The first exact match will dictate recovery management." + ), ) diff --git a/robot-server/robot_server/runs/router/base_router.py b/robot-server/robot_server/runs/router/base_router.py index 3b0e7040e02..b9bd8cd24b2 100644 --- a/robot-server/robot_server/runs/router/base_router.py +++ b/robot-server/robot_server/runs/router/base_router.py @@ -426,11 +426,13 @@ async def update_run( @PydanticResponse.wrap_route( base_router.put, path="/runs/{runId}/errorRecoveryPolicy", - summary="Set run policies", + summary="Set a run's error recovery policy", description=dedent( """ Update how to handle different kinds of command failures. - The following rules will persist during the run. + + For this to have any effect, error recovery must also be enabled globally. + See `PATCH /errorRecovery/settings`. """ ), status_code=status.HTTP_201_CREATED, @@ -451,12 +453,11 @@ async def put_error_recovery_policy( request_body: Request body with run policies data. run_data_manager: Current and historical run data management. """ - policies = request_body.data.policyRules - if policies: - try: - run_data_manager.set_policies(run_id=runId, policies=policies) - except RunNotCurrentError as e: - raise RunStopped(detail=str(e)).as_error(status.HTTP_409_CONFLICT) from e + rules = request_body.data.policyRules + try: + run_data_manager.set_error_recovery_rules(run_id=runId, rules=rules) + except RunNotCurrentError as e: + raise RunStopped(detail=str(e)).as_error(status.HTTP_409_CONFLICT) from e return await PydanticResponse.create( content=SimpleEmptyBody.construct(), diff --git a/robot-server/robot_server/runs/run_data_manager.py b/robot-server/robot_server/runs/run_data_manager.py index b756b185bf1..4168b1d4d5d 100644 --- a/robot-server/robot_server/runs/run_data_manager.py +++ b/robot-server/robot_server/runs/run_data_manager.py @@ -22,6 +22,7 @@ CSVRuntimeParamPaths, ) +from robot_server.error_recovery.settings.store import ErrorRecoverySettingStore from robot_server.protocols.protocol_store import ProtocolResource from robot_server.service.task_runner import TaskRunner from robot_server.service.notifications import RunsPublisher @@ -35,6 +36,9 @@ from opentrons.protocol_engine.types import DeckConfigurationType, RunTimeParameter +_INITIAL_ERROR_RECOVERY_RULES: list[ErrorRecoveryRule] = [] + + def _build_run( run_resource: Union[RunResource, BadRunResource], state_summary: Union[StateSummary, BadStateSummary], @@ -145,11 +149,13 @@ def __init__( self, run_orchestrator_store: RunOrchestratorStore, run_store: RunStore, + error_recovery_setting_store: ErrorRecoverySettingStore, task_runner: TaskRunner, runs_publisher: RunsPublisher, ) -> None: self._run_orchestrator_store = run_orchestrator_store self._run_store = run_store + self._error_recovery_setting_store = error_recovery_setting_store self._task_runner = task_runner self._runs_publisher = runs_publisher @@ -190,6 +196,7 @@ async def create( """ prev_run_id = self._run_orchestrator_store.current_run_id if prev_run_id is not None: + # Allow clear() to propagate RunConflictError. prev_run_result = await self._run_orchestrator_store.clear() self._run_store.update_run_state( run_id=prev_run_id, @@ -197,9 +204,18 @@ async def create( commands=prev_run_result.commands, run_time_parameters=prev_run_result.parameters, ) + + error_recovery_is_enabled = self._error_recovery_setting_store.get_is_enabled() + initial_error_recovery_policy = ( + error_recovery_mapping.create_error_recovery_policy_from_rules( + _INITIAL_ERROR_RECOVERY_RULES, error_recovery_is_enabled + ) + ) + state_summary = await self._run_orchestrator_store.create( run_id=run_id, labware_offsets=labware_offsets, + initial_error_recovery_policy=initial_error_recovery_policy, deck_configuration=deck_configuration, protocol=protocol, run_time_param_values=run_time_param_values, @@ -215,6 +231,7 @@ async def create( self._run_store.insert_csv_rtp( run_id=run_id, run_time_parameters=run_time_parameters ) + self._runs_publisher.start_publishing_for_run( get_current_command=self.get_current_command, get_recovery_target_command=self.get_recovery_target_command, @@ -498,16 +515,23 @@ def get_all_commands_as_preserialized_list( run_id, include_fixit_commands ) - def set_policies(self, run_id: str, policies: List[ErrorRecoveryRule]) -> None: - """Create run policy rules for error recovery.""" + def set_error_recovery_rules( + self, run_id: str, rules: List[ErrorRecoveryRule] + ) -> None: + """Set the run's error recovery policy. + + The input rules get combined with the global error recovery enabled/disabled + setting, which this method retrieves automatically. + """ if run_id != self._run_orchestrator_store.current_run_id: raise RunNotCurrentError( f"Cannot update {run_id} because it is not the current run." ) - policy = error_recovery_mapping.create_error_recovery_policy_from_rules( - policies + is_enabled = self._error_recovery_setting_store.get_is_enabled() + mapped_policy = error_recovery_mapping.create_error_recovery_policy_from_rules( + rules, is_enabled ) - self._run_orchestrator_store.set_error_recovery_policy(policy=policy) + self._run_orchestrator_store.set_error_recovery_policy(policy=mapped_policy) def _get_state_summary(self, run_id: str) -> Union[StateSummary, BadStateSummary]: if run_id == self._run_orchestrator_store.current_run_id: diff --git a/robot-server/robot_server/runs/run_orchestrator_store.py b/robot-server/robot_server/runs/run_orchestrator_store.py index 46a384b96ea..03af7315ef9 100644 --- a/robot-server/robot_server/runs/run_orchestrator_store.py +++ b/robot-server/robot_server/runs/run_orchestrator_store.py @@ -53,8 +53,6 @@ ) from opentrons_shared_data.labware.types import LabwareUri -from .error_recovery_mapping import default_error_recovery_policy - _log = logging.getLogger(__name__) @@ -119,8 +117,6 @@ def run_handler_in_engine_thread_from_hardware_thread( class RunOrchestratorStore: """Factory and in-memory storage for ProtocolEngine.""" - _run_orchestrator: Optional[RunOrchestrator] = None - def __init__( self, hardware_api: HardwareControlAPI, @@ -138,6 +134,7 @@ def __init__( self._hardware_api = hardware_api self._robot_type = robot_type self._deck_type = deck_type + self._run_orchestrator: Optional[RunOrchestrator] = None self._default_run_orchestrator: Optional[RunOrchestrator] = None hardware_api.register_callback(_get_estop_listener(self)) @@ -194,6 +191,7 @@ async def create( self, run_id: str, labware_offsets: List[LabwareOffsetCreate], + initial_error_recovery_policy: error_recovery_policy.ErrorRecoveryPolicy, deck_configuration: DeckConfigurationType, notify_publishers: Callable[[], None], protocol: Optional[ProtocolResource], @@ -235,7 +233,7 @@ async def create( RobotTypeEnum.robot_literal_to_enum(self._robot_type) ), ), - error_recovery_policy=default_error_recovery_policy, + error_recovery_policy=initial_error_recovery_policy, load_fixed_trash=load_fixed_trash, deck_configuration=deck_configuration, notify_publishers=notify_publishers, diff --git a/robot-server/tests/error_recovery/settings/test_store.py b/robot-server/tests/error_recovery/settings/test_store.py index cc69f5d307f..e67f5e72ee9 100644 --- a/robot-server/tests/error_recovery/settings/test_store.py +++ b/robot-server/tests/error_recovery/settings/test_store.py @@ -17,7 +17,7 @@ def subject( def test_error_recovery_setting_store(subject: ErrorRecoverySettingStore) -> None: """Test `ErrorRecoverySettingStore`.""" - assert subject.get_is_enabled() is None + assert subject.get_is_enabled() is True subject.set_is_enabled(is_enabled=False) assert subject.get_is_enabled() is False @@ -26,4 +26,4 @@ def test_error_recovery_setting_store(subject: ErrorRecoverySettingStore) -> Non assert subject.get_is_enabled() is True subject.set_is_enabled(is_enabled=None) - assert subject.get_is_enabled() is None + assert subject.get_is_enabled() is True diff --git a/robot-server/tests/runs/router/test_base_router.py b/robot-server/tests/runs/router/test_base_router.py index 37e5cd6dd3d..8a10af1940d 100644 --- a/robot-server/tests/runs/router/test_base_router.py +++ b/robot-server/tests/runs/router/test_base_router.py @@ -698,8 +698,8 @@ async def test_create_policies( run_data_manager=mock_run_data_manager, ) decoy.verify( - mock_run_data_manager.set_policies( - run_id="rud-id", policies=policies.policyRules + mock_run_data_manager.set_error_recovery_rules( + run_id="rud-id", rules=policies.policyRules ) ) @@ -710,8 +710,8 @@ async def test_create_policies_raises_not_active_run( """It should raise that the run is not current.""" policies = decoy.mock(cls=ErrorRecoveryPolicy) decoy.when( - mock_run_data_manager.set_policies( - run_id="rud-id", policies=policies.policyRules + mock_run_data_manager.set_error_recovery_rules( + run_id="rud-id", rules=policies.policyRules ) ).then_raise(RunNotCurrentError()) with pytest.raises(ApiError) as exc_info: diff --git a/robot-server/tests/runs/test_error_recovery_mapping.py b/robot-server/tests/runs/test_error_recovery_mapping.py index a142fbc5e30..fba8e4315d9 100644 --- a/robot-server/tests/runs/test_error_recovery_mapping.py +++ b/robot-server/tests/runs/test_error_recovery_mapping.py @@ -71,7 +71,7 @@ def test_create_error_recovery_policy_with_rules( mock_rule: ErrorRecoveryRule, ) -> None: """Should return IGNORE_AND_CONTINUE if that's what we specify as the rule.""" - policy = create_error_recovery_policy_from_rules([mock_rule]) + policy = create_error_recovery_policy_from_rules([mock_rule], enabled=True) exampleConfig = Config( robot_type="OT-3 Standard", deck_type=DeckType.OT3_STANDARD, @@ -86,7 +86,7 @@ def test_create_error_recovery_policy_undefined_error( decoy: Decoy, mock_command: LiquidProbe ) -> None: """Should return a FAIL_RUN policy when error is not defined.""" - policy = create_error_recovery_policy_from_rules(rules=[]) + policy = create_error_recovery_policy_from_rules(rules=[], enabled=True) exampleConfig = Config( robot_type="OT-3 Standard", deck_type=DeckType.OT3_STANDARD, @@ -99,7 +99,7 @@ def test_create_error_recovery_policy_defined_error( decoy: Decoy, mock_command: LiquidProbe, mock_error_data: CommandDefinedErrorData ) -> None: """Should return a WAIT_FOR_RECOVERY policy when error is defined.""" - policy = create_error_recovery_policy_from_rules(rules=[]) + policy = create_error_recovery_policy_from_rules(rules=[], enabled=True) exampleConfig = Config( robot_type="OT-3 Standard", deck_type=DeckType.OT3_STANDARD, diff --git a/robot-server/tests/runs/test_run_data_manager.py b/robot-server/tests/runs/test_run_data_manager.py index 49399447597..981a0e7177c 100644 --- a/robot-server/tests/runs/test_run_data_manager.py +++ b/robot-server/tests/runs/test_run_data_manager.py @@ -1,10 +1,10 @@ """Tests for RunDataManager.""" from datetime import datetime from typing import Optional, List, Dict +from unittest.mock import sentinel import pytest from decoy import Decoy, matchers -from pathlib import Path from opentrons.protocol_engine import ( EngineStatus, @@ -21,16 +21,15 @@ LabwareOffset, Liquid, ) -from opentrons.protocol_engine.error_recovery_policy import ErrorRecoveryPolicy from opentrons.protocol_engine.types import BooleanParameter, CSVParameter from opentrons.protocol_runner import RunResult -from opentrons.types import DeckSlotName from opentrons.hardware_control.nozzle_manager import NozzleMap from opentrons_shared_data.errors.exceptions import InvalidStoredData from opentrons_shared_data.labware.labware_definition import LabwareDefinition +from robot_server.error_recovery.settings.store import ErrorRecoverySettingStore from robot_server.protocols.protocol_models import ProtocolKind from robot_server.protocols.protocol_store import ProtocolResource from robot_server.runs import error_recovery_mapping @@ -74,6 +73,12 @@ def mock_run_store(decoy: Decoy) -> RunStore: return decoy.mock(cls=RunStore) +@pytest.fixture +def mock_error_recovery_setting_store(decoy: Decoy) -> ErrorRecoverySettingStore: + """Get a mock ErrorRecoverySettingStore.""" + return decoy.mock(cls=ErrorRecoverySettingStore) + + @pytest.fixture() def mock_task_runner(decoy: Decoy) -> TaskRunner: """Get a mock background TaskRunner.""" @@ -102,6 +107,20 @@ def engine_state_summary() -> StateSummary: ) +@pytest.fixture(autouse=True) +def patch_error_recovery_mapping(decoy: Decoy, monkeypatch: pytest.MonkeyPatch) -> None: + """Replace the members of the error_recovery_mapping module with mocks.""" + monkeypatch.setattr( + error_recovery_mapping, + "create_error_recovery_policy_from_rules", + decoy.mock( + func=decoy.mock( + func=error_recovery_mapping.create_error_recovery_policy_from_rules + ) + ), + ) + + @pytest.fixture() def run_time_parameters() -> List[pe_types.RunTimeParameter]: """Get a RunTimeParameter list.""" @@ -150,6 +169,7 @@ def run_command() -> commands.Command: def subject( mock_run_orchestrator_store: RunOrchestratorStore, mock_run_store: RunStore, + mock_error_recovery_setting_store: ErrorRecoverySettingStore, mock_task_runner: TaskRunner, mock_runs_publisher: RunsPublisher, ) -> RunDataManager: @@ -157,6 +177,7 @@ def subject( return RunDataManager( run_orchestrator_store=mock_run_orchestrator_store, run_store=mock_run_store, + error_recovery_setting_store=mock_error_recovery_setting_store, task_runner=mock_task_runner, runs_publisher=mock_runs_publisher, ) @@ -166,6 +187,7 @@ async def test_create( decoy: Decoy, mock_run_orchestrator_store: RunOrchestratorStore, mock_run_store: RunStore, + mock_error_recovery_setting_store: ErrorRecoverySettingStore, subject: RunDataManager, engine_state_summary: StateSummary, run_resource: RunResource, @@ -173,102 +195,33 @@ async def test_create( """It should create an engine and a persisted run resource.""" run_id = "hello world" created_at = datetime(year=2021, month=1, day=1) - - decoy.when( - await mock_run_orchestrator_store.create( - run_id=run_id, - labware_offsets=[], - protocol=None, - deck_configuration=[], - run_time_param_values=None, - run_time_param_paths=None, - notify_publishers=mock_notify_publishers, - ) - ).then_return(engine_state_summary) - - decoy.when(mock_run_orchestrator_store.get_run_time_parameters()).then_return([]) - - decoy.when( - mock_run_store.insert( - run_id=run_id, - protocol_id=None, - created_at=created_at, - ) - ).then_return(run_resource) - - decoy.when(mock_run_orchestrator_store.get_run_time_parameters()).then_return([]) - - result = await subject.create( - run_id=run_id, - created_at=created_at, - labware_offsets=[], - protocol=None, - deck_configuration=[], - run_time_param_values=None, - run_time_param_paths=None, - notify_publishers=mock_notify_publishers, - ) - - assert result == Run( - id=run_resource.run_id, - protocolId=run_resource.protocol_id, - createdAt=run_resource.created_at, - current=True, - actions=run_resource.actions, - status=engine_state_summary.status, - errors=engine_state_summary.errors, - hasEverEnteredErrorRecovery=engine_state_summary.hasEverEnteredErrorRecovery, - labware=engine_state_summary.labware, - labwareOffsets=engine_state_summary.labwareOffsets, - pipettes=engine_state_summary.pipettes, - modules=engine_state_summary.modules, - liquids=engine_state_summary.liquids, - ) - decoy.verify(mock_run_store.insert_csv_rtp(run_id=run_id, run_time_parameters=[])) - - -async def test_create_with_options( - decoy: Decoy, - mock_run_orchestrator_store: RunOrchestratorStore, - mock_run_store: RunStore, - subject: RunDataManager, - engine_state_summary: StateSummary, - run_resource: RunResource, -) -> None: - """It should handle creation with a protocol, labware offsets and parameters.""" - run_id = "hello world" - created_at = datetime(year=2021, month=1, day=1) - protocol = ProtocolResource( - protocol_id="protocol-id", + protocol_id=sentinel.protocol_id, created_at=datetime(year=2022, month=2, day=2), source=None, # type: ignore[arg-type] protocol_key=None, protocol_kind=ProtocolKind.STANDARD, ) - labware_offset = pe_types.LabwareOffsetCreate( - definitionUri="namespace/load_name/version", - location=pe_types.LabwareOffsetLocation(slotName=DeckSlotName.SLOT_5), - vector=pe_types.LabwareOffsetVector(x=1, y=2, z=3), - ) - decoy.when( await mock_run_orchestrator_store.create( run_id=run_id, - labware_offsets=[labware_offset], + labware_offsets=sentinel.labware_offsets, + initial_error_recovery_policy=sentinel.initial_error_recovery_policy, protocol=protocol, - deck_configuration=[], - run_time_param_values={"foo": "bar"}, - run_time_param_paths={"xyzzy": Path("zork")}, + deck_configuration=sentinel.deck_configuration, + run_time_param_values=sentinel.run_time_param_values, + run_time_param_paths=sentinel.run_time_param_paths, notify_publishers=mock_notify_publishers, ) ).then_return(engine_state_summary) + decoy.when(mock_run_orchestrator_store.get_run_time_parameters()).then_return([]) + decoy.when( mock_run_store.insert( run_id=run_id, - protocol_id="protocol-id", + protocol_id=protocol.protocol_id, created_at=created_at, ) ).then_return(run_resource) @@ -276,21 +229,30 @@ async def test_create_with_options( bool_parameter = BooleanParameter( displayName="foo", variableName="bar", default=True, value=False ) - file_parameter = CSVParameter(displayName="my_file", variableName="file-id") - decoy.when(mock_run_orchestrator_store.get_run_time_parameters()).then_return( [bool_parameter, file_parameter] ) + expected_initial_error_recovery_rules: list[ErrorRecoveryRule] = [] + decoy.when(mock_error_recovery_setting_store.get_is_enabled()).then_return( + sentinel.error_recovery_enabled + ) + decoy.when( + error_recovery_mapping.create_error_recovery_policy_from_rules( + rules=expected_initial_error_recovery_rules, + enabled=sentinel.error_recovery_enabled, + ) + ).then_return(sentinel.initial_error_recovery_policy) + result = await subject.create( run_id=run_id, created_at=created_at, - labware_offsets=[labware_offset], + labware_offsets=sentinel.labware_offsets, protocol=protocol, - deck_configuration=[], - run_time_param_values={"foo": "bar"}, - run_time_param_paths={"xyzzy": Path("zork")}, + deck_configuration=sentinel.deck_configuration, + run_time_param_values=sentinel.run_time_param_values, + run_time_param_paths=sentinel.run_time_param_paths, notify_publishers=mock_notify_publishers, ) @@ -321,12 +283,24 @@ async def test_create_engine_error( decoy: Decoy, mock_run_orchestrator_store: RunOrchestratorStore, mock_run_store: RunStore, + mock_error_recovery_setting_store: ErrorRecoverySettingStore, subject: RunDataManager, ) -> None: """It should not create a resource if engine creation fails.""" run_id = "hello world" created_at = datetime(year=2021, month=1, day=1) + expected_initial_error_recovery_rules: list[ErrorRecoveryRule] = [] + decoy.when(mock_error_recovery_setting_store.get_is_enabled()).then_return( + sentinel.error_recovery_enabled + ) + decoy.when( + error_recovery_mapping.create_error_recovery_policy_from_rules( + rules=expected_initial_error_recovery_rules, + enabled=sentinel.error_recovery_enabled, + ) + ).then_return(sentinel.initial_error_recovery_policy) + decoy.when( await mock_run_orchestrator_store.create( run_id, @@ -336,6 +310,7 @@ async def test_create_engine_error( run_time_param_values=None, run_time_param_paths=None, notify_publishers=mock_notify_publishers, + initial_error_recovery_policy=matchers.Anything(), ) ).then_raise(RunConflictError("oh no")) @@ -783,6 +758,7 @@ async def test_create_archives_existing( run_command: commands.Command, mock_run_orchestrator_store: RunOrchestratorStore, mock_run_store: RunStore, + mock_error_recovery_setting_store: ErrorRecoverySettingStore, subject: RunDataManager, ) -> None: """It should persist the previously current run when a new run is created.""" @@ -798,11 +774,23 @@ async def test_create_archives_existing( ) ) + expected_initial_error_recovery_rules: list[ErrorRecoveryRule] = [] + decoy.when(mock_error_recovery_setting_store.get_is_enabled()).then_return( + sentinel.error_recovery_enabled + ) + decoy.when( + error_recovery_mapping.create_error_recovery_policy_from_rules( + rules=expected_initial_error_recovery_rules, + enabled=sentinel.error_recovery_enabled, + ) + ).then_return(sentinel.initial_error_recovery_policy) + decoy.when( await mock_run_orchestrator_store.create( run_id=run_id_new, labware_offsets=[], protocol=None, + initial_error_recovery_policy=sentinel.initial_error_recovery_policy, deck_configuration=[], run_time_param_values=None, run_time_param_paths=None, @@ -1126,35 +1114,36 @@ async def test_create_policies_raises_run_not_current( "not-current-run-id" ) with pytest.raises(RunNotCurrentError): - subject.set_policies( - run_id="run-id", policies=decoy.mock(cls=List[ErrorRecoveryRule]) + subject.set_error_recovery_rules( + run_id="run-id", rules=decoy.mock(cls=List[ErrorRecoveryRule]) ) async def test_create_policies_translates_and_calls_orchestrator( decoy: Decoy, - monkeypatch: pytest.MonkeyPatch, mock_run_orchestrator_store: RunOrchestratorStore, + mock_error_recovery_setting_store: ErrorRecoverySettingStore, subject: RunDataManager, ) -> None: """Should translate rules into policy and call orchestrator.""" - monkeypatch.setattr( - error_recovery_mapping, - "create_error_recovery_policy_from_rules", - decoy.mock( - func=decoy.mock( - func=error_recovery_mapping.create_error_recovery_policy_from_rules - ) - ), + decoy.when(mock_error_recovery_setting_store.get_is_enabled()).then_return( + sentinel.is_enabled ) - input_rules = decoy.mock(cls=List[ErrorRecoveryRule]) - expected_output = decoy.mock(cls=ErrorRecoveryPolicy) decoy.when( - error_recovery_mapping.create_error_recovery_policy_from_rules(input_rules) - ).then_return(expected_output) - decoy.when(mock_run_orchestrator_store.current_run_id).then_return("run-id") - subject.set_policies(run_id="run-id", policies=input_rules) - decoy.verify(mock_run_orchestrator_store.set_error_recovery_policy(expected_output)) + error_recovery_mapping.create_error_recovery_policy_from_rules( + rules=sentinel.input_rules, + enabled=sentinel.is_enabled, + ) + ).then_return(sentinel.expected_output) + decoy.when(mock_run_orchestrator_store.current_run_id).then_return( + sentinel.current_run_id + ) + subject.set_error_recovery_rules( + run_id=sentinel.current_run_id, rules=sentinel.input_rules + ) + decoy.verify( + mock_run_orchestrator_store.set_error_recovery_policy(sentinel.expected_output) + ) def test_get_nozzle_map_current_run( diff --git a/robot-server/tests/runs/test_engine_store.py b/robot-server/tests/runs/test_run_orchestrator_store.py similarity index 94% rename from robot-server/tests/runs/test_engine_store.py rename to robot-server/tests/runs/test_run_orchestrator_store.py index 46f25f3edb4..e34c1340359 100644 --- a/robot-server/tests/runs/test_engine_store.py +++ b/robot-server/tests/runs/test_run_orchestrator_store.py @@ -6,6 +6,7 @@ from opentrons_shared_data import get_shared_data_root from opentrons_shared_data.robot.types import RobotType +from opentrons.protocol_engine.error_recovery_policy import never_recover from opentrons.protocol_engine.errors.exceptions import EStopActivatedError from opentrons.types import DeckSlotName from opentrons.hardware_control import HardwareControlAPI, API @@ -58,6 +59,7 @@ async def test_create_engine(decoy: Decoy, subject: RunOrchestratorStore) -> Non result = await subject.create( run_id="run-id", labware_offsets=[], + initial_error_recovery_policy=never_recover, protocol=None, deck_configuration=[], notify_publishers=mock_notify_publishers, @@ -85,6 +87,7 @@ async def test_create_engine_uses_robot_type( await subject.create( run_id="run-id", labware_offsets=[], + initial_error_recovery_policy=never_recover, deck_configuration=[], protocol=None, notify_publishers=mock_notify_publishers, @@ -106,6 +109,7 @@ async def test_create_engine_with_labware_offsets( result = await subject.create( run_id="run-id", labware_offsets=[labware_offset], + initial_error_recovery_policy=never_recover, deck_configuration=[], protocol=None, notify_publishers=mock_notify_publishers, @@ -129,6 +133,7 @@ async def test_archives_state_if_engine_already_exists( await subject.create( run_id="run-id-1", labware_offsets=[], + initial_error_recovery_policy=never_recover, deck_configuration=[], protocol=None, notify_publishers=mock_notify_publishers, @@ -138,6 +143,7 @@ async def test_archives_state_if_engine_already_exists( await subject.create( run_id="run-id-2", labware_offsets=[], + initial_error_recovery_policy=never_recover, deck_configuration=[], protocol=None, notify_publishers=mock_notify_publishers, @@ -151,6 +157,7 @@ async def test_clear_engine(subject: RunOrchestratorStore) -> None: await subject.create( run_id="run-id", labware_offsets=[], + initial_error_recovery_policy=never_recover, deck_configuration=[], protocol=None, notify_publishers=mock_notify_publishers, @@ -172,6 +179,7 @@ async def test_clear_engine_not_stopped_or_idle( await subject.create( run_id="run-id", labware_offsets=[], + initial_error_recovery_policy=never_recover, deck_configuration=[], protocol=None, notify_publishers=mock_notify_publishers, @@ -187,6 +195,7 @@ async def test_clear_idle_engine(subject: RunOrchestratorStore) -> None: await subject.create( run_id="run-id", labware_offsets=[], + initial_error_recovery_policy=never_recover, deck_configuration=[], protocol=None, notify_publishers=mock_notify_publishers, @@ -238,6 +247,7 @@ async def test_get_default_orchestrator_current_unstarted( await subject.create( run_id="run-id", labware_offsets=[], + initial_error_recovery_policy=never_recover, deck_configuration=[], protocol=None, notify_publishers=mock_notify_publishers, @@ -252,6 +262,7 @@ async def test_get_default_orchestrator_conflict(subject: RunOrchestratorStore) await subject.create( run_id="run-id", labware_offsets=[], + initial_error_recovery_policy=never_recover, deck_configuration=[], protocol=None, notify_publishers=mock_notify_publishers, @@ -269,6 +280,7 @@ async def test_get_default_orchestrator_run_stopped( await subject.create( run_id="run-id", labware_offsets=[], + initial_error_recovery_policy=never_recover, deck_configuration=[], protocol=None, notify_publishers=mock_notify_publishers, From 7badfeed5cec147f0d69fb88980d108a2792c975 Mon Sep 17 00:00:00 2001 From: TamarZanzouri Date: Mon, 7 Oct 2024 11:44:55 -0400 Subject: [PATCH 12/27] feat(api): allow ungrip gripper labware while door is open (#16394) # Overview closes [EXEC-734](https://opentrons.atlassian.net/browse/EXEC-734). add ungrip command and allow queuing it and executing it while door is open. ## Test Plan and Hands on Testing 1. upload a protocol that will enter ER mode. 2. open door. 3. issue an ungrip command: ``` { "data": { "commandType": "unsafe/ungripLabware", "intent": "fixit", "params": { } } } ``` 4. make sure the gripper opens its jaw. tested with dev server and the command succeeded but still need to test with an actual gripper (@SyntaxColoring thank you Max) ## Changelog 1. added an ungrip command `unsafe/ungripLabware` 2. added logic for queuing while the door is open. 3. added logic for allowing to execute while door is open. ## Review requests 1. gripper command makes sense? 2. logic changes make sense? ## Risk assessment medium. added a new command but need to make sure nothing has changed with the door saftey. [EXEC-734]: https://opentrons.atlassian.net/browse/EXEC-734?atlOrigin=eyJpIjoiNWRkNTljNzYxNjVmNDY3MDlhMDU5Y2ZhYzA5YTRkZjUiLCJwIjoiZ2l0aHViLWNvbS1KU1cifQ --------- Co-authored-by: Max Marrone --- .../commands/command_unions.py | 5 ++ .../commands/unsafe/__init__.py | 15 ++++ .../commands/unsafe/unsafe_ungrip_labware.py | 73 +++++++++++++++++++ .../protocol_engine/state/commands.py | 51 +++++++++++-- .../commands/unsafe/test_ungrip_labware.py | 40 ++++++++++ .../state/test_command_state.py | 73 +++++++++++++++++++ .../state/test_command_view_old.py | 15 ++++ robot-server/simulators/test-flex.json | 4 + shared-data/command/schemas/10.json | 42 ++++++++++- 9 files changed, 312 insertions(+), 6 deletions(-) create mode 100644 api/src/opentrons/protocol_engine/commands/unsafe/unsafe_ungrip_labware.py create mode 100644 api/tests/opentrons/protocol_engine/commands/unsafe/test_ungrip_labware.py diff --git a/api/src/opentrons/protocol_engine/commands/command_unions.py b/api/src/opentrons/protocol_engine/commands/command_unions.py index 604fca50e14..f01e10aa63e 100644 --- a/api/src/opentrons/protocol_engine/commands/command_unions.py +++ b/api/src/opentrons/protocol_engine/commands/command_unions.py @@ -392,6 +392,7 @@ unsafe.UnsafeDropTipInPlace, unsafe.UpdatePositionEstimators, unsafe.UnsafeEngageAxes, + unsafe.UnsafeUngripLabware, ], Field(discriminator="commandType"), ] @@ -467,6 +468,7 @@ unsafe.UnsafeDropTipInPlaceParams, unsafe.UpdatePositionEstimatorsParams, unsafe.UnsafeEngageAxesParams, + unsafe.UnsafeUngripLabwareParams, ] CommandType = Union[ @@ -540,6 +542,7 @@ unsafe.UnsafeDropTipInPlaceCommandType, unsafe.UpdatePositionEstimatorsCommandType, unsafe.UnsafeEngageAxesCommandType, + unsafe.UnsafeUngripLabwareCommandType, ] CommandCreate = Annotated[ @@ -614,6 +617,7 @@ unsafe.UnsafeDropTipInPlaceCreate, unsafe.UpdatePositionEstimatorsCreate, unsafe.UnsafeEngageAxesCreate, + unsafe.UnsafeUngripLabwareCreate, ], Field(discriminator="commandType"), ] @@ -689,6 +693,7 @@ unsafe.UnsafeDropTipInPlaceResult, unsafe.UpdatePositionEstimatorsResult, unsafe.UnsafeEngageAxesResult, + unsafe.UnsafeUngripLabwareResult, ] # todo(mm, 2024-06-12): Ideally, command return types would have specific diff --git a/api/src/opentrons/protocol_engine/commands/unsafe/__init__.py b/api/src/opentrons/protocol_engine/commands/unsafe/__init__.py index 6b92cc2e18e..72698a3b0f2 100644 --- a/api/src/opentrons/protocol_engine/commands/unsafe/__init__.py +++ b/api/src/opentrons/protocol_engine/commands/unsafe/__init__.py @@ -31,6 +31,15 @@ UnsafeEngageAxesCreate, ) +from .unsafe_ungrip_labware import ( + UnsafeUngripLabwareCommandType, + UnsafeUngripLabwareParams, + UnsafeUngripLabwareResult, + UnsafeUngripLabware, + UnsafeUngripLabwareCreate, +) + + __all__ = [ # Unsafe blow-out-in-place command models "UnsafeBlowOutInPlaceCommandType", @@ -56,4 +65,10 @@ "UnsafeEngageAxesResult", "UnsafeEngageAxes", "UnsafeEngageAxesCreate", + # Unsafe ungrip labware + "UnsafeUngripLabwareCommandType", + "UnsafeUngripLabwareParams", + "UnsafeUngripLabwareResult", + "UnsafeUngripLabware", + "UnsafeUngripLabwareCreate", ] diff --git a/api/src/opentrons/protocol_engine/commands/unsafe/unsafe_ungrip_labware.py b/api/src/opentrons/protocol_engine/commands/unsafe/unsafe_ungrip_labware.py new file mode 100644 index 00000000000..e64beaa7ea7 --- /dev/null +++ b/api/src/opentrons/protocol_engine/commands/unsafe/unsafe_ungrip_labware.py @@ -0,0 +1,73 @@ +"""Ungrip labware payload, result, and implementaiton.""" + +from __future__ import annotations +from opentrons.protocol_engine.errors.exceptions import GripperNotAttachedError +from pydantic import BaseModel +from typing import Optional, Type +from typing_extensions import Literal + +from ..command import AbstractCommandImpl, BaseCommand, BaseCommandCreate, SuccessData +from ...errors.error_occurrence import ErrorOccurrence +from ...resources import ensure_ot3_hardware + +from opentrons.hardware_control import HardwareControlAPI + + +UnsafeUngripLabwareCommandType = Literal["unsafe/ungripLabware"] + + +class UnsafeUngripLabwareParams(BaseModel): + """Payload required for an UngripLabware command.""" + + +class UnsafeUngripLabwareResult(BaseModel): + """Result data from the execution of an UngripLabware command.""" + + +class UnsafeUngripLabwareImplementation( + AbstractCommandImpl[ + UnsafeUngripLabwareParams, + SuccessData[UnsafeUngripLabwareResult, None], + ] +): + """Ungrip labware command implementation.""" + + def __init__( + self, + hardware_api: HardwareControlAPI, + **kwargs: object, + ) -> None: + self._hardware_api = hardware_api + + async def execute( + self, params: UnsafeUngripLabwareParams + ) -> SuccessData[UnsafeUngripLabwareResult, None]: + """Ungrip Labware.""" + ot3_hardware_api = ensure_ot3_hardware(self._hardware_api) + if not ot3_hardware_api.has_gripper(): + raise GripperNotAttachedError("No gripper found to perform ungrip.") + await ot3_hardware_api.ungrip() + return SuccessData(public=UnsafeUngripLabwareResult(), private=None) + + +class UnsafeUngripLabware( + BaseCommand[UnsafeUngripLabwareParams, UnsafeUngripLabwareResult, ErrorOccurrence] +): + """UnsafeUngripLabware command model.""" + + commandType: UnsafeUngripLabwareCommandType = "unsafe/ungripLabware" + params: UnsafeUngripLabwareParams + result: Optional[UnsafeUngripLabwareResult] + + _ImplementationCls: Type[ + UnsafeUngripLabwareImplementation + ] = UnsafeUngripLabwareImplementation + + +class UnsafeUngripLabwareCreate(BaseCommandCreate[UnsafeUngripLabwareParams]): + """UnsafeEngageAxes command request model.""" + + commandType: UnsafeUngripLabwareCommandType = "unsafe/ungripLabware" + params: UnsafeUngripLabwareParams + + _CommandCls: Type[UnsafeUngripLabware] = UnsafeUngripLabware diff --git a/api/src/opentrons/protocol_engine/state/commands.py b/api/src/opentrons/protocol_engine/state/commands.py index d01926862de..6723c521892 100644 --- a/api/src/opentrons/protocol_engine/state/commands.py +++ b/api/src/opentrons/protocol_engine/state/commands.py @@ -17,6 +17,9 @@ RunCommandAction, SetErrorRecoveryPolicyAction, ) +from opentrons.protocol_engine.commands.unsafe.unsafe_ungrip_labware import ( + UnsafeUngripLabwareCommandType, +) from opentrons.protocol_engine.error_recovery_policy import ( ErrorRecoveryPolicy, ErrorRecoveryType, @@ -36,7 +39,7 @@ DoorChangeAction, ) -from ..commands import Command, CommandStatus, CommandIntent +from ..commands import Command, CommandStatus, CommandIntent, CommandCreate from ..errors import ( RunStoppedError, ErrorOccurrence, @@ -95,7 +98,9 @@ class QueueStatus(enum.Enum): AWAITING_RECOVERY_PAUSED = enum.auto() """Execution of fixit commands has been paused. - New protocol and fixit commands may be enqueued, but will wait to execute. + New protocol and fixit commands may be enqueued, but will usually wait to execute. + There are certain exceptions where fixit commands will still run. + New setup commands may not be enqueued. """ @@ -740,6 +745,12 @@ def get_next_to_execute(self) -> Optional[str]: next_fixit_cmd = self._state.command_history.get_fixit_queue_ids().head(None) if next_fixit_cmd and self._state.queue_status == QueueStatus.AWAITING_RECOVERY: return next_fixit_cmd + if ( + next_fixit_cmd + and self._state.queue_status == QueueStatus.AWAITING_RECOVERY_PAUSED + and self._may_run_with_door_open(fixit_command=self.get(next_fixit_cmd)) + ): + return next_fixit_cmd # if there is a setup command queued, prioritize it next_setup_cmd = self._state.command_history.get_setup_queue_ids().head(None) @@ -970,12 +981,23 @@ def validate_action_allowed( # noqa: C901 "Setup commands are not allowed after run has started." ) elif action.request.intent == CommandIntent.FIXIT: - if self._state.queue_status != QueueStatus.AWAITING_RECOVERY: + if self.get_status() == EngineStatus.AWAITING_RECOVERY: + return action + elif self.get_status() in ( + EngineStatus.AWAITING_RECOVERY_BLOCKED_BY_OPEN_DOOR, + EngineStatus.AWAITING_RECOVERY_PAUSED, + ): + if self._may_run_with_door_open(fixit_command=action.request): + return action + else: + raise FixitCommandNotAllowedError( + f"{action.request.commandType} fixit command may not run" + " until the door is closed and the run is played again." + ) + else: raise FixitCommandNotAllowedError( "Fixit commands are not allowed when the run is not in a recoverable state." ) - else: - return action else: return action @@ -1060,3 +1082,22 @@ def get_error_recovery_policy(self) -> ErrorRecoveryPolicy: higher-level code. """ return self._state.error_recovery_policy + + def _may_run_with_door_open( + self, *, fixit_command: Command | CommandCreate + ) -> bool: + """Return whether the given fixit command is exempt from the usual open-door auto pause. + + This is required for certain error recovery flows, where we want the robot to + do stuff while the door is open. + """ + # CommandIntent.PROTOCOL and CommandIntent.SETUP have their own rules for whether + # they run while the door is open. Passing one of those commands to this function + # is probably a mistake in the caller's logic. + assert fixit_command.intent == CommandIntent.FIXIT + + # This type annotation is to make sure the string constant stays in sync and isn't typo'd. + required_command_type: UnsafeUngripLabwareCommandType = "unsafe/ungripLabware" + # todo(mm, 2024-10-04): Instead of allowlisting command types, maybe we should + # add a `mayRunWithDoorOpen: bool` field to command requests. + return fixit_command.commandType == required_command_type diff --git a/api/tests/opentrons/protocol_engine/commands/unsafe/test_ungrip_labware.py b/api/tests/opentrons/protocol_engine/commands/unsafe/test_ungrip_labware.py new file mode 100644 index 00000000000..1a41244d556 --- /dev/null +++ b/api/tests/opentrons/protocol_engine/commands/unsafe/test_ungrip_labware.py @@ -0,0 +1,40 @@ +"""Test update-position-estimator commands.""" +from decoy import Decoy + +from opentrons.protocol_engine.commands.unsafe.unsafe_ungrip_labware import ( + UnsafeUngripLabwareParams, + UnsafeUngripLabwareResult, + UnsafeUngripLabwareImplementation, +) +from opentrons.protocol_engine.commands.command import SuccessData +from opentrons.protocol_engine.errors.exceptions import GripperNotAttachedError +from opentrons.hardware_control import OT3HardwareControlAPI +import pytest + + +async def test_ungrip_labware_implementation( + decoy: Decoy, ot3_hardware_api: OT3HardwareControlAPI +) -> None: + """Test UngripLabware command execution.""" + subject = UnsafeUngripLabwareImplementation(hardware_api=ot3_hardware_api) + + decoy.when(ot3_hardware_api.has_gripper()).then_return(True) + + result = await subject.execute(params=UnsafeUngripLabwareParams()) + + assert result == SuccessData(public=UnsafeUngripLabwareResult(), private=None) + + decoy.verify( + await ot3_hardware_api.ungrip(), + ) + + +async def test_ungrip_labware_implementation_raises_no_gripper_attached( + decoy: Decoy, ot3_hardware_api: OT3HardwareControlAPI +) -> None: + """Test UngripLabware command execution.""" + subject = UnsafeUngripLabwareImplementation(hardware_api=ot3_hardware_api) + + decoy.when(ot3_hardware_api.has_gripper()).then_return(False) + with pytest.raises(GripperNotAttachedError): + await subject.execute(params=UnsafeUngripLabwareParams()) diff --git a/api/tests/opentrons/protocol_engine/state/test_command_state.py b/api/tests/opentrons/protocol_engine/state/test_command_state.py index afafcc3cabe..6f090612a74 100644 --- a/api/tests/opentrons/protocol_engine/state/test_command_state.py +++ b/api/tests/opentrons/protocol_engine/state/test_command_state.py @@ -557,6 +557,79 @@ def test_door_during_error_recovery() -> None: assert subject.state.failed_command_errors == [expected_error_occurance] +@pytest.mark.parametrize("close_door_before_queueing", [False, True]) +def test_door_ungrip_labware(close_door_before_queueing: bool) -> None: + """Ungrip commands should be able to run even when the door is open.""" + subject = CommandStore( + is_door_open=False, + error_recovery_policy=_placeholder_error_recovery_policy, + config=Config( + block_on_door_open=True, + # Choice of robot and deck type are arbitrary. + robot_type="OT-2 Standard", + deck_type=DeckType.OT2_STANDARD, + ), + ) + subject_view = CommandView(subject.state) + + # Fail a command to put the subject in recovery mode. + queue_failing = actions.QueueCommandAction( + request=commands.CommentCreate( + params=commands.CommentParams(message=""), key="command-key-1" + ), + request_hash=None, + created_at=datetime(year=2021, month=1, day=1), + command_id="failing-command-id", + ) + subject.handle_action(queue_failing) + run_failing = actions.RunCommandAction( + command_id="failing-command-id", + started_at=datetime(year=2022, month=2, day=2), + ) + subject.handle_action(run_failing) + expected_error = errors.ProtocolEngineError(message="oh no") + fail_failing = actions.FailCommandAction( + command_id="failing-command-id", + running_command=subject_view.get("failing-command-id"), + error_id="error-id", + failed_at=datetime(year=2023, month=3, day=3), + error=expected_error, + notes=[], + type=ErrorRecoveryType.WAIT_FOR_RECOVERY, + ) + subject.handle_action(fail_failing) + + # Open the door: + subject.handle_action(actions.DoorChangeAction(DoorState.OPEN)) + assert ( + subject_view.get_status() == EngineStatus.AWAITING_RECOVERY_BLOCKED_BY_OPEN_DOOR + ) + assert subject_view.get_next_to_execute() is None + + if close_door_before_queueing: + subject.handle_action(actions.DoorChangeAction(DoorState.CLOSED)) + + assert subject_view.get_status() in ( + EngineStatus.AWAITING_RECOVERY_PAUSED, # If we closed the door. + EngineStatus.AWAITING_RECOVERY_BLOCKED_BY_OPEN_DOOR, # If we didn't. + ) + + # Make sure the special ungrip command can be queued and that it will be returned + # as next to execute: + queue_fixit = actions.QueueCommandAction( + request=commands.unsafe.UnsafeUngripLabwareCreate( + params=commands.unsafe.UnsafeUngripLabwareParams(), + intent=CommandIntent.FIXIT, + ), + request_hash=None, + created_at=datetime(year=2021, month=1, day=1), + command_id="fixit-command-id", + ) + subject_view.validate_action_allowed(queue_fixit) + subject.handle_action(queue_fixit) + assert subject_view.get_next_to_execute() == "fixit-command-id" + + @pytest.mark.parametrize( ("door_initially_open", "expected_engine_status_after_play"), [ diff --git a/api/tests/opentrons/protocol_engine/state/test_command_view_old.py b/api/tests/opentrons/protocol_engine/state/test_command_view_old.py index 48918eec6eb..06318cb8d36 100644 --- a/api/tests/opentrons/protocol_engine/state/test_command_view_old.py +++ b/api/tests/opentrons/protocol_engine/state/test_command_view_old.py @@ -595,6 +595,21 @@ class ActionAllowedSpec(NamedTuple): action=ResumeFromRecoveryAction(), expected_error=errors.ResumeFromRecoveryNotAllowedError, ), + ActionAllowedSpec( + subject=get_command_view( + queue_status=QueueStatus.AWAITING_RECOVERY_PAUSED, is_door_blocking=True + ), + action=QueueCommandAction( + request=cmd.unsafe.UnsafeUngripLabwareCreate( + params=cmd.unsafe.UnsafeUngripLabwareParams(), + intent=cmd.CommandIntent.FIXIT, + ), + request_hash=None, + command_id="command-id", + created_at=datetime(year=2021, month=1, day=1), + ), + expected_error=None, + ), ] diff --git a/robot-server/simulators/test-flex.json b/robot-server/simulators/test-flex.json index ed694a8cb92..34544cfa099 100644 --- a/robot-server/simulators/test-flex.json +++ b/robot-server/simulators/test-flex.json @@ -9,6 +9,10 @@ "left": { "model": "p50_single_3.4", "id": "123" + }, + "gripper":{ + "model": "gripper_1.3", + "id": "1234" } }, "attached_modules": { diff --git a/shared-data/command/schemas/10.json b/shared-data/command/schemas/10.json index d83ec30e388..07afff241a1 100644 --- a/shared-data/command/schemas/10.json +++ b/shared-data/command/schemas/10.json @@ -74,7 +74,8 @@ "unsafe/blowOutInPlace": "#/definitions/UnsafeBlowOutInPlaceCreate", "unsafe/dropTipInPlace": "#/definitions/UnsafeDropTipInPlaceCreate", "unsafe/updatePositionEstimators": "#/definitions/UpdatePositionEstimatorsCreate", - "unsafe/engageAxes": "#/definitions/UnsafeEngageAxesCreate" + "unsafe/engageAxes": "#/definitions/UnsafeEngageAxesCreate", + "unsafe/ungripLabware": "#/definitions/UnsafeUngripLabwareCreate" } }, "oneOf": [ @@ -287,6 +288,9 @@ }, { "$ref": "#/definitions/UnsafeEngageAxesCreate" + }, + { + "$ref": "#/definitions/UnsafeUngripLabwareCreate" } ], "definitions": { @@ -4526,6 +4530,42 @@ } }, "required": ["params"] + }, + "UnsafeUngripLabwareParams": { + "title": "UnsafeUngripLabwareParams", + "description": "Payload required for an UngripLabware command.", + "type": "object", + "properties": {} + }, + "UnsafeUngripLabwareCreate": { + "title": "UnsafeUngripLabwareCreate", + "description": "UnsafeEngageAxes command request model.", + "type": "object", + "properties": { + "commandType": { + "title": "Commandtype", + "default": "unsafe/ungripLabware", + "enum": ["unsafe/ungripLabware"], + "type": "string" + }, + "params": { + "$ref": "#/definitions/UnsafeUngripLabwareParams" + }, + "intent": { + "description": "The reason the command was added. If not specified or `protocol`, the command will be treated as part of the protocol run itself, and added to the end of the existing command queue.\n\nIf `setup`, the command will be treated as part of run setup. A setup command may only be enqueued if the run has not started.\n\nUse setup commands for activities like pre-run calibration checks and module setup, like pre-heating.", + "allOf": [ + { + "$ref": "#/definitions/CommandIntent" + } + ] + }, + "key": { + "title": "Key", + "description": "A key value, unique in this run, that can be used to track the same logical command across multiple runs of the same protocol. If a value is not provided, one will be generated.", + "type": "string" + } + }, + "required": ["params"] } }, "$id": "opentronsCommandSchemaV10", From fb6e437b95b7649142c593e1b80b59b06db7be24 Mon Sep 17 00:00:00 2001 From: Sanniti Pimpley Date: Mon, 7 Oct 2024 13:49:11 -0400 Subject: [PATCH 13/27] refactor(api, robot-server): remove/ update outdated TODOs (#16413) # Overview Removes TODOs that have been addressed or are no longer relevant. Updates outdated ones. Details in comments. ## Risk assessment None. --- api/src/opentrons/execute.py | 3 +-- .../hardware_control/modules/heater_shaker.py | 1 - .../opentrons/protocol_api/core/engine/protocol.py | 1 - .../protocol_api/core/legacy/legacy_protocol_core.py | 1 - api/src/opentrons/protocol_api/core/protocol.py | 1 - api/src/opentrons/protocol_api/protocol_context.py | 1 - .../protocol_engine/commands/move_labware.py | 1 - .../execution/heater_shaker_movement_flagger.py | 3 --- .../protocol_engine/execution/labware_movement.py | 2 -- api/src/opentrons/protocol_engine/state/modules.py | 1 - api/src/opentrons/simulate.py | 3 +-- .../robot_server/instruments/instrument_models.py | 5 ----- robot-server/robot_server/instruments/router.py | 11 ++++++++--- .../maintenance_runs/maintenance_run_data_manager.py | 2 +- .../maintenance_runs/router/commands_router.py | 3 --- .../robot_server/service/legacy/routers/motors.py | 2 -- robot-server/tests/instruments/test_router.py | 2 -- 17 files changed, 11 insertions(+), 32 deletions(-) diff --git a/api/src/opentrons/execute.py b/api/src/opentrons/execute.py index 1e8d3771f59..ade74b1aadd 100644 --- a/api/src/opentrons/execute.py +++ b/api/src/opentrons/execute.py @@ -609,8 +609,6 @@ def _run_file_non_pe( context.home() try: - # TODO (spp, 2024-03-18): use true run-time param overrides once enabled - # for cli protocol simulation/ execution execute_apiv2.run_protocol( protocol, context, run_time_parameters_with_overrides=None ) @@ -626,6 +624,7 @@ def _run_file_pe( """Run a protocol file with Protocol Engine.""" async def run(protocol_source: ProtocolSource) -> None: + # TODO (spp, 2024-03-18): use run-time param overrides once enabled for cli protocol execution hardware_api_wrapped = hardware_api.wrapped() protocol_engine = await create_protocol_engine( hardware_api=hardware_api_wrapped, diff --git a/api/src/opentrons/hardware_control/modules/heater_shaker.py b/api/src/opentrons/hardware_control/modules/heater_shaker.py index e52de0bf49c..cc592d3c514 100644 --- a/api/src/opentrons/hardware_control/modules/heater_shaker.py +++ b/api/src/opentrons/hardware_control/modules/heater_shaker.py @@ -201,7 +201,6 @@ def device_info(self) -> Mapping[str, str]: @property def live_data(self) -> LiveData: return { - # TODO (spp, 2022-2-22): Revise what status includes "status": self.status.value, "data": { "temperatureStatus": self.temperature_status.value, diff --git a/api/src/opentrons/protocol_api/core/engine/protocol.py b/api/src/opentrons/protocol_api/core/engine/protocol.py index 04ddaf55a48..360740cbfcd 100644 --- a/api/src/opentrons/protocol_api/core/engine/protocol.py +++ b/api/src/opentrons/protocol_api/core/engine/protocol.py @@ -311,7 +311,6 @@ def load_adapter( return labware_core - # TODO (spp, 2022-12-14): https://opentrons.atlassian.net/browse/RLAB-237 def move_labware( self, labware_core: LabwareCore, diff --git a/api/src/opentrons/protocol_api/core/legacy/legacy_protocol_core.py b/api/src/opentrons/protocol_api/core/legacy/legacy_protocol_core.py index d698604ac30..eb1a7386e38 100644 --- a/api/src/opentrons/protocol_api/core/legacy/legacy_protocol_core.py +++ b/api/src/opentrons/protocol_api/core/legacy/legacy_protocol_core.py @@ -267,7 +267,6 @@ def load_adapter( """Load an adapter using its identifying parameters""" raise APIVersionError(api_element="Loading adapter") - # TODO (spp, 2022-12-14): https://opentrons.atlassian.net/browse/RLAB-237 def move_labware( self, labware_core: LegacyLabwareCore, diff --git a/api/src/opentrons/protocol_api/core/protocol.py b/api/src/opentrons/protocol_api/core/protocol.py index a8403cc40da..687291c390a 100644 --- a/api/src/opentrons/protocol_api/core/protocol.py +++ b/api/src/opentrons/protocol_api/core/protocol.py @@ -93,7 +93,6 @@ def load_adapter( """Load an adapter using its identifying parameters""" ... - # TODO (spp, 2022-12-14): https://opentrons.atlassian.net/browse/RLAB-237 @abstractmethod def move_labware( self, diff --git a/api/src/opentrons/protocol_api/protocol_context.py b/api/src/opentrons/protocol_api/protocol_context.py index 64a73457608..5c21f662a62 100644 --- a/api/src/opentrons/protocol_api/protocol_context.py +++ b/api/src/opentrons/protocol_api/protocol_context.py @@ -661,7 +661,6 @@ def loaded_labwares(self) -> Dict[int, Labware]: if slot is not None } - # TODO (spp, 2022-12-14): https://opentrons.atlassian.net/browse/RLAB-237 @requires_version(2, 15) def move_labware( self, diff --git a/api/src/opentrons/protocol_engine/commands/move_labware.py b/api/src/opentrons/protocol_engine/commands/move_labware.py index c4381dd6865..d5c188d219f 100644 --- a/api/src/opentrons/protocol_engine/commands/move_labware.py +++ b/api/src/opentrons/protocol_engine/commands/move_labware.py @@ -47,7 +47,6 @@ _TRASH_CHUTE_DROP_BUFFER_MM = 8 -# TODO (spp, 2022-12-14): https://opentrons.atlassian.net/browse/RLAB-237 class MoveLabwareParams(BaseModel): """Input parameters for a ``moveLabware`` command.""" diff --git a/api/src/opentrons/protocol_engine/execution/heater_shaker_movement_flagger.py b/api/src/opentrons/protocol_engine/execution/heater_shaker_movement_flagger.py index 78b8f2e9bfa..efe8190f04a 100644 --- a/api/src/opentrons/protocol_engine/execution/heater_shaker_movement_flagger.py +++ b/api/src/opentrons/protocol_engine/execution/heater_shaker_movement_flagger.py @@ -61,9 +61,6 @@ async def raise_if_labware_latched_on_heater_shaker( return # Labware on a module, but not a Heater-Shaker. if hs_substate.labware_latch_status == HeaterShakerLatchStatus.CLOSED: - # TODO (spp, 2022-10-27): This only raises if latch status is 'idle_closed'. - # We need to update the flagger to raise if latch status is anything other - # than 'idle_open' raise HeaterShakerLabwareLatchNotOpenError( "Heater-Shaker labware latch must be open when moving labware to/from it." ) diff --git a/api/src/opentrons/protocol_engine/execution/labware_movement.py b/api/src/opentrons/protocol_engine/execution/labware_movement.py index b7d03914793..30feb6517ff 100644 --- a/api/src/opentrons/protocol_engine/execution/labware_movement.py +++ b/api/src/opentrons/protocol_engine/execution/labware_movement.py @@ -37,8 +37,6 @@ _GRIPPER_HOMED_POSITION_Z = 166.125 # Height of the center of the gripper critical point from the deck when homed -# TODO (spp, 2022-10-20): name this GripperMovementHandler if it doesn't handle -# any non-gripper implementations class LabwareMovementHandler: """Implementation logic for labware movement.""" diff --git a/api/src/opentrons/protocol_engine/state/modules.py b/api/src/opentrons/protocol_engine/state/modules.py index 7120025da89..ca8973b405c 100644 --- a/api/src/opentrons/protocol_engine/state/modules.py +++ b/api/src/opentrons/protocol_engine/state/modules.py @@ -580,7 +580,6 @@ def _handle_thermocycler_module_commands( target_block_temperature=block_temperature, target_lid_temperature=None, ) - # TODO (spp, 2022-08-01): set is_lid_open to False upon lid commands' failure elif isinstance(command.result, thermocycler.OpenLidResult): self._state.substate_by_module_id[module_id] = ThermocyclerModuleSubState( module_id=ThermocyclerModuleId(module_id), diff --git a/api/src/opentrons/simulate.py b/api/src/opentrons/simulate.py index 62806edb048..23f6c7fdfb9 100644 --- a/api/src/opentrons/simulate.py +++ b/api/src/opentrons/simulate.py @@ -883,8 +883,6 @@ def _run_file_non_pe( context.home() with scraper.scrape(): try: - # TODO (spp, 2024-03-18): use true run-time param overrides once enabled - # for cli protocol simulation/ execution execute.run_protocol( protocol, context, run_time_parameters_with_overrides=None ) @@ -914,6 +912,7 @@ def _run_file_pe( log_level: str, ) -> _SimulateResult: """Run a protocol file with Protocol Engine.""" + # TODO (spp, 2024-03-18): use run-time param overrides once enabled for cli protocol simulation. async def run(protocol_source: ProtocolSource) -> _SimulateResult: hardware_api_wrapped = hardware_api.wrapped() diff --git a/robot-server/robot_server/instruments/instrument_models.py b/robot-server/robot_server/instruments/instrument_models.py index 3bd9885d26d..f6a8ed0f82f 100644 --- a/robot-server/robot_server/instruments/instrument_models.py +++ b/robot-server/robot_server/instruments/instrument_models.py @@ -76,8 +76,6 @@ class GripperData(BaseModel): """Data from attached gripper.""" jawState: str = Field(..., description="Gripper Jaw state.") - # TODO (spp, 2023-01-03): update calibration field as decided after - # spike https://opentrons.atlassian.net/browse/RSS-167 calibratedOffset: Optional[InstrumentCalibrationData] = Field( None, description="Calibrated gripper offset." ) @@ -93,9 +91,6 @@ class PipetteData(BaseModel): None, description="Calibrated pipette offset." ) - # TODO (spp, 2022-12-20): update/ add fields according to client needs. - # add calibration data as decided by https://opentrons.atlassian.net/browse/RSS-167 - class PipetteState(BaseModel): """State from an attached pipette.""" diff --git a/robot-server/robot_server/instruments/router.py b/robot-server/robot_server/instruments/router.py index b34a5d0c749..a9a3e3bbed3 100644 --- a/robot-server/robot_server/instruments/router.py +++ b/robot-server/robot_server/instruments/router.py @@ -267,10 +267,15 @@ async def _get_attached_instruments_ot2( async def get_attached_instruments( hardware: Annotated[HardwareControlAPI, Depends(get_hardware)], ) -> PydanticResponse[SimpleMultiBody[AttachedItem]]: - """Get a list of all attached instruments.""" + """Get a list of all attached instruments. + + Note: This endpoint returns the full AttachedItem data for Flex instruments only. + + On an OT-2, this endpoint will provide partial data of the OT-2 pipettes + (no pipette fw and calibration data), and will not fetch new data after + a pipette attachment/ removal. + """ try: - # TODO (spp, 2023-01-06): revise according to - # https://opentrons.atlassian.net/browse/RET-1295 ot3_hardware = ensure_ot3_hardware(hardware_api=hardware) return await _get_attached_instruments_ot3(ot3_hardware) except HardwareNotSupportedError: diff --git a/robot-server/robot_server/maintenance_runs/maintenance_run_data_manager.py b/robot-server/robot_server/maintenance_runs/maintenance_run_data_manager.py index c1c733a8e12..589aaf5614d 100644 --- a/robot-server/robot_server/maintenance_runs/maintenance_run_data_manager.py +++ b/robot-server/robot_server/maintenance_runs/maintenance_run_data_manager.py @@ -39,7 +39,7 @@ def _build_run( id=run_id, createdAt=created_at, status=state_summary.status, - actions=[], # TODO (spp, 2023-04-23): wire up actions once they are allowed + actions=[], errors=state_summary.errors, labware=state_summary.labware, labwareOffsets=state_summary.labwareOffsets, diff --git a/robot-server/robot_server/maintenance_runs/router/commands_router.py b/robot-server/robot_server/maintenance_runs/router/commands_router.py index 9df5f9630b9..afc5e03779b 100644 --- a/robot-server/robot_server/maintenance_runs/router/commands_router.py +++ b/robot-server/robot_server/maintenance_runs/router/commands_router.py @@ -156,9 +156,6 @@ async def create_run_command( # behavior is to pass through `command_intent` without overriding it command_intent = pe_commands.CommandIntent.SETUP command_create = request_body.data.copy(update={"intent": command_intent}) - - # TODO (spp): re-add `RunStoppedError` exception catching if/when maintenance runs - # have actions. command = await run_orchestrator_store.add_command_and_wait_for_interval( request=command_create, wait_until_complete=waitUntilComplete, timeout=timeout ) diff --git a/robot-server/robot_server/service/legacy/routers/motors.py b/robot-server/robot_server/service/legacy/routers/motors.py index d142ab2466f..1bcae9a2c38 100644 --- a/robot-server/robot_server/service/legacy/routers/motors.py +++ b/robot-server/robot_server/service/legacy/routers/motors.py @@ -30,8 +30,6 @@ async def get_engaged_motors( hardware: Annotated[HardwareControlAPI, Depends(get_hardware)], ) -> model.EngagedMotors: - # TODO (spp, 2023-07-06): Implement fetching Flex's engaged motors - # https://opentrons.atlassian.net/browse/RET-1371 try: engaged_axes = hardware.engaged_axes axes_dict = { diff --git a/robot-server/tests/instruments/test_router.py b/robot-server/tests/instruments/test_router.py index 01ba0cdf7c6..fe401828284 100644 --- a/robot-server/tests/instruments/test_router.py +++ b/robot-server/tests/instruments/test_router.py @@ -100,8 +100,6 @@ async def test_get_instruments_empty( assert result.status_code == 200 -# TODO (spp, 2022-01-17): remove xfail once robot server test flow is set up to handle -# OT2 vs OT3 tests correclty @pytest.mark.ot3_only async def test_get_all_attached_instruments( decoy: Decoy, From 528326fd7f1f7314b9fa07d890e7b29b1a7e75e4 Mon Sep 17 00:00:00 2001 From: Max Marrone Date: Mon, 7 Oct 2024 15:01:37 -0400 Subject: [PATCH 14/27] test(robot-server): Add more unit tests for error_recovery_mapping.py (#16426) --- .../tests/runs/test_error_recovery_mapping.py | 95 +++++++++++++++++-- 1 file changed, 89 insertions(+), 6 deletions(-) diff --git a/robot-server/tests/runs/test_error_recovery_mapping.py b/robot-server/tests/runs/test_error_recovery_mapping.py index fba8e4315d9..a125d12649d 100644 --- a/robot-server/tests/runs/test_error_recovery_mapping.py +++ b/robot-server/tests/runs/test_error_recovery_mapping.py @@ -2,6 +2,7 @@ import pytest from decoy import Decoy +from opentrons_shared_data.robot.types import RobotType from opentrons.protocol_engine.commands.pipetting_common import LiquidNotFoundError from opentrons.protocol_engine.commands.command import ( @@ -12,6 +13,7 @@ from opentrons.protocol_engine.error_recovery_policy import ErrorRecoveryType from opentrons.protocol_engine.state.config import Config from opentrons.protocol_engine.types import DeckType + from robot_server.runs.error_recovery_mapping import ( create_error_recovery_policy_from_rules, ) @@ -72,12 +74,12 @@ def test_create_error_recovery_policy_with_rules( ) -> None: """Should return IGNORE_AND_CONTINUE if that's what we specify as the rule.""" policy = create_error_recovery_policy_from_rules([mock_rule], enabled=True) - exampleConfig = Config( + example_config = Config( robot_type="OT-3 Standard", deck_type=DeckType.OT3_STANDARD, ) assert ( - policy(exampleConfig, mock_command, mock_error_data) + policy(example_config, mock_command, mock_error_data) == ErrorRecoveryType.IGNORE_AND_CONTINUE ) @@ -87,12 +89,12 @@ def test_create_error_recovery_policy_undefined_error( ) -> None: """Should return a FAIL_RUN policy when error is not defined.""" policy = create_error_recovery_policy_from_rules(rules=[], enabled=True) - exampleConfig = Config( + example_config = Config( robot_type="OT-3 Standard", deck_type=DeckType.OT3_STANDARD, ) - assert policy(exampleConfig, mock_command, None) == ErrorRecoveryType.FAIL_RUN + assert policy(example_config, mock_command, None) == ErrorRecoveryType.FAIL_RUN def test_create_error_recovery_policy_defined_error( @@ -100,12 +102,93 @@ def test_create_error_recovery_policy_defined_error( ) -> None: """Should return a WAIT_FOR_RECOVERY policy when error is defined.""" policy = create_error_recovery_policy_from_rules(rules=[], enabled=True) - exampleConfig = Config( + example_config = Config( robot_type="OT-3 Standard", deck_type=DeckType.OT3_STANDARD, ) assert ( - policy(exampleConfig, mock_command, mock_error_data) + policy(example_config, mock_command, mock_error_data) == ErrorRecoveryType.WAIT_FOR_RECOVERY ) + + +@pytest.mark.parametrize("enabled", [True, False]) +def test_enabled_boolean(enabled: bool) -> None: + """enabled=False should override any rules and always fail the run.""" + command = LiquidProbe.construct() # type: ignore[call-arg] + error_data = DefinedErrorData[LiquidNotFoundError]( + public=LiquidNotFoundError.construct() # type: ignore[call-arg] + ) + + rules = [ + ErrorRecoveryRule( + matchCriteria=MatchCriteria( + command=CommandMatcher( + commandType=command.commandType, + error=ErrorMatcher(errorType=error_data.public.errorType), + ), + ), + ifMatch=ReactionIfMatch.IGNORE_AND_CONTINUE, + ) + ] + + example_config = Config( + robot_type="OT-3 Standard", + deck_type=DeckType.OT3_STANDARD, + ) + + policy = create_error_recovery_policy_from_rules(rules, enabled) + result = policy(example_config, command, error_data) + expected_result = ( + ErrorRecoveryType.IGNORE_AND_CONTINUE if enabled else ErrorRecoveryType.FAIL_RUN + ) + assert result == expected_result + + +@pytest.mark.parametrize( + ( + "robot_type", + "expect_error_recovery_to_be_enabled", + ), + [ + ("OT-2 Standard", False), + ("OT-3 Standard", True), + ], +) +def test_enabled_on_flex_disabled_on_ot2( + robot_type: RobotType, expect_error_recovery_to_be_enabled: bool +) -> None: + """On OT-2s, the run should always fail regardless of any input rules.""" + command = LiquidProbe.construct() # type: ignore[call-arg] + error_data = DefinedErrorData[LiquidNotFoundError]( + public=LiquidNotFoundError.construct() # type: ignore[call-arg] + ) + + rules = [ + ErrorRecoveryRule( + matchCriteria=MatchCriteria( + command=CommandMatcher( + commandType=command.commandType, + error=ErrorMatcher(errorType=error_data.public.errorType), + ), + ), + ifMatch=ReactionIfMatch.IGNORE_AND_CONTINUE, + ) + ] + + example_config = Config( + robot_type=robot_type, + # This is a "wrong" deck_type that doesn't necessarily match robot_type + # but that shouldn't matter for our purposes. + deck_type=DeckType.OT3_STANDARD, + ) + + policy = create_error_recovery_policy_from_rules(rules, enabled=True) + result = policy(example_config, command, error_data) + expected_result = ( + ErrorRecoveryType.IGNORE_AND_CONTINUE + if expect_error_recovery_to_be_enabled + else ErrorRecoveryType.FAIL_RUN + ) + assert result == expected_result From d1de8082a27ea7c76a39f663db19cd429bb42869 Mon Sep 17 00:00:00 2001 From: Josh McVey Date: Mon, 7 Oct 2024 16:04:22 -0500 Subject: [PATCH 15/27] fix(app): get back unboxingFlow path update function (#16411) (#16428) ## Cherry-pick 4bca02a947 #16411 - [ ] Reviewer please validate that I resolved the conflicts correctly as edge has the import pathing updates. Co-authored-by: koji --- app/src/pages/ODD/RobotDashboard/WelcomeModal.tsx | 10 ++++++++++ .../ODD/RobotDashboard/__tests__/WelcomeModal.test.tsx | 5 +++++ 2 files changed, 15 insertions(+) diff --git a/app/src/pages/ODD/RobotDashboard/WelcomeModal.tsx b/app/src/pages/ODD/RobotDashboard/WelcomeModal.tsx index 99c1ff41b21..450bdb689bf 100644 --- a/app/src/pages/ODD/RobotDashboard/WelcomeModal.tsx +++ b/app/src/pages/ODD/RobotDashboard/WelcomeModal.tsx @@ -1,5 +1,6 @@ import { useEffect } from 'react' import { useTranslation } from 'react-i18next' +import { useDispatch } from 'react-redux' import { COLORS, @@ -14,10 +15,12 @@ import { useCreateLiveCommandMutation } from '@opentrons/react-api-client' import { SmallButton } from '/app/atoms/buttons' import { OddModal } from '/app/molecules/OddModal' +import { updateConfigValue } from '/app/redux/config' import welcomeModalImage from '/app/assets/images/on-device-display/welcome_dashboard_modal.png' import type { SetStatusBarCreateCommand } from '@opentrons/shared-data' +import type { Dispatch } from '/app/redux/types' interface WelcomeModalProps { setShowWelcomeModal: (showWelcomeModal: boolean) => void @@ -27,6 +30,7 @@ export function WelcomeModal({ setShowWelcomeModal, }: WelcomeModalProps): JSX.Element { const { t } = useTranslation(['device_details', 'shared']) + const dispatch = useDispatch() const { createLiveCommand } = useCreateLiveCommandMutation() const animationCommand: SetStatusBarCreateCommand = { @@ -44,6 +48,12 @@ export function WelcomeModal({ } const handleCloseModal = (): void => { + dispatch( + updateConfigValue( + 'onDeviceDisplaySettings.unfinishedUnboxingFlowRoute', + null + ) + ) setShowWelcomeModal(false) } diff --git a/app/src/pages/ODD/RobotDashboard/__tests__/WelcomeModal.test.tsx b/app/src/pages/ODD/RobotDashboard/__tests__/WelcomeModal.test.tsx index 9d9f59d75b5..7fc9bf46ea2 100644 --- a/app/src/pages/ODD/RobotDashboard/__tests__/WelcomeModal.test.tsx +++ b/app/src/pages/ODD/RobotDashboard/__tests__/WelcomeModal.test.tsx @@ -6,6 +6,7 @@ import { useCreateLiveCommandMutation } from '@opentrons/react-api-client' import { renderWithProviders } from '/app/__testing-utils__' import { i18n } from '/app/i18n' +import { updateConfigValue } from '/app/redux/config' import { WelcomeModal } from '../WelcomeModal' import type { SetStatusBarCreateCommand } from '@opentrons/shared-data' @@ -61,6 +62,10 @@ describe('WelcomeModal', () => { it('should call a mock function when tapping next button', () => { render(props) fireEvent.click(screen.getByText('Next')) + expect(vi.mocked(updateConfigValue)).toHaveBeenCalledWith( + 'onDeviceDisplaySettings.unfinishedUnboxingFlowRoute', + null + ) expect(props.setShowWelcomeModal).toHaveBeenCalled() }) }) From a9b219e395c75c014680e161236775560991215a Mon Sep 17 00:00:00 2001 From: koji Date: Tue, 8 Oct 2024 09:22:04 -0400 Subject: [PATCH 16/27] fix(protocol-designer): fix issues in select pipette screen (#16404) * fix(protocol-designer): fix issues in select pipette screen --- .../localization/en/create_new_protocol.json | 2 +- .../localization/en/protocol_steps.json | 2 +- .../organisms/EditInstrumentsModal/index.tsx | 2 - .../__tests__/PipetteInfoItem.test.tsx | 19 +- .../src/organisms/PipetteInfoItem/index.tsx | 44 ++-- .../CreateNewProtocolWizard/SelectGripper.tsx | 4 + .../SelectPipettes.tsx | 194 +++++++++++------- .../__tests__/SelectGripper.test.tsx | 11 + .../__tests__/SelectPipettes.test.tsx | 10 + 9 files changed, 175 insertions(+), 113 deletions(-) diff --git a/protocol-designer/src/assets/localization/en/create_new_protocol.json b/protocol-designer/src/assets/localization/en/create_new_protocol.json index a10a1653685..52c03ca7b50 100644 --- a/protocol-designer/src/assets/localization/en/create_new_protocol.json +++ b/protocol-designer/src/assets/localization/en/create_new_protocol.json @@ -32,7 +32,7 @@ "show_tips": "Show incompatible tips", "slots_limit_reached": "Slots limit reached", "stagingArea": "Staging area", - "swap": "Swap pipettes", + "swap_pipettes": "Swap pipettes", "tell_us": "Tell us about your protocol", "trash_required": "A trash entity is required", "trashBin": "Trash Bin", diff --git a/protocol-designer/src/assets/localization/en/protocol_steps.json b/protocol-designer/src/assets/localization/en/protocol_steps.json index 3ab8b590dcc..3b00d2f7d5c 100644 --- a/protocol-designer/src/assets/localization/en/protocol_steps.json +++ b/protocol-designer/src/assets/localization/en/protocol_steps.json @@ -6,8 +6,8 @@ "delete": "Delete step", "dispensed": "Dispensed", "duplicate": "Duplicate step", - "engage_height": "Engage height", "edit_step": "Edit step", + "engage_height": "Engage height", "final_deck_state": "Final deck state", "from": "from", "heater_shaker_settings": "Heater-shaker settings", diff --git a/protocol-designer/src/organisms/EditInstrumentsModal/index.tsx b/protocol-designer/src/organisms/EditInstrumentsModal/index.tsx index c01e4ee859f..c11a62a678c 100644 --- a/protocol-designer/src/organisms/EditInstrumentsModal/index.tsx +++ b/protocol-designer/src/organisms/EditInstrumentsModal/index.tsx @@ -242,7 +242,6 @@ export function EditInstrumentsModal( leftInfo != null ? ( { @@ -277,7 +276,6 @@ export function EditInstrumentsModal( rightInfo != null ? ( { diff --git a/protocol-designer/src/organisms/PipetteInfoItem/__tests__/PipetteInfoItem.test.tsx b/protocol-designer/src/organisms/PipetteInfoItem/__tests__/PipetteInfoItem.test.tsx index 8a35eb66e87..5b6f51e414c 100644 --- a/protocol-designer/src/organisms/PipetteInfoItem/__tests__/PipetteInfoItem.test.tsx +++ b/protocol-designer/src/organisms/PipetteInfoItem/__tests__/PipetteInfoItem.test.tsx @@ -25,10 +25,6 @@ describe('PipetteInfoItem', () => { tiprackDefURIs: ['mockDefUri'], pipetteName: 'p1000_single', mount: 'left', - formPipettesByMount: { - left: { pipetteName: 'p1000_single' }, - right: { pipetteName: 'p50_single' }, - }, } vi.mocked(getLabwareDefsByURI).mockReturnValue({ @@ -45,4 +41,19 @@ describe('PipetteInfoItem', () => { fireEvent.click(screen.getByText('Remove')) expect(props.cleanForm).toHaveBeenCalled() }) + + it('renders pipette with edit and remove buttons right pipette', () => { + props = { + ...props, + mount: 'right', + } + render(props) + screen.getByText('P1000 Single-Channel GEN1') + screen.getByText('Right pipette') + screen.getByText('mock display name') + fireEvent.click(screen.getByText('Edit')) + expect(props.editClick).toHaveBeenCalled() + fireEvent.click(screen.getByText('Remove')) + expect(props.cleanForm).toHaveBeenCalled() + }) }) diff --git a/protocol-designer/src/organisms/PipetteInfoItem/index.tsx b/protocol-designer/src/organisms/PipetteInfoItem/index.tsx index 25c9855ea95..220b08cb823 100644 --- a/protocol-designer/src/organisms/PipetteInfoItem/index.tsx +++ b/protocol-designer/src/organisms/PipetteInfoItem/index.tsx @@ -15,7 +15,6 @@ import { getPipetteSpecsV2 } from '@opentrons/shared-data' import { BUTTON_LINK_STYLE } from '../../atoms' import { getLabwareDefsByURI } from '../../labware-defs/selectors' import type { PipetteMount, PipetteName } from '@opentrons/shared-data' -import type { FormPipettesByMount, PipetteOnDeck } from '../../step-forms' interface PipetteInfoItemProps { mount: PipetteMount @@ -23,22 +22,11 @@ interface PipetteInfoItemProps { tiprackDefURIs: string[] editClick: () => void cleanForm: () => void - formPipettesByMount?: FormPipettesByMount - pipetteOnDeck?: PipetteOnDeck[] } export function PipetteInfoItem(props: PipetteInfoItemProps): JSX.Element { - const { - mount, - pipetteName, - tiprackDefURIs, - editClick, - cleanForm, - formPipettesByMount, - pipetteOnDeck, - } = props + const { mount, pipetteName, tiprackDefURIs, editClick, cleanForm } = props const { t, i18n } = useTranslation('create_new_protocol') - const oppositeMount = mount === 'left' ? 'right' : 'left' const allLabware = useSelector(getLabwareDefsByURI) const is96Channel = pipetteName === 'p1000_96' return ( @@ -73,33 +61,31 @@ export function PipetteInfoItem(props: PipetteInfoItemProps): JSX.Element { {t('edit')} - {(formPipettesByMount != null && - formPipettesByMount[oppositeMount].pipetteName == null) || - (pipetteOnDeck != null && pipetteOnDeck.length === 1) ? null : ( - { - cleanForm() - }} - textDecoration={TYPOGRAPHY.textDecorationUnderline} - css={BUTTON_LINK_STYLE} - > - - {t('remove')} - - - )} + { + cleanForm() + }} + textDecoration={TYPOGRAPHY.textDecorationUnderline} + css={BUTTON_LINK_STYLE} + padding={SPACING.spacing4} + > + + {t('remove')} + + diff --git a/protocol-designer/src/pages/CreateNewProtocolWizard/SelectGripper.tsx b/protocol-designer/src/pages/CreateNewProtocolWizard/SelectGripper.tsx index f4067689fa4..88dc6ab031d 100644 --- a/protocol-designer/src/pages/CreateNewProtocolWizard/SelectGripper.tsx +++ b/protocol-designer/src/pages/CreateNewProtocolWizard/SelectGripper.tsx @@ -1,6 +1,8 @@ import { useState } from 'react' import { useTranslation } from 'react-i18next' import without from 'lodash/without' +import { useLocation } from 'react-router-dom' + import { Flex, SPACING, @@ -16,6 +18,7 @@ import type { WizardTileProps } from './types' export function SelectGripper(props: WizardTileProps): JSX.Element | null { const { goBack, setValue, proceed, watch } = props const { t } = useTranslation(['create_new_protocol', 'shared']) + const location = useLocation() const [gripperStatus, setGripperStatus] = useState<'yes' | 'no' | null>(null) const additionalEquipment = watch('additionalEquipment') @@ -44,6 +47,7 @@ export function SelectGripper(props: WizardTileProps): JSX.Element | null { header={t('add_gripper')} disabled={gripperStatus == null} goBack={() => { + location.state = 'gripper' goBack(1) }} proceed={handleProceed} diff --git a/protocol-designer/src/pages/CreateNewProtocolWizard/SelectPipettes.tsx b/protocol-designer/src/pages/CreateNewProtocolWizard/SelectPipettes.tsx index 7602b091c8f..b9f16f5e23c 100644 --- a/protocol-designer/src/pages/CreateNewProtocolWizard/SelectPipettes.tsx +++ b/protocol-designer/src/pages/CreateNewProtocolWizard/SelectPipettes.tsx @@ -2,6 +2,7 @@ import { useState, useEffect } from 'react' import { useTranslation } from 'react-i18next' import styled, { css } from 'styled-components' import { useDispatch, useSelector } from 'react-redux' +import { useLocation } from 'react-router-dom' import { FLEX_ROBOT_TYPE, getAllPipetteNames, @@ -57,6 +58,7 @@ const MAX_TIPRACKS_ALLOWED = 3 export function SelectPipettes(props: WizardTileProps): JSX.Element | null { const { goBack, proceed, watch, setValue } = props const { t } = useTranslation(['create_new_protocol', 'shared']) + const location = useLocation() const pipettesByMount = watch('pipettesByMount') const fields = watch('fields') const { makeSnackbar } = useKitchen() @@ -101,8 +103,21 @@ export function SelectPipettes(props: WizardTileProps): JSX.Element | null { } }, [pipetteType, pipetteGen, pipetteVolume, selectedPipetteName]) + const noPipette = + (pipettesByMount.left.pipetteName == null || + pipettesByMount.left.tiprackDefURI == null) && + (pipettesByMount.right.pipetteName == null || + pipettesByMount.right.tiprackDefURI == null) + const isDisabled = - page === 'add' && pipettesByMount[defaultMount].tiprackDefURI == null + (page === 'add' && pipettesByMount[defaultMount].tiprackDefURI == null) || + noPipette + + const targetPipetteMount = + pipettesByMount.left.pipetteName == null || + pipettesByMount.left.tiprackDefURI == null + ? 'left' + : 'right' const handleProceed = (): void => { if (!isDisabled) { @@ -113,6 +128,34 @@ export function SelectPipettes(props: WizardTileProps): JSX.Element | null { } } } + + const handleGoBack = (): void => { + if (page === 'add') { + resetFields() + setValue(`pipettesByMount.${defaultMount}.pipetteName`, undefined) + setValue(`pipettesByMount.${defaultMount}.tiprackDefURI`, undefined) + if ( + pipettesByMount.left.pipetteName != null || + pipettesByMount.left.tiprackDefURI != null || + pipettesByMount.right.pipetteName != null || + pipettesByMount.right.tiprackDefURI != null + ) { + setPage('overview') + } else { + goBack(1) + } + } + if (page === 'overview') { + setPage('add') + } + } + + useEffect(() => { + if (location.state === 'gripper') { + setPage('overview') + } + }, [location]) + return ( <> {showIncompatibleTip ? ( @@ -129,17 +172,7 @@ export function SelectPipettes(props: WizardTileProps): JSX.Element | null { subHeader={page === 'add' ? t('which_pipette') : undefined} proceed={handleProceed} goBack={() => { - if (page === 'add') { - resetFields() - setValue(`pipettesByMount.${defaultMount}.pipetteName`, undefined) - setValue( - `pipettesByMount.${defaultMount}.tiprackDefURI`, - undefined - ) - goBack(1) - } else { - setPage('add') - } + handleGoBack() }} disabled={isDisabled} > @@ -375,7 +408,11 @@ export function SelectPipettes(props: WizardTileProps): JSX.Element | null { {t('your_pipettes')} - {has96Channel ? null : ( + {has96Channel || + (pipettesByMount.left.pipetteName == null && + pipettesByMount.right.pipetteName == null) || + (pipettesByMount.left.tiprackDefURI == null && + pipettesByMount.right.tiprackDefURI == null) ? null : ( { @@ -411,76 +448,81 @@ export function SelectPipettes(props: WizardTileProps): JSX.Element | null { transform="rotate(90deg)" /> - {t('swap')} + {t('swap_pipettes')} )} - {pipettesByMount.left.pipetteName != null && - pipettesByMount.left.tiprackDefURI != null ? ( - { - setPage('add') - setMount('left') - }} - cleanForm={() => { - setValue(`pipettesByMount.left.pipetteName`, undefined) - setValue(`pipettesByMount.left.tiprackDefURI`, undefined) + + {pipettesByMount.left.pipetteName != null && + pipettesByMount.left.tiprackDefURI != null ? ( + { + setPage('add') + setMount('left') + }} + cleanForm={() => { + setValue(`pipettesByMount.left.pipetteName`, undefined) + setValue( + `pipettesByMount.left.tiprackDefURI`, + undefined + ) - resetFields() - }} - /> - ) : ( - { - setPage('add') - setMount('left') - resetFields() - }} - text={t('add_pipette')} - textAlignment="left" - iconName="plus" - /> - )} - {pipettesByMount.right.pipetteName != null && - pipettesByMount.right.tiprackDefURI != null ? ( - { - setPage('add') - setMount('right') - }} - cleanForm={() => { - setValue(`pipettesByMount.right.pipetteName`, undefined) - setValue(`pipettesByMount.right.tiprackDefURI`, undefined) - resetFields() - }} - /> - ) : has96Channel ? null : ( - { - setPage('add') - setMount('right') - resetFields() - }} - text={t('add_pipette')} - textAlignment="left" - iconName="plus" - /> - )} + resetFields() + }} + /> + ) : null} + {pipettesByMount.right.pipetteName != null && + pipettesByMount.right.tiprackDefURI != null ? ( + { + setPage('add') + setMount('right') + }} + cleanForm={() => { + setValue(`pipettesByMount.right.pipetteName`, undefined) + setValue( + `pipettesByMount.right.tiprackDefURI`, + undefined + ) + resetFields() + }} + /> + ) : null} + + <> + {has96Channel || + (pipettesByMount.left.pipetteName != null && + pipettesByMount.right.pipetteName != null && + pipettesByMount.left.tiprackDefURI != null && + pipettesByMount.right.tiprackDefURI != null) ? null : ( + { + setPage('add') + setMount(targetPipetteMount) + resetFields() + }} + text={t('add_pipette')} + textAlignment="left" + iconName="plus" + /> + )} + )} diff --git a/protocol-designer/src/pages/CreateNewProtocolWizard/__tests__/SelectGripper.test.tsx b/protocol-designer/src/pages/CreateNewProtocolWizard/__tests__/SelectGripper.test.tsx index d6c25eef7d1..87ab1bb07e3 100644 --- a/protocol-designer/src/pages/CreateNewProtocolWizard/__tests__/SelectGripper.test.tsx +++ b/protocol-designer/src/pages/CreateNewProtocolWizard/__tests__/SelectGripper.test.tsx @@ -7,8 +7,19 @@ import { i18n } from '../../../assets/localization' import { renderWithProviders } from '../../../__testing-utils__' import { SelectGripper } from '../SelectGripper' +import type { NavigateFunction } from 'react-router-dom' import type { WizardFormState, WizardTileProps } from '../types' +const mockLocation = vi.fn() + +vi.mock('react-router-dom', async importOriginal => { + const actual = await importOriginal() + return { + ...actual, + useLocation: () => mockLocation, + } +}) + const render = (props: React.ComponentProps) => { return renderWithProviders(, { i18nInstance: i18n, diff --git a/protocol-designer/src/pages/CreateNewProtocolWizard/__tests__/SelectPipettes.test.tsx b/protocol-designer/src/pages/CreateNewProtocolWizard/__tests__/SelectPipettes.test.tsx index 6426b9ee083..922c48a0959 100644 --- a/protocol-designer/src/pages/CreateNewProtocolWizard/__tests__/SelectPipettes.test.tsx +++ b/protocol-designer/src/pages/CreateNewProtocolWizard/__tests__/SelectPipettes.test.tsx @@ -12,6 +12,7 @@ import { createCustomTiprackDef } from '../../../labware-defs/actions' import { SelectPipettes } from '../SelectPipettes' import { getTiprackOptions } from '../utils' +import type { NavigateFunction } from 'react-router-dom' import type { WizardFormState, WizardTileProps } from '../types' vi.mock('../../../labware-defs/selectors') @@ -19,6 +20,15 @@ vi.mock('../../../feature-flags/selectors') vi.mock('../../../organisms') vi.mock('../../../labware-defs/actions') vi.mock('../utils') +const mockLocation = vi.fn() + +vi.mock('react-router-dom', async importOriginal => { + const actual = await importOriginal() + return { + ...actual, + useLocation: () => mockLocation, + } +}) const render = (props: React.ComponentProps) => { return renderWithProviders(, { From 519482dc34bfcf60015c558546553494b7f47125 Mon Sep 17 00:00:00 2001 From: koji Date: Tue, 8 Oct 2024 09:23:14 -0400 Subject: [PATCH 17/27] fix(protocol-designer): fix EditInstrumentsModal issue (#16421) * fix(protocol-designer): fix EditInstrumentsModal issue --- .../localization/en/create_new_protocol.json | 2 +- .../src/assets/localization/en/shared.json | 3 +- .../organisms/EditInstrumentsModal/index.tsx | 147 +++++++++--------- .../SelectPipettes.tsx | 78 +++++----- .../__tests__/SelectPipettes.test.tsx | 4 +- 5 files changed, 120 insertions(+), 114 deletions(-) diff --git a/protocol-designer/src/assets/localization/en/create_new_protocol.json b/protocol-designer/src/assets/localization/en/create_new_protocol.json index 52c03ca7b50..b75005152d7 100644 --- a/protocol-designer/src/assets/localization/en/create_new_protocol.json +++ b/protocol-designer/src/assets/localization/en/create_new_protocol.json @@ -3,7 +3,7 @@ "add_fixtures": "Add your fixtures", "add_gripper": "Add a gripper", "add_modules": "Add your modules", - "add_pipette": "Add a pipette and tips", + "add_pipette": "Add a pipette", "author_org": "Author/Organization", "basics": "Let’s start with the basics", "description": "Description", diff --git a/protocol-designer/src/assets/localization/en/shared.json b/protocol-designer/src/assets/localization/en/shared.json index 4da0ce66196..fcf63f043da 100644 --- a/protocol-designer/src/assets/localization/en/shared.json +++ b/protocol-designer/src/assets/localization/en/shared.json @@ -14,7 +14,8 @@ "developer_ff": "Developer feature flags", "done": "Done", "edit_existing": "Edit existing protocol", - "edit_instruments": "Edit instruments", + "edit_instruments": "Edit Instruments", + "edit_pipette": "Edit Pipette", "edit_protocol_metadata": "Edit protocol metadata", "edit": "edit", "eight_channel": "8-Channel", diff --git a/protocol-designer/src/organisms/EditInstrumentsModal/index.tsx b/protocol-designer/src/organisms/EditInstrumentsModal/index.tsx index c11a62a678c..6f1729a2110 100644 --- a/protocol-designer/src/organisms/EditInstrumentsModal/index.tsx +++ b/protocol-designer/src/organisms/EditInstrumentsModal/index.tsx @@ -6,6 +6,7 @@ import styled, { css } from 'styled-components' import mapValues from 'lodash/mapValues' import { ALIGN_CENTER, + ALIGN_STRETCH, Box, Btn, Checkbox, @@ -17,11 +18,13 @@ import { DISPLAY_INLINE_BLOCK, EmptySelectorButton, Flex, + FLEX_MAX_CONTENT, Icon, JUSTIFY_END, JUSTIFY_SPACE_BETWEEN, ListItem, Modal, + OVERFLOW_AUTO, PrimaryButton, PRODUCT, RadioButton, @@ -141,11 +144,24 @@ export function EditInstrumentsModal( ? getSectionsFromPipetteName(leftPip.name, leftPip.spec) : null + const removeOpentronsPhrases = (input: string): string => { + const phrasesToRemove = ['Opentrons Flex 96', 'Opentrons OT-2 96'] + + return phrasesToRemove + .reduce((text, phrase) => { + return text.replace(new RegExp(phrase, 'gi'), '') + }, input) + .trim() + } + return createPortal( { resetFields() onClose() @@ -154,7 +170,7 @@ export function EditInstrumentsModal( {page === 'overview' ? null : ( {page === 'overview' ? ( - <> - + + @@ -307,13 +322,9 @@ export function EditInstrumentsModal( {robotType === FLEX_ROBOT_TYPE ? ( - + @@ -368,18 +379,15 @@ export function EditInstrumentsModal( ) : null} - + ) : ( - <> - + + {t('pipette_type')} @@ -400,16 +408,10 @@ export function EditInstrumentsModal( ) })} - + {pipetteType != null && robotType === OT2_ROBOT_TYPE ? ( - - + + {t('pipette_gen')} @@ -435,12 +437,10 @@ export function EditInstrumentsModal( robotType === OT2_ROBOT_TYPE) ? ( - + {t('pipette_vol')} @@ -488,19 +488,16 @@ export function EditInstrumentsModal( {allPipetteOptions.includes(selectedPip as PipetteName) ? (() => { const tiprackOptions = getTiprackOptions({ - allLabware: allLabware, - allowAllTipracks: allowAllTipracks, + allLabware, + allowAllTipracks, selectedPipetteName: selectedPip, }) return ( - + {t('pipette_tips')} {tiprackOptions.map(option => ( @@ -518,7 +518,7 @@ export function EditInstrumentsModal( !selectedTips.includes(option.value) } isChecked={selectedTips.includes(option.value)} - labelText={option.name} + labelText={removeOpentronsPhrases(option.name)} onClick={() => { const updatedTips = selectedTips.includes( option.value @@ -529,41 +529,42 @@ export function EditInstrumentsModal( }} /> ))} - - - - - {t('add_custom_tips')} - - dispatch(createCustomTiprackDef(e))} - /> - - {pipetteVolume === 'p1000' && - robotType === FLEX_ROBOT_TYPE ? null : ( - { - dispatch( - setFeatureFlags({ - OT_PD_ALLOW_ALL_TIPRACKS: !allowAllTipracks, - }) - ) - }} - textDecoration={TYPOGRAPHY.textDecorationUnderline} - > + + - {allowAllTipracks - ? t('show_default_tips') - : t('show_all_tips')} + {t('add_custom_tips')} - - )} - + dispatch(createCustomTiprackDef(e))} + /> + + {pipetteVolume === 'p1000' && + robotType === FLEX_ROBOT_TYPE ? null : ( + { + dispatch( + setFeatureFlags({ + OT_PD_ALLOW_ALL_TIPRACKS: !allowAllTipracks, + }) + ) + }} + textDecoration={TYPOGRAPHY.textDecorationUnderline} + > + + {allowAllTipracks + ? t('show_default_tips') + : t('show_all_tips')} + + + )} + + ) })() diff --git a/protocol-designer/src/pages/CreateNewProtocolWizard/SelectPipettes.tsx b/protocol-designer/src/pages/CreateNewProtocolWizard/SelectPipettes.tsx index b9f16f5e23c..f63d8532e60 100644 --- a/protocol-designer/src/pages/CreateNewProtocolWizard/SelectPipettes.tsx +++ b/protocol-designer/src/pages/CreateNewProtocolWizard/SelectPipettes.tsx @@ -10,6 +10,7 @@ import { } from '@opentrons/shared-data' import { ALIGN_CENTER, + ALIGN_STRETCH, Box, Btn, Checkbox, @@ -323,6 +324,9 @@ export function SelectPipettes(props: WizardTileProps): JSX.Element | null { gap: ${SPACING.spacing4}; display: ${DISPLAY_FLEX}; flex-wrap: ${WRAP}; + align-items: ${ALIGN_CENTER}; + align-content: ${ALIGN_CENTER}; + align-self: ${ALIGN_STRETCH}; `} > {Object.entries(tiprackOptions).map( @@ -354,45 +358,45 @@ export function SelectPipettes(props: WizardTileProps): JSX.Element | null { ) )} - - - - - {t('add_custom_tips')} - - - dispatch(createCustomTiprackDef(e)) - } - /> - - {pipetteVolume === 'p1000' && - robotType === FLEX_ROBOT_TYPE ? null : ( - { - if (allowAllTipracks) { - dispatch( - setFeatureFlags({ - OT_PD_ALLOW_ALL_TIPRACKS: !allowAllTipracks, - }) - ) - } else { - setIncompatibleTip(true) - } - }} - textDecoration={ - TYPOGRAPHY.textDecorationUnderline - } - > + + - {allowAllTipracks - ? t('show_default_tips') - : t('show_all_tips')} + {t('add_custom_tips')} - - )} + + dispatch(createCustomTiprackDef(e)) + } + /> + + {pipetteVolume === 'p1000' && + robotType === FLEX_ROBOT_TYPE ? null : ( + { + if (allowAllTipracks) { + dispatch( + setFeatureFlags({ + OT_PD_ALLOW_ALL_TIPRACKS: !allowAllTipracks, + }) + ) + } else { + setIncompatibleTip(true) + } + }} + textDecoration={ + TYPOGRAPHY.textDecorationUnderline + } + > + + {allowAllTipracks + ? t('show_default_tips') + : t('show_all_tips')} + + + )} + ) diff --git a/protocol-designer/src/pages/CreateNewProtocolWizard/__tests__/SelectPipettes.test.tsx b/protocol-designer/src/pages/CreateNewProtocolWizard/__tests__/SelectPipettes.test.tsx index 922c48a0959..3efc8ec11b4 100644 --- a/protocol-designer/src/pages/CreateNewProtocolWizard/__tests__/SelectPipettes.test.tsx +++ b/protocol-designer/src/pages/CreateNewProtocolWizard/__tests__/SelectPipettes.test.tsx @@ -77,7 +77,7 @@ describe('SelectPipettes', () => { it('renders the first page of select pipettes for a Flex', () => { render(props) screen.getByText('Step 2') - screen.getByText('Add a pipette and tips') + screen.getByText('Add a pipette') screen.getByText( 'Pick your first pipette. If you need a second pipette, you can add it next.' ) @@ -125,7 +125,7 @@ describe('SelectPipettes', () => { } render(props) screen.getByText('Step 2') - screen.getByText('Add a pipette and tips') + screen.getByText('Add a pipette') screen.getByText( 'Pick your first pipette. If you need a second pipette, you can add it next.' ) From 9d16384320715389a1418014694d2a7da0c59a60 Mon Sep 17 00:00:00 2001 From: Seth Foster Date: Tue, 8 Oct 2024 09:31:54 -0400 Subject: [PATCH 18/27] fix(app,api): Display thermocycler profile cycles (#16414) We identified a simple bug with the app: it displays wonky numbers for thermocycler profile cycles: ![image (1)](https://github.com/user-attachments/assets/8005c0b6-c55e-4b48-bf50-7d90f91fa63b) This wouldn't repeat anything at all, what's going on? Well, it turns out that when Protocol Designer added thermocycler support, they wanted something a bit more in depth than the Python protocol API's "list of steps, number of times to repeat the cycle" format. They wanted users to be able to add single steps and cycles, in arbitrary order. To make the two styles work with the engine, we made the engine's `thermocycler/runProfile` command take a flat list of steps - any of the structure of repeated commands was removed. In the app's `CommandText` display, we then had to fix up the way we displayed profiles to remove references to a `repetitions` value that now didn't exist... and we just didn't, instead setting the `repetitions` element to just be the number of steps in the profile. Fixing this ended up being a bit involved. ## summary - ad172608c64c8d00844a7748ae282a1c8284b745 Make a new interface for the hardware controller `execute_profile` function of the thermocycler, since it's important that thermocycler cycles execute inside an asyncio worker so that they won't be interrupted by e.g. pausing. This new interface takes the PD style of protocol. It relies under the hood on the same function that actually sends stuff to the thermocycler, so there shouldn't be any functional execution changes. - 335e25ad61ec36927060993a21342c20ec325c52 Make a new `thermocycler/runExtendedProfile` command in the protocol engine, that takes as its parameters a structured list of either steps or cycles, adhering to PD's expectations since the PAPI's expectations are a strict subset of PD. This implements its command by using the new hardware controller. - e842a2a47da30a62437c093516292b48a676369b Use the new structured data to implement a command text for the new command that can render the equivalent of what PD makes (and, again, what the PAPI does, which is a strict subset) - e842a2a47da30a62437c093516292b48a676369b Also make the old command text not use a "repetitions" keyword that doesn't exist - 0043ab7cf281b4dff4277c1350831671232559ea Switch the PAPI to emitting the new command in api 2.21 ## new UI These UI changes will be on https://s3-us-west-2.amazonaws.com/opentrons-components/rqa-2771-thermocycler-extended-profiles/index.html?path=/docs/app-molecules-command-commandtext--docs for the desktop and general text and https://s3-us-west-2.amazonaws.com/opentrons-components/rqa-2771-thermocycler-extended-profiles/index.html?path=/docs/app-molecules-command-command--docs for the ODD colored-background elements whenever they upload. Here's a screenshot of what they were like when the PR was opened: `CommandText` of `thermocycler/runProfile` : ![runProfileCommandText](https://github.com/user-attachments/assets/dcad4ce8-2f0e-418d-8618-066a084dc832) Note the change to the first line. This needs wordsmithing. `CommandText` of `thermocycler/runExtendedProfile`: ![runProfileExtended](https://github.com/user-attachments/assets/6b1a1977-9200-4d78-84dc-2961d76cfff9) Note the two-level rendering. The common case will probably be that there's only cycles ## todo - [x] wordsmith - ~[ ] add to PD?~ no, but structured in a way that it will be easy eventually - [x] Test. Oh boy Closes RQA-2771 --------- Co-authored-by: Ed Cormany --- .../hardware_control/modules/thermocycler.py | 61 +- .../hardware_control/modules/types.py | 5 + .../protocol_api/core/engine/module_core.py | 56 +- .../opentrons/protocol_api/module_contexts.py | 10 +- api/src/opentrons/protocol_api/validation.py | 3 +- .../commands/command_unions.py | 5 + .../commands/thermocycler/__init__.py | 19 + .../thermocycler/run_extended_profile.py | 166 + .../opentrons/protocols/api_support/types.py | 15 +- .../modules/test_hc_thermocycler.py | 61 + .../core/engine/test_thermocycler_core.py | 81 +- .../thermocycler/test_run_extended_profile.py | 115 + .../en/protocol_command_text.json | 6 +- app/src/molecules/Command/Command.stories.tsx | 22 +- app/src/molecules/Command/CommandText.tsx | 163 +- .../Command/__fixtures__/doItAllV10.json | 4863 +++++++++++++++++ .../molecules/Command/__fixtures__/index.ts | 2 +- .../Command/__tests__/CommandText.test.tsx | 130 +- app/src/molecules/Command/hooks/index.ts | 2 + .../hooks/useCommandTextString/index.tsx | 58 +- .../getTCRunExtendedProfileCommandText.ts | 67 + .../utils/getTCRunProfileCommandText.ts | 15 +- .../hooks/useCommandTextString/utils/index.ts | 1 + .../CategorizedStepContent.stories.tsx | 14 +- .../__tests__/useRecoveryToasts.test.tsx | 34 +- .../hooks/useRecoveryToasts.ts | 24 +- .../__tests__/formatDuration.test.tsx | 55 +- .../transformations/formatDuration.ts | 39 +- shared-data/command/schemas/10.json | 106 + shared-data/command/types/module.ts | 23 + 30 files changed, 6132 insertions(+), 89 deletions(-) create mode 100644 api/src/opentrons/protocol_engine/commands/thermocycler/run_extended_profile.py create mode 100644 api/tests/opentrons/protocol_engine/commands/thermocycler/test_run_extended_profile.py create mode 100644 app/src/molecules/Command/__fixtures__/doItAllV10.json create mode 100644 app/src/molecules/Command/hooks/useCommandTextString/utils/getTCRunExtendedProfileCommandText.ts diff --git a/api/src/opentrons/hardware_control/modules/thermocycler.py b/api/src/opentrons/hardware_control/modules/thermocycler.py index bcaac8650d9..4a1b2fe038b 100644 --- a/api/src/opentrons/hardware_control/modules/thermocycler.py +++ b/api/src/opentrons/hardware_control/modules/thermocycler.py @@ -2,7 +2,7 @@ import asyncio import logging -from typing import Callable, Optional, List, Dict, Mapping +from typing import Callable, Optional, List, Dict, Mapping, Union, cast from opentrons.drivers.rpi_drivers.types import USBPort from opentrons.drivers.types import ThermocyclerLidStatus, Temperature, PlateTemperature from opentrons.hardware_control.modules.lid_temp_status import LidTemperatureStatus @@ -363,6 +363,39 @@ async def cycle_temperatures( self.make_cancellable(task) await task + async def execute_profile( + self, + profile: List[Union[types.ThermocyclerCycle, types.ThermocyclerStep]], + volume: Optional[float] = None, + ) -> None: + """Begin a set temperature profile, with both repeating and non-repeating steps. + + Args: + profile: The temperature profile to follow. + volume: Optional volume + + Returns: None + """ + await self.wait_for_is_running() + self._total_cycle_count = 0 + self._total_step_count = 0 + self._current_cycle_index = 0 + self._current_step_index = 0 + for step_or_cycle in profile: + if "steps" in step_or_cycle: + # basically https://github.com/python/mypy/issues/14766 + this_cycle = cast(types.ThermocyclerCycle, step_or_cycle) + self._total_cycle_count += this_cycle["repetitions"] + self._total_step_count += ( + len(this_cycle["steps"]) * this_cycle["repetitions"] + ) + else: + self._total_step_count += 1 + self._total_cycle_count += 1 + task = self._loop.create_task(self._execute_profile(profile, volume)) + self.make_cancellable(task) + await task + async def set_lid_temperature(self, temperature: float) -> None: """Set the lid temperature in degrees Celsius""" await self.wait_for_is_running() @@ -574,7 +607,7 @@ async def _execute_cycles( self, steps: List[types.ThermocyclerStep], repetitions: int, - volume: Optional[float] = None, + volume: Optional[float], ) -> None: """ Execute cycles. @@ -592,6 +625,30 @@ async def _execute_cycles( self._current_step_index = step_idx + 1 # science starts at 1 await self._execute_cycle_step(step, volume) + async def _execute_profile( + self, + profile: List[Union[types.ThermocyclerCycle, types.ThermocyclerStep]], + volume: Optional[float], + ) -> None: + """ + Execute profiles. + + Profiles command a thermocycler pattern that can contain multiple cycles and out-of-cycle steps. + """ + self._current_cycle_index = 0 + self._current_step_index = 0 + for step_or_cycle in profile: + self._current_cycle_index += 1 + if "repetitions" in step_or_cycle: + # basically https://github.com/python/mypy/issues/14766 + this_cycle = cast(types.ThermocyclerCycle, step_or_cycle) + for rep in range(this_cycle["repetitions"]): + for step in this_cycle["steps"]: + self._current_step_index += 1 + await self._execute_cycle_step(step, volume) + else: + await self._execute_cycle_step(step_or_cycle, volume) + # TODO(mc, 2022-10-13): why does this exist? # Do the driver and poller really need to be disconnected? # Could we accomplish the same thing by latching the error state diff --git a/api/src/opentrons/hardware_control/modules/types.py b/api/src/opentrons/hardware_control/modules/types.py index 6c9f6a3e915..9b7c33058d4 100644 --- a/api/src/opentrons/hardware_control/modules/types.py +++ b/api/src/opentrons/hardware_control/modules/types.py @@ -39,6 +39,11 @@ class ThermocyclerStep(ThermocyclerStepBase, total=False): hold_time_minutes: float +class ThermocyclerCycle(TypedDict): + steps: List[ThermocyclerStep] + repetitions: int + + UploadFunction = Callable[[str, str, Dict[str, Any]], Awaitable[Tuple[bool, str]]] diff --git a/api/src/opentrons/protocol_api/core/engine/module_core.py b/api/src/opentrons/protocol_api/core/engine/module_core.py index 729037425a8..47b49c54e23 100644 --- a/api/src/opentrons/protocol_api/core/engine/module_core.py +++ b/api/src/opentrons/protocol_api/core/engine/module_core.py @@ -1,14 +1,13 @@ """Protocol API module implementation logic.""" from __future__ import annotations -from typing import Optional, List, Dict +from typing import Optional, List, Dict, Union from opentrons.hardware_control import SynchronousAdapter, modules as hw_modules from opentrons.hardware_control.modules.types import ( ModuleModel, TemperatureStatus, MagneticStatus, - ThermocyclerStep, SpeedStatus, module_model_from_string, ) @@ -27,7 +26,7 @@ CannotPerformModuleAction, ) -from opentrons.protocols.api_support.types import APIVersion +from opentrons.protocols.api_support.types import APIVersion, ThermocyclerStep from ... import validation from ..module import ( @@ -327,15 +326,13 @@ def wait_for_lid_temperature(self) -> None: cmd.thermocycler.WaitForLidTemperatureParams(moduleId=self.module_id) ) - def execute_profile( + def _execute_profile_pre_221( self, steps: List[ThermocyclerStep], repetitions: int, - block_max_volume: Optional[float] = None, + block_max_volume: Optional[float], ) -> None: - """Execute a Thermocycler Profile.""" - self._repetitions = repetitions - self._step_count = len(steps) + """Execute a thermocycler profile using thermocycler/runProfile and flattened steps.""" engine_steps = [ cmd.thermocycler.RunProfileStepParams( celsius=step["temperature"], @@ -352,6 +349,49 @@ def execute_profile( ) ) + def _execute_profile_post_221( + self, + steps: List[ThermocyclerStep], + repetitions: int, + block_max_volume: Optional[float], + ) -> None: + """Execute a thermocycler profile using thermocycler/runExtendedProfile.""" + engine_steps: List[ + Union[cmd.thermocycler.ProfileCycle, cmd.thermocycler.ProfileStep] + ] = [ + cmd.thermocycler.ProfileCycle( + repetitions=repetitions, + steps=[ + cmd.thermocycler.ProfileStep( + celsius=step["temperature"], + holdSeconds=step["hold_time_seconds"], + ) + for step in steps + ], + ) + ] + self._engine_client.execute_command( + cmd.thermocycler.RunExtendedProfileParams( + moduleId=self.module_id, + profileElements=engine_steps, + blockMaxVolumeUl=block_max_volume, + ) + ) + + def execute_profile( + self, + steps: List[ThermocyclerStep], + repetitions: int, + block_max_volume: Optional[float] = None, + ) -> None: + """Execute a Thermocycler Profile.""" + self._repetitions = repetitions + self._step_count = len(steps) + if self.api_version >= APIVersion(2, 21): + return self._execute_profile_post_221(steps, repetitions, block_max_volume) + else: + return self._execute_profile_pre_221(steps, repetitions, block_max_volume) + def deactivate_lid(self) -> None: """Turn off the heated lid.""" self._engine_client.execute_command( diff --git a/api/src/opentrons/protocol_api/module_contexts.py b/api/src/opentrons/protocol_api/module_contexts.py index f9fcc18ca00..5d182843dcc 100644 --- a/api/src/opentrons/protocol_api/module_contexts.py +++ b/api/src/opentrons/protocol_api/module_contexts.py @@ -8,10 +8,9 @@ from opentrons_shared_data.module.types import ModuleModel, ModuleType from opentrons.legacy_broker import LegacyBroker -from opentrons.hardware_control.modules import ThermocyclerStep from opentrons.legacy_commands import module_commands as cmds from opentrons.legacy_commands.publisher import CommandPublisher, publish -from opentrons.protocols.api_support.types import APIVersion +from opentrons.protocols.api_support.types import APIVersion, ThermocyclerStep from opentrons.protocols.api_support.util import ( APIVersionError, requires_version, @@ -629,6 +628,13 @@ def execute_profile( ``hold_time_minutes`` and ``hold_time_seconds`` must be defined and for each step. + .. note: + + Before API Version 2.21, Thermocycler profiles run with this command + would be listed in the app as having a number of repetitions equal to + their step count. At or above API Version 2.21, the structure of the + Thermocycler cycles is preserved. + """ repetitions = validation.ensure_thermocycler_repetition_count(repetitions) validated_steps = validation.ensure_thermocycler_profile_steps(steps) diff --git a/api/src/opentrons/protocol_api/validation.py b/api/src/opentrons/protocol_api/validation.py index 08e56fdef8f..43c83eca2e0 100644 --- a/api/src/opentrons/protocol_api/validation.py +++ b/api/src/opentrons/protocol_api/validation.py @@ -18,7 +18,7 @@ from opentrons_shared_data.pipette.types import PipetteNameType from opentrons_shared_data.robot.types import RobotType -from opentrons.protocols.api_support.types import APIVersion +from opentrons.protocols.api_support.types import APIVersion, ThermocyclerStep from opentrons.protocols.api_support.util import APIVersionError from opentrons.protocols.models import LabwareDefinition from opentrons.types import Mount, DeckSlotName, StagingSlotName, Location @@ -30,7 +30,6 @@ HeaterShakerModuleModel, MagneticBlockModel, AbsorbanceReaderModel, - ThermocyclerStep, ) from .disposal_locations import TrashBin, WasteChute diff --git a/api/src/opentrons/protocol_engine/commands/command_unions.py b/api/src/opentrons/protocol_engine/commands/command_unions.py index f01e10aa63e..2c7f768945f 100644 --- a/api/src/opentrons/protocol_engine/commands/command_unions.py +++ b/api/src/opentrons/protocol_engine/commands/command_unions.py @@ -380,6 +380,7 @@ thermocycler.OpenLid, thermocycler.CloseLid, thermocycler.RunProfile, + thermocycler.RunExtendedProfile, absorbance_reader.CloseLid, absorbance_reader.OpenLid, absorbance_reader.Initialize, @@ -456,6 +457,7 @@ thermocycler.OpenLidParams, thermocycler.CloseLidParams, thermocycler.RunProfileParams, + thermocycler.RunExtendedProfileParams, absorbance_reader.CloseLidParams, absorbance_reader.OpenLidParams, absorbance_reader.InitializeParams, @@ -530,6 +532,7 @@ thermocycler.OpenLidCommandType, thermocycler.CloseLidCommandType, thermocycler.RunProfileCommandType, + thermocycler.RunExtendedProfileCommandType, absorbance_reader.CloseLidCommandType, absorbance_reader.OpenLidCommandType, absorbance_reader.InitializeCommandType, @@ -605,6 +608,7 @@ thermocycler.OpenLidCreate, thermocycler.CloseLidCreate, thermocycler.RunProfileCreate, + thermocycler.RunExtendedProfileCreate, absorbance_reader.CloseLidCreate, absorbance_reader.OpenLidCreate, absorbance_reader.InitializeCreate, @@ -681,6 +685,7 @@ thermocycler.OpenLidResult, thermocycler.CloseLidResult, thermocycler.RunProfileResult, + thermocycler.RunExtendedProfileResult, absorbance_reader.CloseLidResult, absorbance_reader.OpenLidResult, absorbance_reader.InitializeResult, diff --git a/api/src/opentrons/protocol_engine/commands/thermocycler/__init__.py b/api/src/opentrons/protocol_engine/commands/thermocycler/__init__.py index b0ffdd53ce9..60e5c62591c 100644 --- a/api/src/opentrons/protocol_engine/commands/thermocycler/__init__.py +++ b/api/src/opentrons/protocol_engine/commands/thermocycler/__init__.py @@ -73,6 +73,16 @@ RunProfileCreate, ) +from .run_extended_profile import ( + RunExtendedProfileCommandType, + RunExtendedProfileParams, + RunExtendedProfileResult, + RunExtendedProfile, + RunExtendedProfileCreate, + ProfileCycle, + ProfileStep, +) + __all__ = [ # Set target block temperature command models @@ -130,4 +140,13 @@ "RunProfileResult", "RunProfile", "RunProfileCreate", + # Run extended profile command models. + "RunExtendedProfileCommandType", + "RunExtendedProfileParams", + "RunExtendedProfileStepParams", + "RunExtendedProfileResult", + "RunExtendedProfile", + "RunExtendedProfileCreate", + "ProfileCycle", + "ProfileStep", ] diff --git a/api/src/opentrons/protocol_engine/commands/thermocycler/run_extended_profile.py b/api/src/opentrons/protocol_engine/commands/thermocycler/run_extended_profile.py new file mode 100644 index 00000000000..3cf8a67bf41 --- /dev/null +++ b/api/src/opentrons/protocol_engine/commands/thermocycler/run_extended_profile.py @@ -0,0 +1,166 @@ +"""Command models to execute a Thermocycler profile.""" +from __future__ import annotations +from typing import List, Optional, TYPE_CHECKING, overload, Union +from typing_extensions import Literal, Type + +from pydantic import BaseModel, Field + +from opentrons.hardware_control.modules.types import ThermocyclerStep, ThermocyclerCycle + +from ..command import AbstractCommandImpl, BaseCommand, BaseCommandCreate, SuccessData +from ...errors.error_occurrence import ErrorOccurrence + +if TYPE_CHECKING: + from opentrons.protocol_engine.state.state import StateView + from opentrons.protocol_engine.execution import EquipmentHandler + from opentrons.protocol_engine.state.module_substates.thermocycler_module_substate import ( + ThermocyclerModuleSubState, + ) + + +RunExtendedProfileCommandType = Literal["thermocycler/runExtendedProfile"] + + +class ProfileStep(BaseModel): + """An individual step in a Thermocycler extended profile.""" + + celsius: float = Field(..., description="Target temperature in °C.") + holdSeconds: float = Field( + ..., description="Time to hold target temperature in seconds." + ) + + +class ProfileCycle(BaseModel): + """An individual cycle in a Thermocycler extended profile.""" + + steps: List[ProfileStep] = Field(..., description="Steps to repeat.") + repetitions: int = Field(..., description="Number of times to repeat the steps.") + + +class RunExtendedProfileParams(BaseModel): + """Input parameters for an individual Thermocycler profile step.""" + + moduleId: str = Field(..., description="Unique ID of the Thermocycler.") + profileElements: List[Union[ProfileStep, ProfileCycle]] = Field( + ..., + description="Elements of the profile. Each can be either a step or a cycle.", + ) + blockMaxVolumeUl: Optional[float] = Field( + None, + description="Amount of liquid in uL of the most-full well" + " in labware loaded onto the thermocycler.", + ) + + +class RunExtendedProfileResult(BaseModel): + """Result data from running a Thermocycler profile.""" + + +def _transform_profile_step( + step: ProfileStep, thermocycler_state: ThermocyclerModuleSubState +) -> ThermocyclerStep: + + return ThermocyclerStep( + temperature=thermocycler_state.validate_target_block_temperature(step.celsius), + hold_time_seconds=step.holdSeconds, + ) + + +@overload +def _transform_profile_element( + element: ProfileStep, thermocycler_state: ThermocyclerModuleSubState +) -> ThermocyclerStep: + ... + + +@overload +def _transform_profile_element( + element: ProfileCycle, thermocycler_state: ThermocyclerModuleSubState +) -> ThermocyclerCycle: + ... + + +def _transform_profile_element( + element: Union[ProfileStep, ProfileCycle], + thermocycler_state: ThermocyclerModuleSubState, +) -> Union[ThermocyclerStep, ThermocyclerCycle]: + if isinstance(element, ProfileStep): + return _transform_profile_step(element, thermocycler_state) + else: + return ThermocyclerCycle( + steps=[ + _transform_profile_step(step, thermocycler_state) + for step in element.steps + ], + repetitions=element.repetitions, + ) + + +class RunExtendedProfileImpl( + AbstractCommandImpl[ + RunExtendedProfileParams, SuccessData[RunExtendedProfileResult, None] + ] +): + """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: RunExtendedProfileParams + ) -> SuccessData[RunExtendedProfileResult, None]: + """Run a Thermocycler profile.""" + thermocycler_state = self._state_view.modules.get_thermocycler_module_substate( + params.moduleId + ) + thermocycler_hardware = self._equipment.get_module_hardware_api( + thermocycler_state.module_id + ) + + profile = [ + _transform_profile_element(element, thermocycler_state) + for element in params.profileElements + ] + target_volume: Optional[float] + if params.blockMaxVolumeUl is not None: + target_volume = thermocycler_state.validate_max_block_volume( + params.blockMaxVolumeUl + ) + else: + target_volume = None + + if thermocycler_hardware is not None: + # TODO(jbl 2022-06-27) hardcoded constant 1 for `repetitions` should be + # moved from HardwareControlAPI to the Python ProtocolContext + await thermocycler_hardware.execute_profile( + profile=profile, volume=target_volume + ) + + return SuccessData(public=RunExtendedProfileResult(), private=None) + + +class RunExtendedProfile( + BaseCommand[RunExtendedProfileParams, RunExtendedProfileResult, ErrorOccurrence] +): + """A command to execute a Thermocycler profile run.""" + + commandType: RunExtendedProfileCommandType = "thermocycler/runExtendedProfile" + params: RunExtendedProfileParams + result: Optional[RunExtendedProfileResult] + + _ImplementationCls: Type[RunExtendedProfileImpl] = RunExtendedProfileImpl + + +class RunExtendedProfileCreate(BaseCommandCreate[RunExtendedProfileParams]): + """A request to execute a Thermocycler profile run.""" + + commandType: RunExtendedProfileCommandType = "thermocycler/runExtendedProfile" + params: RunExtendedProfileParams + + _CommandCls: Type[RunExtendedProfile] = RunExtendedProfile diff --git a/api/src/opentrons/protocols/api_support/types.py b/api/src/opentrons/protocols/api_support/types.py index 6d3af89bcf9..d16fa8ddf73 100644 --- a/api/src/opentrons/protocols/api_support/types.py +++ b/api/src/opentrons/protocols/api_support/types.py @@ -1,5 +1,5 @@ from __future__ import annotations -from typing import NamedTuple +from typing import NamedTuple, TypedDict class APIVersion(NamedTuple): @@ -17,3 +17,16 @@ def from_string(cls, inp: str) -> APIVersion: def __str__(self) -> str: return f"{self.major}.{self.minor}" + + +class ThermocyclerStepBase(TypedDict): + """Required elements of a thermocycler step: the temperature.""" + + temperature: float + + +class ThermocyclerStep(ThermocyclerStepBase, total=False): + """Optional elements of a thermocycler step: the hold time. One of these must be present.""" + + hold_time_seconds: float + hold_time_minutes: float diff --git a/api/tests/opentrons/hardware_control/modules/test_hc_thermocycler.py b/api/tests/opentrons/hardware_control/modules/test_hc_thermocycler.py index d893d9912d0..6e90068ac1f 100644 --- a/api/tests/opentrons/hardware_control/modules/test_hc_thermocycler.py +++ b/api/tests/opentrons/hardware_control/modules/test_hc_thermocycler.py @@ -329,6 +329,67 @@ async def test_cycle_temperature( ) +async def test_execute_profile( + set_temperature_subject: modules.Thermocycler, set_plate_temp_spy: mock.AsyncMock +) -> None: + """It should send a series of set_plate_temperatures from a profile.""" + await set_temperature_subject.execute_profile( + [ + {"temperature": 42, "hold_time_seconds": 30}, + { + "repetitions": 5, + "steps": [ + {"temperature": 20, "hold_time_minutes": 1}, + {"temperature": 30, "hold_time_seconds": 1}, + ], + }, + {"temperature": 90, "hold_time_seconds": 2}, + { + "repetitions": 10, + "steps": [ + {"temperature": 10, "hold_time_minutes": 2}, + {"temperature": 20, "hold_time_seconds": 5}, + ], + }, + ], + volume=123, + ) + assert set_plate_temp_spy.call_args_list == [ + mock.call(temp=42, hold_time=30, volume=123), + mock.call(temp=20, hold_time=60, volume=123), + mock.call(temp=30, hold_time=1, volume=123), + mock.call(temp=20, hold_time=60, volume=123), + mock.call(temp=30, hold_time=1, volume=123), + mock.call(temp=20, hold_time=60, volume=123), + mock.call(temp=30, hold_time=1, volume=123), + mock.call(temp=20, hold_time=60, volume=123), + mock.call(temp=30, hold_time=1, volume=123), + mock.call(temp=20, hold_time=60, volume=123), + mock.call(temp=30, hold_time=1, volume=123), + mock.call(temp=90, hold_time=2, volume=123), + mock.call(temp=10, hold_time=120, volume=123), + mock.call(temp=20, hold_time=5, volume=123), + mock.call(temp=10, hold_time=120, volume=123), + mock.call(temp=20, hold_time=5, volume=123), + mock.call(temp=10, hold_time=120, volume=123), + mock.call(temp=20, hold_time=5, volume=123), + mock.call(temp=10, hold_time=120, volume=123), + mock.call(temp=20, hold_time=5, volume=123), + mock.call(temp=10, hold_time=120, volume=123), + mock.call(temp=20, hold_time=5, volume=123), + mock.call(temp=10, hold_time=120, volume=123), + mock.call(temp=20, hold_time=5, volume=123), + mock.call(temp=10, hold_time=120, volume=123), + mock.call(temp=20, hold_time=5, volume=123), + mock.call(temp=10, hold_time=120, volume=123), + mock.call(temp=20, hold_time=5, volume=123), + mock.call(temp=10, hold_time=120, volume=123), + mock.call(temp=20, hold_time=5, volume=123), + mock.call(temp=10, hold_time=120, volume=123), + mock.call(temp=20, hold_time=5, volume=123), + ] + + async def test_sync_error_response_to_poller( subject_mocked_driver: modules.Thermocycler, mock_driver: mock.AsyncMock, diff --git a/api/tests/opentrons/protocol_api/core/engine/test_thermocycler_core.py b/api/tests/opentrons/protocol_api/core/engine/test_thermocycler_core.py index eb429065d0a..1ee868ad84b 100644 --- a/api/tests/opentrons/protocol_api/core/engine/test_thermocycler_core.py +++ b/api/tests/opentrons/protocol_api/core/engine/test_thermocycler_core.py @@ -1,5 +1,7 @@ """Tests for the engine based Protocol API module core implementations.""" +from typing import cast import pytest +from _pytest.fixtures import SubRequest from decoy import Decoy from opentrons.drivers.types import ThermocyclerLidStatus @@ -13,6 +15,8 @@ from opentrons.protocol_engine.clients import SyncClient as EngineClient from opentrons.protocol_api.core.engine.module_core import ThermocyclerModuleCore from opentrons.protocol_api import MAX_SUPPORTED_VERSION +from opentrons.protocols.api_support.types import APIVersion +from ... import versions_below, versions_at_or_above SyncThermocyclerHardware = SynchronousAdapter[Thermocycler] @@ -34,7 +38,7 @@ def subject( mock_engine_client: EngineClient, mock_sync_module_hardware: SyncThermocyclerHardware, ) -> ThermocyclerModuleCore: - """Get a HeaterShakerModuleCore test subject.""" + """Get a ThermocyclerModuleCore test subject.""" return ThermocyclerModuleCore( module_id="1234", engine_client=mock_engine_client, @@ -43,6 +47,36 @@ def subject( ) +@pytest.fixture(params=versions_below(APIVersion(2, 21), flex_only=False)) +def subject_below_221( + request: SubRequest, + mock_engine_client: EngineClient, + mock_sync_module_hardware: SyncThermocyclerHardware, +) -> ThermocyclerModuleCore: + """Get a ThermocyclerCore below API version 2.21.""" + return ThermocyclerModuleCore( + module_id="1234", + engine_client=mock_engine_client, + api_version=cast(APIVersion, request.param), + sync_module_hardware=mock_sync_module_hardware, + ) + + +@pytest.fixture(params=versions_at_or_above(APIVersion(2, 21))) +def subject_at_or_above_221( + request: SubRequest, + mock_engine_client: EngineClient, + mock_sync_module_hardware: SyncThermocyclerHardware, +) -> ThermocyclerModuleCore: + """Get a ThermocyclerCore below API version 2.21.""" + return ThermocyclerModuleCore( + module_id="1234", + engine_client=mock_engine_client, + api_version=cast(APIVersion, request.param), + sync_module_hardware=mock_sync_module_hardware, + ) + + def test_create( decoy: Decoy, mock_engine_client: EngineClient, @@ -159,11 +193,13 @@ def test_wait_for_lid_temperature( ) -def test_execute_profile( - decoy: Decoy, mock_engine_client: EngineClient, subject: ThermocyclerModuleCore +def test_execute_profile_below_221( + decoy: Decoy, + mock_engine_client: EngineClient, + subject_below_221: ThermocyclerModuleCore, ) -> None: """It should run a thermocycler profile with the engine client.""" - subject.execute_profile( + subject_below_221.execute_profile( steps=[{"temperature": 45.6, "hold_time_seconds": 12.3}], repetitions=2, block_max_volume=78.9, @@ -187,6 +223,43 @@ def test_execute_profile( ) +def test_execute_profile_above_221( + decoy: Decoy, + mock_engine_client: EngineClient, + subject_at_or_above_221: ThermocyclerModuleCore, +) -> None: + """It should run a thermocycler profile with the engine client.""" + subject_at_or_above_221.execute_profile( + steps=[ + {"temperature": 45.6, "hold_time_seconds": 12.3}, + {"temperature": 78.9, "hold_time_seconds": 45.6}, + ], + repetitions=2, + block_max_volume=25, + ) + decoy.verify( + mock_engine_client.execute_command( + cmd.thermocycler.RunExtendedProfileParams( + moduleId="1234", + profileElements=[ + cmd.thermocycler.ProfileCycle( + repetitions=2, + steps=[ + cmd.thermocycler.ProfileStep( + celsius=45.6, holdSeconds=12.3 + ), + cmd.thermocycler.ProfileStep( + celsius=78.9, holdSeconds=45.6 + ), + ], + ) + ], + blockMaxVolumeUl=25, + ) + ) + ) + + def test_deactivate_lid( decoy: Decoy, mock_engine_client: EngineClient, subject: ThermocyclerModuleCore ) -> None: diff --git a/api/tests/opentrons/protocol_engine/commands/thermocycler/test_run_extended_profile.py b/api/tests/opentrons/protocol_engine/commands/thermocycler/test_run_extended_profile.py new file mode 100644 index 00000000000..9dcefceb9f1 --- /dev/null +++ b/api/tests/opentrons/protocol_engine/commands/thermocycler/test_run_extended_profile.py @@ -0,0 +1,115 @@ +"""Test Thermocycler run profile command implementation.""" +from typing import List, Union + +from decoy import Decoy + +from opentrons.hardware_control.modules import Thermocycler + +from opentrons.protocol_engine.state.state import StateView +from opentrons.protocol_engine.state.module_substates import ( + ThermocyclerModuleSubState, + ThermocyclerModuleId, +) +from opentrons.protocol_engine.execution import EquipmentHandler +from opentrons.protocol_engine.commands import thermocycler as tc_commands +from opentrons.protocol_engine.commands.command import SuccessData +from opentrons.protocol_engine.commands.thermocycler.run_extended_profile import ( + RunExtendedProfileImpl, + ProfileStep, + ProfileCycle, +) + + +async def test_run_extended_profile( + decoy: Decoy, + state_view: StateView, + equipment: EquipmentHandler, +) -> None: + """It should be able to execute the specified module's profile run.""" + subject = RunExtendedProfileImpl(state_view=state_view, equipment=equipment) + + step_data: List[Union[ProfileStep, ProfileCycle]] = [ + ProfileStep(celsius=12.3, holdSeconds=45), + ProfileCycle( + steps=[ + ProfileStep(celsius=78.9, holdSeconds=910), + ProfileStep(celsius=12, holdSeconds=1), + ], + repetitions=2, + ), + ProfileStep(celsius=45.6, holdSeconds=78), + ProfileCycle( + steps=[ + ProfileStep(celsius=56, holdSeconds=11), + ProfileStep(celsius=34, holdSeconds=10), + ], + repetitions=1, + ), + ] + data = tc_commands.RunExtendedProfileParams( + moduleId="input-thermocycler-id", + profileElements=step_data, + blockMaxVolumeUl=56.7, + ) + expected_result = tc_commands.RunExtendedProfileResult() + + tc_module_substate = decoy.mock(cls=ThermocyclerModuleSubState) + tc_hardware = decoy.mock(cls=Thermocycler) + + decoy.when( + state_view.modules.get_thermocycler_module_substate("input-thermocycler-id") + ).then_return(tc_module_substate) + + decoy.when(tc_module_substate.module_id).then_return( + ThermocyclerModuleId("thermocycler-id") + ) + + # Stub temperature validation from hs module view + decoy.when(tc_module_substate.validate_target_block_temperature(12.3)).then_return( + 32.1 + ) + decoy.when(tc_module_substate.validate_target_block_temperature(78.9)).then_return( + 78.9 + ) + decoy.when(tc_module_substate.validate_target_block_temperature(12)).then_return(12) + decoy.when(tc_module_substate.validate_target_block_temperature(45.6)).then_return( + 65.4 + ) + decoy.when(tc_module_substate.validate_target_block_temperature(56)).then_return(56) + decoy.when(tc_module_substate.validate_target_block_temperature(34)).then_return(34) + + # Stub volume validation from hs module view + decoy.when(tc_module_substate.validate_max_block_volume(56.7)).then_return(76.5) + + # Get attached hardware modules + decoy.when( + equipment.get_module_hardware_api(ThermocyclerModuleId("thermocycler-id")) + ).then_return(tc_hardware) + + result = await subject.execute(data) + + decoy.verify( + await tc_hardware.execute_profile( + profile=[ + {"temperature": 32.1, "hold_time_seconds": 45}, + { + "steps": [ + {"temperature": 78.9, "hold_time_seconds": 910}, + {"temperature": 12, "hold_time_seconds": 1}, + ], + "repetitions": 2, + }, + {"temperature": 65.4, "hold_time_seconds": 78}, + { + "steps": [ + {"temperature": 56, "hold_time_seconds": 11}, + {"temperature": 34, "hold_time_seconds": 10}, + ], + "repetitions": 1, + }, + ], + volume=76.5, + ), + times=1, + ) + assert result == SuccessData(public=expected_result, private=None) diff --git a/app/src/assets/localization/en/protocol_command_text.json b/app/src/assets/localization/en/protocol_command_text.json index 17d60a8f967..c78aef13785 100644 --- a/app/src/assets/localization/en/protocol_command_text.json +++ b/app/src/assets/localization/en/protocol_command_text.json @@ -71,8 +71,10 @@ "slot": "Slot {{slot_name}}", "target_temperature": "target temperature", "tc_awaiting_for_duration": "Waiting for Thermocycler profile to complete", - "tc_run_profile_steps": "temperature: {{celsius}}°C, seconds: {{seconds}}", - "tc_starting_profile": "Thermocycler starting {{repetitions}} repetitions of cycle composed of the following steps:", + "tc_run_profile_steps": "Temperature: {{celsius}}°C, hold time: {{duration}}", + "tc_starting_extended_profile_cycle": "{{repetitions}} repetitions of the following steps:", + "tc_starting_extended_profile": "Running thermocycler profile with {{elementCount}} total steps and cycles:", + "tc_starting_profile": "Running thermocycler profile with {{stepCount}} steps:", "touch_tip": "Touching tip", "trash_bin_in_slot": "Trash Bin in {{slot_name}}", "unlatching_hs_latch": "Unlatching labware on Heater-Shaker", diff --git a/app/src/molecules/Command/Command.stories.tsx b/app/src/molecules/Command/Command.stories.tsx index 1fe64215ef3..43e81fa5541 100644 --- a/app/src/molecules/Command/Command.stories.tsx +++ b/app/src/molecules/Command/Command.stories.tsx @@ -18,7 +18,7 @@ interface StorybookArgs { } const availableCommandTypes = uniq( - Fixtures.mockQIASeqTextData.commands.map(command => command.commandType) + Fixtures.mockDoItAllTextData.commands.map(command => command.commandType) ) const commandsByType: Partial> = {} @@ -26,7 +26,7 @@ function commandsOfType(type: CommandType): RunTimeCommand[] { if (type in commandsByType) { return commandsByType[type] } - commandsByType[type] = Fixtures.mockQIASeqTextData.commands.filter( + commandsByType[type] = Fixtures.mockDoItAllTextData.commands.filter( command => command.commandType === type ) return commandsByType[type] @@ -43,8 +43,8 @@ function safeCommandOfType(type: CommandType, index: number): RunTimeCommand { function Wrapper(props: StorybookArgs): JSX.Element { const command = props.selectCommandBy === 'protocol index' - ? Fixtures.mockQIASeqTextData.commands[ - props.commandIndex < Fixtures.mockQIASeqTextData.commands.length + ? Fixtures.mockDoItAllTextData.commands[ + props.commandIndex < Fixtures.mockDoItAllTextData.commands.length ? props.commandIndex : -1 ] @@ -52,7 +52,7 @@ function Wrapper(props: StorybookArgs): JSX.Element { return command == null ? null : ( = { control: { type: 'range', min: 0, - max: Fixtures.mockQIASeqTextData.commands.length - 1, + max: Fixtures.mockDoItAllTextData.commands.length - 1, }, defaultValue: 0, if: { arg: 'selectCommandBy', eq: 'protocol index' }, @@ -161,6 +161,16 @@ export const ThermocyclerProfile: Story = { }, } +export const ThermocyclerExtendedProfile: Story = { + args: { + selectCommandBy: 'command type', + commandType: 'thermocycler/runExtendedProfile', + commandTypeIndex: 0, + aligned: 'left', + state: 'current', + }, +} + export const VeryLongCommand: Story = { args: { selectCommandBy: 'command type', diff --git a/app/src/molecules/Command/CommandText.tsx b/app/src/molecules/Command/CommandText.tsx index 70fb5281817..00c7337104b 100644 --- a/app/src/molecules/Command/CommandText.tsx +++ b/app/src/molecules/Command/CommandText.tsx @@ -16,6 +16,10 @@ import { useCommandTextString } from './hooks' import type { RobotType, RunTimeCommand } from '@opentrons/shared-data' import type { StyleProps } from '@opentrons/components' import type { CommandTextData } from './types' +import type { + GetTCRunExtendedProfileCommandTextResult, + GetTCRunProfileCommandTextResult, +} from './hooks' interface LegacySTProps { as?: React.ComponentProps['as'] @@ -39,22 +43,35 @@ interface BaseProps extends StyleProps { propagateTextLimit?: boolean } export function CommandText(props: BaseProps & STProps): JSX.Element | null { - const { commandText, stepTexts } = useCommandTextString({ + const commandText = useCommandTextString({ ...props, }) - switch (props.command.commandType) { + switch (commandText.kind) { case 'thermocycler/runProfile': { return ( + ) + } + case 'thermocycler/runExtendedProfile': { + return ( + ) } default: { - return {commandText} + return ( + + {commandText.commandText} + + ) } } } @@ -91,11 +108,18 @@ function CommandStyledText( } } +const shouldPropagateCenter = ( + propagateCenter: boolean, + isOnDevice?: boolean +): boolean => isOnDevice === true || propagateCenter +const shouldPropagateTextLimit = ( + propagateTextLimit: boolean, + isOnDevice?: boolean +): boolean => isOnDevice === true || propagateTextLimit + type ThermocyclerRunProfileProps = BaseProps & - STProps & { - commandText: string - stepTexts?: string[] - } + STProps & + Omit function ThermocyclerRunProfile( props: ThermocyclerRunProfileProps @@ -109,9 +133,6 @@ function ThermocyclerRunProfile( ...styleProps } = props - const shouldPropagateCenter = isOnDevice === true || propagateCenter - const shouldPropagateTextLimit = isOnDevice === true || propagateTextLimit - // TODO(sfoster): Command sometimes wraps this in a cascaded display: -webkit-box // to achieve multiline text clipping with an automatically inserted ellipsis, which works // everywhere except for here where it overrides this property in the flex since this is @@ -124,7 +145,11 @@ function ThermocyclerRunProfile(
    - {shouldPropagateTextLimit ? ( + {shouldPropagateTextLimit(propagateTextLimit, isOnDevice) ? (
  • - {stepTexts?.[0]} + {stepTexts[0]}
    • ) : ( - stepTexts?.map((step: string, index: number) => ( + stepTexts.map((step: string, index: number) => (
  • ) } + +type ThermocyclerRunExtendedProfileProps = BaseProps & + STProps & + Omit + +function ThermocyclerRunExtendedProfile( + props: ThermocyclerRunExtendedProfileProps +): JSX.Element { + const { + isOnDevice, + propagateCenter = false, + propagateTextLimit = false, + commandText, + profileElementTexts, + ...styleProps + } = props + + // TODO(sfoster): Command sometimes wraps this in a cascaded display: -webkit-box + // to achieve multiline text clipping with an automatically inserted ellipsis, which works + // everywhere except for here where it overrides this property in the flex since this is + // the only place where CommandText uses a flex. + // The right way to handle this is probably to take the css that's in Command and make it + // live here instead, but that should be done in a followup since it would touch everything. + // See also the margin-left on the
  • s, which is needed to prevent their bullets from + // clipping if a container set overflow: hidden. + return ( + + + {commandText} + + +
      + {shouldPropagateTextLimit(propagateTextLimit, isOnDevice) ? ( +
    • + {profileElementTexts[0].kind === 'step' + ? profileElementTexts[0].stepText + : profileElementTexts[0].cycleText} +
      • + ) : ( + profileElementTexts.map((element, index: number) => + element.kind === 'step' ? ( +
    • + {' '} + {element.stepText} +
      • + ) : ( +
    • + {element.cycleText} +
        + {element.stepTexts.map( + ({ stepText }, stepIndex: number) => ( +
      • + {' '} + {stepText} +
        • + ) + )} +
      +
      • + ) + ) + )} +
    +     +     + ) +} diff --git a/app/src/molecules/Command/__fixtures__/doItAllV10.json b/app/src/molecules/Command/__fixtures__/doItAllV10.json new file mode 100644 index 00000000000..83030179e79 --- /dev/null +++ b/app/src/molecules/Command/__fixtures__/doItAllV10.json @@ -0,0 +1,4863 @@ +{ + "id": "lasdlakjjflaksjdlkajsldkasd", + "result": "ok", + "status": "completed", + "createdAt": "2024-06-12T17:21:56.919263+00:00", + "files": [ + { "name": "doItAllV8.json", "role": "main" }, + { "name": "cpx_4_tuberack_100ul.json", "role": "labware" } + ], + "config": { "protocolType": "json", "schemaVersion": 8 }, + "metadata": { + "protocolName": "doItAllV10", + "author": "", + "description": "", + "created": 1701659107408, + "lastModified": 1714570438503, + "category": null, + "subcategory": null, + "tags": [] + }, + "robotType": "OT-3 Standard", + "runTimeParameters": [], + "commands": [ + { + "id": "70fbbc6c-d86a-4e66-9361-25de75552da6", + "createdAt": "2024-06-12T17:21:57.915484+00:00", + "commandType": "thermocycler/runProfile", + "key": "5ec88b6a-2c2c-4ffc-961f-c6e0dd300b49", + "status": "succeeded", + "params": { + "moduleId": "fd6da9f1-d63b-414b-929e-c646b64790e9:thermocyclerModuleType", + "profile": [ + { "holdSeconds": 1, "celsius": 9 }, + { "holdSeconds": 2, "celsius": 10 }, + { "holdSeconds": 3, "celsius": 11 }, + { "holdSeconds": 4, "celsius": 12 }, + { "holdSeconds": 5, "celsius": 13 }, + { "holdSeconds": 6, "celsius": 14 }, + { "holdSeconds": 7, "celsius": 15 }, + { "holdSeconds": 8, "celsius": 16 }, + { "holdSeconds": 9, "celsius": 17 }, + { "holdSeconds": 10, "celsius": 18 }, + { "holdSeconds": 11, "celsius": 19 }, + { "holdSeconds": 12, "celsius": 20 }, + { "holdSeconds": 1, "celsius": 9 }, + { "holdSeconds": 2, "celsius": 10 }, + { "holdSeconds": 3, "celsius": 11 }, + { "holdSeconds": 4, "celsius": 12 }, + { "holdSeconds": 5, "celsius": 13 }, + { "holdSeconds": 6, "celsius": 14 }, + { "holdSeconds": 7, "celsius": 15 }, + { "holdSeconds": 8, "celsius": 16 }, + { "holdSeconds": 9, "celsius": 17 }, + { "holdSeconds": 10, "celsius": 18 }, + { "holdSeconds": 11, "celsius": 19 }, + { "holdSeconds": 12, "celsius": 20 } + ], + "blockMaxVolumeUl": 10 + }, + "result": {}, + "startedAt": "2024-06-12T17:21:57.915517+00:00", + "completedAt": "2024-06-12T17:21:57.915543+00:00", + "notes": [] + }, + { + "id": "70fbbc6c-d86a-4e66-9361-25de75552da6", + "createdAt": "2024-06-12T17:21:57.915484+00:00", + "commandType": "thermocycler/runExtendedProfile", + "key": "5ec22b6a-2c2c-4bbc-961f-c6e0aa211b49", + "status": "succeeded", + "params": { + "moduleId": "f99da9f1-d63b-414b-929e-c646b23790fd:thermocyclerModuleType", + "profileElements": [ + { + "repetitions": 10, + "steps": [ + { "holdSeconds": 2, "celsius": 10 }, + { "holdSeconds": 3, "celsius": 11 }, + { "holdSeconds": 4, "celsius": 12 } + ] + }, + { "holdSeconds": 1, "celsius": 9 }, + { "holdSeconds": 5, "celsius": 13 }, + { + "repetitions": 20, + "steps": [ + { "holdSeconds": 6, "celsius": 14 }, + { "holdSeconds": 7, "celsius": 15 }, + { "holdSeconds": 8, "celsius": 16 } + ] + }, + { "holdSeconds": 9, "celsius": 17 }, + { + "repetitions": 30, + "steps": [ + { "holdSeconds": 10, "celsius": 18 }, + { "holdSeconds": 11, "celsius": 19 }, + { "holdSeconds": 12, "celsius": 20 } + ] + }, + { "holdSeconds": 1, "celsius": 9 }, + { + "repetitions": 40, + "steps": [ + { "holdSeconds": 2, "celsius": 10 }, + { "holdSeconds": 3, "celsius": 11 }, + { "holdSeconds": 4, "celsius": 12 } + ] + }, + { "holdSeconds": 5, "celsius": 13 }, + { + "repetitions": 50, + "steps": [ + { "holdSeconds": 6, "celsius": 14 }, + { "holdSeconds": 7, "celsius": 15 }, + { "holdSeconds": 8, "celsius": 16 } + ] + }, + { "holdSeconds": 9, "celsius": 17 }, + { + "repetitions": 60, + "steps": [ + { "holdSeconds": 10, "celsius": 18 }, + { "holdSeconds": 11, "celsius": 19 }, + { "holdSeconds": 12, "celsius": 20 } + ] + } + ], + "blockMaxVolumeUl": 10 + }, + "result": {}, + "startedAt": "2024-06-12T17:21:57.915517+00:00", + "completedAt": "2024-06-12T17:21:57.915543+00:00", + "notes": [] + }, + { + "id": "8f0be368-dc25-4f2a-92b9-a734ad622d4b", + "createdAt": "2024-06-12T17:21:56.894269+00:00", + "commandType": "home", + "key": "50c7ae73a4e3f7129874f39dfb514803", + "status": "succeeded", + "params": {}, + "result": {}, + "startedAt": "2024-06-12T17:21:56.894479+00:00", + "completedAt": "2024-06-12T17:21:56.894522+00:00", + "notes": [] + }, + { + "id": "c744767e-f5a4-408d-bc28-d46a2bd17297", + "createdAt": "2024-06-12T17:21:56.894706+00:00", + "commandType": "loadPipette", + "key": "a1b95079-5b17-428d-b40c-a8236a9890c5", + "status": "succeeded", + "params": { + "pipetteName": "p1000_single_flex", + "mount": "left", + "pipetteId": "9fcd50d9-92b2-45ac-acf1-e2cf773feffc" + }, + "result": { "pipetteId": "9fcd50d9-92b2-45ac-acf1-e2cf773feffc" }, + "startedAt": "2024-06-12T17:21:56.894767+00:00", + "completedAt": "2024-06-12T17:21:56.898018+00:00", + "notes": [] + }, + { + "id": "684793b1-7401-4291-ac0f-e95d61e49e07", + "createdAt": "2024-06-12T17:21:56.898252+00:00", + "commandType": "loadModule", + "key": "6f1e3ad3-8f03-4583-8031-be6be2fcd903", + "status": "succeeded", + "params": { + "model": "heaterShakerModuleV1", + "location": { "slotName": "D1" }, + "moduleId": "23347241-80bb-4a7e-9c91-5d9727a9e483:heaterShakerModuleType" + }, + "result": { + "moduleId": "23347241-80bb-4a7e-9c91-5d9727a9e483:heaterShakerModuleType", + "definition": { + "otSharedSchema": "module/schemas/2", + "moduleType": "heaterShakerModuleType", + "model": "heaterShakerModuleV1", + "labwareOffset": { "x": -0.125, "y": 1.125, "z": 68.275 }, + "dimensions": { "bareOverallHeight": 82.0, "overLabwareHeight": 0.0 }, + "calibrationPoint": { "x": 12.0, "y": 8.75, "z": 68.275 }, + "displayName": "Heater-Shaker Module GEN1", + "quirks": [], + "slotTransforms": { + "ot2_standard": { + "3": { + "labwareOffset": [ + [-1, 0, 0, 0], + [0, -1, 0, 0], + [0, 0, 1, 0], + [0, 0, 0, 1] + ] + }, + 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"2024-06-12T17:21:56.916715+00:00", + "notes": [] + }, + { + "id": "487eee54-9fdc-4dcd-b948-6ff860855887", + "createdAt": "2024-06-12T17:21:56.916808+00:00", + "commandType": "heaterShaker/deactivateHeater", + "key": "a6970f26-4800-4949-8592-d977df547d8b", + "status": "succeeded", + "params": { + "moduleId": "23347241-80bb-4a7e-9c91-5d9727a9e483:heaterShakerModuleType" + }, + "result": {}, + "startedAt": "2024-06-12T17:21:56.916832+00:00", + "completedAt": "2024-06-12T17:21:56.916851+00:00", + "notes": [] + }, + { + "id": "917f4e1b-d622-4602-9c13-75177b2119b2", + "createdAt": "2024-06-12T17:21:56.916913+00:00", + "commandType": "heaterShaker/setAndWaitForShakeSpeed", + "key": "ef808dac-1e14-47a1-843d-ce4ce63bdfce", + "status": "succeeded", + "params": { + "moduleId": "23347241-80bb-4a7e-9c91-5d9727a9e483:heaterShakerModuleType", + "rpm": 200.0 + }, + "result": { "pipetteRetracted": true }, + "startedAt": "2024-06-12T17:21:56.916939+00:00", + "completedAt": "2024-06-12T17:21:56.916969+00:00", + "notes": [] + }, + { + "id": "0807dfa8-3c0c-4125-964d-985c642afc34", + "createdAt": "2024-06-12T17:21:56.917053+00:00", + "commandType": "waitForDuration", + "key": "5b47f11e-0755-47d2-b844-f1363e28a54e", + "status": "succeeded", + "params": { "seconds": 60.0 }, + "result": {}, + "startedAt": "2024-06-12T17:21:56.917077+00:00", + "completedAt": "2024-06-12T17:21:56.917095+00:00", + "notes": [] + }, + { + "id": "0a40eee2-8902-4914-86f1-af3d961e7dcd", + "createdAt": "2024-06-12T17:21:56.917156+00:00", + "commandType": "heaterShaker/deactivateShaker", + "key": "614ec8d0-8abf-4aa4-b771-23ff2bde2881", + "status": "succeeded", + "params": { + "moduleId": "23347241-80bb-4a7e-9c91-5d9727a9e483:heaterShakerModuleType" + }, + "result": {}, + "startedAt": "2024-06-12T17:21:56.917187+00:00", + "completedAt": "2024-06-12T17:21:56.917208+00:00", + "notes": [] + }, + { + "id": "ddffeaa1-9f97-4bd3-99ee-5e0d8aee28bc", + "createdAt": "2024-06-12T17:21:56.917290+00:00", + "commandType": "heaterShaker/deactivateHeater", + "key": "dbbe307e-d361-4cb9-afe7-afeab944bfce", + "status": "succeeded", + "params": { + "moduleId": "23347241-80bb-4a7e-9c91-5d9727a9e483:heaterShakerModuleType" + }, + "result": {}, + "startedAt": "2024-06-12T17:21:56.917314+00:00", + "completedAt": "2024-06-12T17:21:56.917333+00:00", + "notes": [] + }, + { + "id": "176fe5ea-4a4f-4a78-a2b9-160fdd1a7be1", + "createdAt": "2024-06-12T17:21:56.917404+00:00", + "commandType": "heaterShaker/deactivateHeater", + "key": "62f98610-cbff-4acb-ba36-a3fbb9527ba9", + "status": "succeeded", + "params": { + "moduleId": "23347241-80bb-4a7e-9c91-5d9727a9e483:heaterShakerModuleType" + }, + "result": {}, + "startedAt": "2024-06-12T17:21:56.917427+00:00", + "completedAt": "2024-06-12T17:21:56.917445+00:00", + "notes": [] + }, + { + "id": "26022284-0a3c-48ad-b864-91f7c48ea19c", + "createdAt": "2024-06-12T17:21:56.917509+00:00", + "commandType": "heaterShaker/openLabwareLatch", + "key": "81cfeab1-175f-4501-8732-1ea1bc9b528b", + "status": "succeeded", + "params": { + "moduleId": "23347241-80bb-4a7e-9c91-5d9727a9e483:heaterShakerModuleType" + }, + "result": { "pipetteRetracted": true }, + "startedAt": "2024-06-12T17:21:56.917532+00:00", + "completedAt": "2024-06-12T17:21:56.917554+00:00", + "notes": [] + }, + { + "id": "5e8711de-7231-47d1-ab55-541dd21cef48", + "createdAt": "2024-06-12T17:21:56.917627+00:00", + "commandType": "moveLabware", + "key": "279df4d0-2c87-4f01-b016-5c42d5edce96", + "status": "succeeded", + "params": { + "labwareId": "54370838-4fca-4a14-b88a-7840e4903649:opentrons/opentrons_96_wellplate_200ul_pcr_full_skirt/2", + "newLocation": { "addressableAreaName": "B4" }, + "strategy": "usingGripper" + }, + "result": {}, + "startedAt": "2024-06-12T17:21:56.917651+00:00", + "completedAt": "2024-06-12T17:21:56.917738+00:00", + "notes": [] + }, + { + "id": "abf5283b-dc04-457e-b1ea-4dc848620954", + "createdAt": "2024-06-12T17:21:56.917841+00:00", + "commandType": "moveLabware", + "key": "f88f41dc-ddf9-4242-9ba4-21bd728ca25f", + "status": "succeeded", + "params": { + "labwareId": "f2d371ea-5146-4c89-8200-9c056a7f321a:opentrons/opentrons_flex_96_tiprack_1000ul/1", + "newLocation": { "addressableAreaName": "gripperWasteChute" }, + "strategy": "usingGripper" + }, + "result": {}, + "startedAt": "2024-06-12T17:21:56.917866+00:00", + "completedAt": "2024-06-12T17:21:56.917941+00:00", + "notes": [] + } + ], + "labware": [ + { + "id": "7c4d59fa-0e50-442f-adce-9e4b0c7f0b88:opentrons/opentrons_96_pcr_adapter/1", + "loadName": "opentrons_96_pcr_adapter", + "definitionUri": "opentrons/opentrons_96_pcr_adapter/1", + "location": { + "moduleId": "23347241-80bb-4a7e-9c91-5d9727a9e483:heaterShakerModuleType" + }, + "displayName": "Opentrons 96 PCR Heater-Shaker Adapter" + }, + { + "id": "f2d371ea-5146-4c89-8200-9c056a7f321a:opentrons/opentrons_flex_96_tiprack_1000ul/1", + "loadName": "opentrons_flex_96_tiprack_1000ul", + "definitionUri": "opentrons/opentrons_flex_96_tiprack_1000ul/1", + "location": "offDeck", + "displayName": "Opentrons Flex 96 Tip Rack 1000 \u00b5L" + }, + { + "id": "54370838-4fca-4a14-b88a-7840e4903649:opentrons/opentrons_96_wellplate_200ul_pcr_full_skirt/2", + "loadName": "opentrons_96_wellplate_200ul_pcr_full_skirt", + "definitionUri": "opentrons/opentrons_96_wellplate_200ul_pcr_full_skirt/2", + "location": { "addressableAreaName": "B4" }, + "displayName": "Opentrons Tough 96 Well Plate 200 \u00b5L PCR Full Skirt" + }, + { + "id": "8bacda22-9e05-45e8-bef4-cc04414a204f:opentrons/axygen_1_reservoir_90ml/1", + "loadName": "axygen_1_reservoir_90ml", + "definitionUri": "opentrons/axygen_1_reservoir_90ml/1", + "location": { "slotName": "C1" }, + "displayName": "Axygen 1 Well Reservoir 90 mL" + } + ], + "pipettes": [ + { + "id": "9fcd50d9-92b2-45ac-acf1-e2cf773feffc", + "pipetteName": "p1000_single_flex", + "mount": "left" + } + ], + "modules": [ + { + "id": "23347241-80bb-4a7e-9c91-5d9727a9e483:heaterShakerModuleType", + "model": "heaterShakerModuleV1", + "location": { "slotName": "D1" }, + "serialNumber": "fake-serial-number-0d06c2c1-3ee4-467d-b1cb-31ce8a260ff5" + }, + { + "id": "fd6da9f1-d63b-414b-929e-c646b64790e9:thermocyclerModuleType", + "model": "thermocyclerModuleV2", + "location": { "slotName": "B1" }, + "serialNumber": "fake-serial-number-abe43d5b-1dd7-4fa9-bf8b-b089236d5adb" + } + ], + "liquids": [ + { + "id": "0", + "displayName": "h20", + "description": "", + "displayColor": "#b925ff" + }, + { + "id": "1", + "displayName": "sample", + "description": "", + "displayColor": "#ffd600" + } + ], + "errors": [] +} diff --git a/app/src/molecules/Command/__fixtures__/index.ts b/app/src/molecules/Command/__fixtures__/index.ts index 447a935d3dc..ba988a5197a 100644 --- a/app/src/molecules/Command/__fixtures__/index.ts +++ b/app/src/molecules/Command/__fixtures__/index.ts @@ -1,5 +1,5 @@ import robotSideAnalysis from './mockRobotSideAnalysis.json' -import doItAllAnalysis from './doItAllV8.json' +import doItAllAnalysis from './doItAllV10.json' import qiaseqAnalysis from './analysis_QIAseqFX24xv4_8.json' import type { CompletedProtocolAnalysis } from '@opentrons/shared-data' import type { CommandTextData } from '../types' diff --git a/app/src/molecules/Command/__tests__/CommandText.test.tsx b/app/src/molecules/Command/__tests__/CommandText.test.tsx index 7425c2e1853..a6614c6b330 100644 --- a/app/src/molecules/Command/__tests__/CommandText.test.tsx +++ b/app/src/molecules/Command/__tests__/CommandText.test.tsx @@ -821,11 +821,9 @@ describe('CommandText', () => { i18nInstance: i18n, } ) - screen.getByText( - 'Thermocycler starting 2 repetitions of cycle composed of the following steps:' - ) - screen.getByText('temperature: 20°C, seconds: 10') - screen.getByText('temperature: 40°C, seconds: 30') + screen.getByText('Running thermocycler profile with 2 steps:') + screen.getByText('Temperature: 20°C, hold time: 0h 00m 10s') + screen.getByText('Temperature: 40°C, hold time: 0h 00m 30s') }) it('renders correct text for thermocycler/runProfile on ODD', () => { const mockProfileSteps = [ @@ -853,12 +851,128 @@ describe('CommandText', () => { i18nInstance: i18n, } ) + screen.getByText('Running thermocycler profile with 2 steps:') + screen.getByText('Temperature: 20°C, hold time: 0h 00m 10s') + expect( + screen.queryByText('Temperature: 40°C, hold time: 0h 00m 30s') + ).not.toBeInTheDocument() + }) + it('renders correct text for thermocycler/runExtendedProfile on Desktop', () => { + const mockProfileSteps = [ + { holdSeconds: 10, celsius: 20 }, + { + repetitions: 10, + steps: [ + { holdSeconds: 15, celsius: 10 }, + { holdSeconds: 12, celsius: 11 }, + ], + }, + { holdSeconds: 30, celsius: 40 }, + { + repetitions: 9, + steps: [ + { holdSeconds: 13000, celsius: 12 }, + { holdSeconds: 14, celsius: 13 }, + ], + }, + ] + renderWithProviders( + , + { + i18nInstance: i18n, + } + ) screen.getByText( - 'Thermocycler starting 2 repetitions of cycle composed of the following steps:' + 'Running thermocycler profile with 4 total steps and cycles:' + ) + screen.getByText('Temperature: 20°C, hold time: 0h 00m 10s') + screen.getByText('10 repetitions of the following steps:') + screen.getByText('Temperature: 10°C, hold time: 0h 00m 15s') + screen.getByText('Temperature: 11°C, hold time: 0h 00m 12s') + screen.getByText('Temperature: 40°C, hold time: 0h 00m 30s') + screen.getByText('9 repetitions of the following steps:') + screen.getByText('Temperature: 12°C, hold time: 3h 36m 40s') + screen.getByText('Temperature: 13°C, hold time: 0h 00m 14s') + }) + it('renders correct text for thermocycler/runExtendedProfile on ODD', () => { + const mockProfileSteps = [ + { holdSeconds: 10, celsius: 20 }, + { + repetitions: 10, + steps: [ + { holdSeconds: 15, celsius: 10 }, + { holdSeconds: 12, celsius: 11 }, + ], + }, + { holdSeconds: 30, celsius: 40 }, + { + repetitions: 9, + steps: [ + { holdSeconds: 13, celsius: 12 }, + { holdSeconds: 14, celsius: 13 }, + ], + }, + ] + renderWithProviders( + , + { + i18nInstance: i18n, + } + ) + screen.getByText( + 'Running thermocycler profile with 4 total steps and cycles:' ) - screen.getByText('temperature: 20°C, seconds: 10') + screen.getByText('Temperature: 20°C, hold time: 0h 00m 10s') + + expect( + screen.queryByText('10 repetitions of the following steps:') + ).not.toBeInTheDocument() + expect( + screen.queryByText('Temperature: 10°C, hold time: 0h 00m 15s') + ).not.toBeInTheDocument() + expect( + screen.queryByText('Temperature: 11°C, hold time: 0h 00m 12s') + ).not.toBeInTheDocument() + expect( + screen.queryByText('Temperature: 40°C, hold time: 0h 00m 30s') + ).not.toBeInTheDocument() + expect( + screen.queryByText('9 repetitions of the following steps:') + ).not.toBeInTheDocument() + expect( + screen.queryByText('Temperature: 12°C, hold time: 0h 00m 13s') + ).not.toBeInTheDocument() expect( - screen.queryByText('temperature: 40°C, seconds: 30') + screen.queryByText('Temperature: 13°C, hold time: 0h 00m 14s') ).not.toBeInTheDocument() }) it('renders correct text for heaterShaker/setAndWaitForShakeSpeed', () => { diff --git a/app/src/molecules/Command/hooks/index.ts b/app/src/molecules/Command/hooks/index.ts index 6b6545c7689..6f0457c174f 100644 --- a/app/src/molecules/Command/hooks/index.ts +++ b/app/src/molecules/Command/hooks/index.ts @@ -4,4 +4,6 @@ export type { UseCommandTextStringParams, GetCommandText, GetCommandTextResult, + GetTCRunExtendedProfileCommandTextResult, + GetTCRunProfileCommandTextResult, } from './useCommandTextString' diff --git a/app/src/molecules/Command/hooks/useCommandTextString/index.tsx b/app/src/molecules/Command/hooks/useCommandTextString/index.tsx index d10a9aa3211..1cf39cc0d1f 100644 --- a/app/src/molecules/Command/hooks/useCommandTextString/index.tsx +++ b/app/src/molecules/Command/hooks/useCommandTextString/index.tsx @@ -5,6 +5,10 @@ import type { TFunction } from 'i18next' import type { RunTimeCommand, RobotType } from '@opentrons/shared-data' import type { CommandTextData } from '../../types' import type { GetDirectTranslationCommandText } from './utils/getDirectTranslationCommandText' +import type { + TCProfileStepText, + TCProfileCycleText, +} from './utils/getTCRunExtendedProfileCommandText' export interface UseCommandTextStringParams { command: RunTimeCommand | null @@ -12,13 +16,32 @@ export interface UseCommandTextStringParams { robotType: RobotType } +export type CommandTextKind = + | 'generic' + | 'thermocycler/runProfile' + | 'thermocycler/runExtendedProfile' + export type GetCommandText = UseCommandTextStringParams & { t: TFunction } -export interface GetCommandTextResult { +export interface GetGenericCommandTextResult { + kind: 'generic' /* The actual command text. Ex "Homing all gantry, pipette, and plunger axes" */ commandText: string +} +export interface GetTCRunProfileCommandTextResult { + kind: 'thermocycler/runProfile' + commandText: string /* The TC run profile steps. */ - stepTexts?: string[] + stepTexts: string[] } +export interface GetTCRunExtendedProfileCommandTextResult { + kind: 'thermocycler/runExtendedProfile' + commandText: string + profileElementTexts: Array +} +export type GetCommandTextResult = + | GetGenericCommandTextResult + | GetTCRunProfileCommandTextResult + | GetTCRunExtendedProfileCommandTextResult // TODO(jh, 07-18-24): Move the testing that covers this from CommandText to a new file, and verify that all commands are // properly tested. @@ -52,6 +75,7 @@ export function useCommandTextString( case 'heaterShaker/deactivateShaker': case 'heaterShaker/waitForTemperature': return { + kind: 'generic', commandText: utils.getDirectTranslationCommandText( fullParams as GetDirectTranslationCommandText ), @@ -67,6 +91,7 @@ export function useCommandTextString( case 'dropTipInPlace': case 'pickUpTip': return { + kind: 'generic', commandText: utils.getPipettingCommandText(fullParams), } @@ -76,12 +101,14 @@ export function useCommandTextString( case 'loadModule': case 'loadLiquid': return { + kind: 'generic', commandText: utils.getLoadCommandText(fullParams), } case 'liquidProbe': case 'tryLiquidProbe': return { + kind: 'generic', commandText: utils.getLiquidProbeCommandText({ ...fullParams, command, @@ -94,6 +121,7 @@ export function useCommandTextString( case 'thermocycler/setTargetLidTemperature': case 'heaterShaker/setTargetTemperature': return { + kind: 'generic', commandText: utils.getTemperatureCommandText({ ...fullParams, command, @@ -103,8 +131,15 @@ export function useCommandTextString( case 'thermocycler/runProfile': return utils.getTCRunProfileCommandText({ ...fullParams, command }) + case 'thermocycler/runExtendedProfile': + return utils.getTCRunExtendedProfileCommandText({ + ...fullParams, + command, + }) + case 'heaterShaker/setAndWaitForShakeSpeed': return { + kind: 'generic', commandText: utils.getHSShakeSpeedCommandText({ ...fullParams, command, @@ -113,11 +148,13 @@ export function useCommandTextString( case 'moveToSlot': return { + kind: 'generic', commandText: utils.getMoveToSlotCommandText({ ...fullParams, command }), } case 'moveRelative': return { + kind: 'generic', commandText: utils.getMoveRelativeCommandText({ ...fullParams, command, @@ -126,6 +163,7 @@ export function useCommandTextString( case 'moveToCoordinates': return { + kind: 'generic', commandText: utils.getMoveToCoordinatesCommandText({ ...fullParams, command, @@ -134,11 +172,13 @@ export function useCommandTextString( case 'moveToWell': return { + kind: 'generic', commandText: utils.getMoveToWellCommandText({ ...fullParams, command }), } case 'moveLabware': return { + kind: 'generic', commandText: utils.getMoveLabwareCommandText({ ...fullParams, command, @@ -147,6 +187,7 @@ export function useCommandTextString( case 'configureForVolume': return { + kind: 'generic', commandText: utils.getConfigureForVolumeCommandText({ ...fullParams, command, @@ -155,6 +196,7 @@ export function useCommandTextString( case 'configureNozzleLayout': return { + kind: 'generic', commandText: utils.getConfigureNozzleLayoutCommandText({ ...fullParams, command, @@ -163,6 +205,7 @@ export function useCommandTextString( case 'prepareToAspirate': return { + kind: 'generic', commandText: utils.getPrepareToAspirateCommandText({ ...fullParams, command, @@ -171,6 +214,7 @@ export function useCommandTextString( case 'moveToAddressableArea': return { + kind: 'generic', commandText: utils.getMoveToAddressableAreaCommandText({ ...fullParams, command, @@ -179,6 +223,7 @@ export function useCommandTextString( case 'moveToAddressableAreaForDropTip': return { + kind: 'generic', commandText: utils.getMoveToAddressableAreaForDropTipCommandText({ ...fullParams, command, @@ -187,6 +232,7 @@ export function useCommandTextString( case 'waitForDuration': return { + kind: 'generic', commandText: utils.getWaitForDurationCommandText({ ...fullParams, command, @@ -196,6 +242,7 @@ export function useCommandTextString( case 'pause': // legacy pause command case 'waitForResume': return { + kind: 'generic', commandText: utils.getWaitForResumeCommandText({ ...fullParams, command, @@ -204,27 +251,31 @@ export function useCommandTextString( case 'delay': return { + kind: 'generic', commandText: utils.getDelayCommandText({ ...fullParams, command }), } case 'comment': return { + kind: 'generic', commandText: utils.getCommentCommandText({ ...fullParams, command }), } case 'custom': return { + kind: 'generic', commandText: utils.getCustomCommandText({ ...fullParams, command }), } case 'setRailLights': return { + kind: 'generic', commandText: utils.getRailLightsCommandText({ ...fullParams, command }), } case undefined: case null: - return { commandText: '' } + return { kind: 'generic', commandText: '' } default: console.warn( @@ -232,6 +283,7 @@ export function useCommandTextString( command ) return { + kind: 'generic', commandText: utils.getUnknownCommandText({ ...fullParams, command }), } } diff --git a/app/src/molecules/Command/hooks/useCommandTextString/utils/getTCRunExtendedProfileCommandText.ts b/app/src/molecules/Command/hooks/useCommandTextString/utils/getTCRunExtendedProfileCommandText.ts new file mode 100644 index 00000000000..4c4acde0b6f --- /dev/null +++ b/app/src/molecules/Command/hooks/useCommandTextString/utils/getTCRunExtendedProfileCommandText.ts @@ -0,0 +1,67 @@ +import { formatDurationLabeled } from '/app/transformations/commands' +import type { + TCRunExtendedProfileRunTimeCommand, + TCProfileCycle, + AtomicProfileStep, +} from '@opentrons/shared-data/command' +import type { GetTCRunExtendedProfileCommandTextResult } from '..' +import type { HandlesCommands } from './types' + +export interface TCProfileStepText { + kind: 'step' + stepText: string +} + +export interface TCProfileCycleText { + kind: 'cycle' + cycleText: string + stepTexts: TCProfileStepText[] +} + +export function getTCRunExtendedProfileCommandText({ + command, + t, +}: HandlesCommands): GetTCRunExtendedProfileCommandTextResult { + const { profileElements } = command.params + + const stepText = ({ + celsius, + holdSeconds, + }: AtomicProfileStep): TCProfileStepText => ({ + kind: 'step', + stepText: t('tc_run_profile_steps', { + celsius, + duration: formatDurationLabeled({ seconds: holdSeconds }), + }).trim(), + }) + + const stepTexts = (cycle: AtomicProfileStep[]): TCProfileStepText[] => + cycle.map(stepText) + + const startingCycleText = (cycle: TCProfileCycle): string => + t('tc_starting_extended_profile_cycle', { + repetitions: cycle.repetitions, + }) + + const cycleText = (cycle: TCProfileCycle): TCProfileCycleText => ({ + kind: 'cycle', + cycleText: startingCycleText(cycle), + stepTexts: stepTexts(cycle.steps), + }) + const profileElementTexts = ( + profile: Array + ): Array => + profile.map(element => + Object.hasOwn(element, 'repetitions') + ? cycleText(element as TCProfileCycle) + : stepText(element as AtomicProfileStep) + ) + + return { + kind: 'thermocycler/runExtendedProfile', + commandText: t('tc_starting_extended_profile', { + elementCount: profileElements.length, + }), + profileElementTexts: profileElementTexts(profileElements), + } +} diff --git a/app/src/molecules/Command/hooks/useCommandTextString/utils/getTCRunProfileCommandText.ts b/app/src/molecules/Command/hooks/useCommandTextString/utils/getTCRunProfileCommandText.ts index 2d279fca850..cbc56b02635 100644 --- a/app/src/molecules/Command/hooks/useCommandTextString/utils/getTCRunProfileCommandText.ts +++ b/app/src/molecules/Command/hooks/useCommandTextString/utils/getTCRunProfileCommandText.ts @@ -1,24 +1,29 @@ +import { formatDurationLabeled } from '/app/transformations/commands' import type { TCRunProfileRunTimeCommand } from '@opentrons/shared-data/command' -import type { GetCommandTextResult } from '..' +import type { GetTCRunProfileCommandTextResult } from '..' import type { HandlesCommands } from './types' export function getTCRunProfileCommandText({ command, t, -}: HandlesCommands): GetCommandTextResult { +}: HandlesCommands): GetTCRunProfileCommandTextResult { const { profile } = command.params const stepTexts = profile.map( ({ holdSeconds, celsius }: { holdSeconds: number; celsius: number }) => t('tc_run_profile_steps', { celsius, - seconds: holdSeconds, + duration: formatDurationLabeled({ seconds: holdSeconds }), }).trim() ) const startingProfileText = t('tc_starting_profile', { - repetitions: Object.keys(stepTexts).length, + stepCount: Object.keys(stepTexts).length, }) - return { commandText: startingProfileText, stepTexts } + return { + kind: 'thermocycler/runProfile', + commandText: startingProfileText, + stepTexts, + } } diff --git a/app/src/molecules/Command/hooks/useCommandTextString/utils/index.ts b/app/src/molecules/Command/hooks/useCommandTextString/utils/index.ts index ff3ad43fc8c..590824e558d 100644 --- a/app/src/molecules/Command/hooks/useCommandTextString/utils/index.ts +++ b/app/src/molecules/Command/hooks/useCommandTextString/utils/index.ts @@ -1,6 +1,7 @@ export { getLoadCommandText } from './getLoadCommandText' export { getTemperatureCommandText } from './getTemperatureCommandText' export { getTCRunProfileCommandText } from './getTCRunProfileCommandText' +export { getTCRunExtendedProfileCommandText } from './getTCRunExtendedProfileCommandText' export { getHSShakeSpeedCommandText } from './getHSShakeSpeedCommandText' export { getMoveToSlotCommandText } from './getMoveToSlotCommandText' export { getMoveRelativeCommandText } from './getMoveRelativeCommandText' diff --git a/app/src/molecules/InterventionModal/CategorizedStepContent.stories.tsx b/app/src/molecules/InterventionModal/CategorizedStepContent.stories.tsx index 04c04c0f3c6..79d83fd57ef 100644 --- a/app/src/molecules/InterventionModal/CategorizedStepContent.stories.tsx +++ b/app/src/molecules/InterventionModal/CategorizedStepContent.stories.tsx @@ -14,7 +14,7 @@ import type { Meta, StoryObj } from '@storybook/react' type CommandType = RunTimeCommand['commandType'] const availableCommandTypes = uniq( - Fixtures.mockQIASeqTextData.commands.map(command => command.commandType) + Fixtures.mockDoItAllTextData.commands.map(command => command.commandType) ) const commandsByType: Partial> = {} @@ -22,7 +22,7 @@ function commandsOfType(type: CommandType): RunTimeCommand[] { if (type in commandsByType) { return commandsByType[type] } - commandsByType[type] = Fixtures.mockQIASeqTextData.commands.filter( + commandsByType[type] = Fixtures.mockDoItAllTextData.commands.filter( command => command.commandType === type ) return commandsByType[type] @@ -62,22 +62,22 @@ function Wrapper(props: WrapperProps): JSX.Element { const topCommandIndex = topCommand == null ? undefined - : Fixtures.mockQIASeqTextData.commands.indexOf(topCommand) + : Fixtures.mockDoItAllTextData.commands.indexOf(topCommand) const bottomCommand1Index = bottomCommand1 == null ? undefined - : Fixtures.mockQIASeqTextData.commands.indexOf(bottomCommand1) + : Fixtures.mockDoItAllTextData.commands.indexOf(bottomCommand1) const bottomCommand2Index = bottomCommand2 == null ? undefined - : Fixtures.mockQIASeqTextData.commands.indexOf(bottomCommand2) + : Fixtures.mockDoItAllTextData.commands.indexOf(bottomCommand2) return ( { mockMakeToast = vi.fn() vi.mocked(useToaster).mockReturnValue({ makeToast: mockMakeToast } as any) vi.mocked(useCommandTextString).mockReturnValue({ + kind: 'generic', commandText: TEST_COMMAND, }) }) @@ -69,6 +71,7 @@ describe('useRecoveryToasts', () => { it('should make toast with correct parameters for desktop', () => { vi.mocked(useCommandTextString).mockReturnValue({ + kind: 'generic', commandText: TEST_COMMAND, }) @@ -80,8 +83,8 @@ describe('useRecoveryToasts', () => { ) vi.mocked(useCommandTextString).mockReturnValue({ + kind: 'generic', commandText: TEST_COMMAND, - stepTexts: undefined, }) result.current.makeSuccessToast() @@ -120,8 +123,8 @@ describe('useRecoveryToasts', () => { it('should use recoveryToastText when desktopFullCommandText is null', () => { vi.mocked(useCommandTextString).mockReturnValue({ + kind: 'generic', commandText: '', - stepTexts: undefined, }) const { result } = renderHook(() => @@ -196,8 +199,8 @@ describe('getStepNumber', () => { describe('useRecoveryFullCommandText', () => { it('should return the correct command text', () => { vi.mocked(useCommandTextString).mockReturnValue({ + kind: 'generic', commandText: TEST_COMMAND, - stepTexts: undefined, }) const { result } = renderHook(() => @@ -213,8 +216,8 @@ describe('useRecoveryFullCommandText', () => { it('should return null when relevantCmd is null', () => { vi.mocked(useCommandTextString).mockReturnValue({ + kind: 'generic', commandText: '', - stepTexts: undefined, }) const { result } = renderHook(() => @@ -242,6 +245,7 @@ describe('useRecoveryFullCommandText', () => { it('should truncate TC command', () => { vi.mocked(useCommandTextString).mockReturnValue({ + kind: 'thermocycler/runProfile', commandText: TC_COMMAND, stepTexts: ['step'], }) @@ -255,7 +259,25 @@ describe('useRecoveryFullCommandText', () => { } as any, }) ) + expect(result.current).toBe('tc starting profile of 1231231 element steps') + }) - expect(result.current).toBe('tc command cycle') + it('should truncate new TC command', () => { + vi.mocked(useCommandTextString).mockReturnValue({ + kind: 'thermocycler/runExtendedProfile', + commandText: TC_COMMAND, + profileElementTexts: [{ kind: 'step', stepText: 'blah blah blah' }], + }) + + const { result } = renderHook(() => + useRecoveryFullCommandText({ + robotType: FLEX_ROBOT_TYPE, + stepNumber: 0, + commandTextData: { + commands: [TC_COMMAND], + } as any, + }) + ) + expect(result.current).toBe('tc starting profile of 1231231 element steps') }) }) diff --git a/app/src/organisms/ErrorRecoveryFlows/hooks/useRecoveryToasts.ts b/app/src/organisms/ErrorRecoveryFlows/hooks/useRecoveryToasts.ts index ff530c5fdb0..ed5aaaeaae5 100644 --- a/app/src/organisms/ErrorRecoveryFlows/hooks/useRecoveryToasts.ts +++ b/app/src/organisms/ErrorRecoveryFlows/hooks/useRecoveryToasts.ts @@ -105,7 +105,7 @@ export function useRecoveryFullCommandText( const relevantCmdIdx = typeof stepNumber === 'number' ? stepNumber : -1 const relevantCmd = commandTextData?.commands[relevantCmdIdx] ?? null - const { commandText, stepTexts } = useCommandTextString({ + const { commandText, kind } = useCommandTextString({ ...props, command: relevantCmd, }) @@ -117,7 +117,12 @@ export function useRecoveryFullCommandText( else if (relevantCmd === null) { return null } else { - return truncateIfTCCommand(commandText, stepTexts != null) + return truncateIfTCCommand( + commandText, + ['thermocycler/runProfile', 'thermocycler/runExtendedProfile'].includes( + kind + ) + ) } } @@ -164,17 +169,20 @@ function handleRecoveryOptionAction( } // Special case the TC text, so it make sense in a success toast. -function truncateIfTCCommand(commandText: string, isTCText: boolean): string { - if (isTCText) { - const indexOfCycle = commandText.indexOf('cycle') - - if (indexOfCycle === -1) { +function truncateIfTCCommand( + commandText: string, + isTCCommand: boolean +): string { + if (isTCCommand) { + const indexOfProfile = commandText.indexOf('steps') + + if (indexOfProfile === -1) { console.warn( 'TC cycle text has changed. Update Error Recovery TC text utility.' ) } - return commandText.slice(0, indexOfCycle + 5) // +5 to include "cycle" + return commandText.slice(0, indexOfProfile + 5) // +5 to include "steps" } else { return commandText } diff --git a/app/src/transformations/commands/transformations/__tests__/formatDuration.test.tsx b/app/src/transformations/commands/transformations/__tests__/formatDuration.test.tsx index 21ffb0f565b..fa6c3a954d2 100644 --- a/app/src/transformations/commands/transformations/__tests__/formatDuration.test.tsx +++ b/app/src/transformations/commands/transformations/__tests__/formatDuration.test.tsx @@ -1,5 +1,5 @@ import { describe, it, expect } from 'vitest' -import { formatDuration } from '../formatDuration' +import { formatDuration, formatDurationLabeled } from '../formatDuration' describe('formatDuration', () => { it('should format a duration', () => { @@ -36,4 +36,57 @@ describe('formatDuration', () => { expect(formatDuration(duration)).toEqual(expected) }) + + it('should format a non-normalized duration', () => { + const duration = { + seconds: 360002, + } + const expected = '100:00:02' + expect(formatDuration(duration)).toEqual(expected) + }) +}) + +describe('formatDurationLabeled', () => { + it('should format a duration', () => { + const duration = { + hours: 2, + minutes: 40, + seconds: 2, + } + + const expected = '2h 40m 02s' + + expect(formatDurationLabeled(duration)).toEqual(expected) + }) + + it('should format a short duration with plenty of zeroes', () => { + const duration = { + seconds: 2, + } + + const expected = '0h 00m 02s' + + expect(formatDurationLabeled(duration)).toEqual(expected) + }) + + it('should format a longer duration', () => { + const duration = { + days: 3, + hours: 2, + minutes: 40, + seconds: 2, + } + + const expected = '74h 40m 02s' + + expect(formatDurationLabeled(duration)).toEqual(expected) + }) + + it('should format a non-normalized duration', () => { + const duration = { + seconds: 360002, + } + const expected = '100h 00m 02s' + expect(formatDurationLabeled(duration)).toEqual(expected) + }) }) diff --git a/app/src/transformations/commands/transformations/formatDuration.ts b/app/src/transformations/commands/transformations/formatDuration.ts index f744d9dba5d..1bef1591874 100644 --- a/app/src/transformations/commands/transformations/formatDuration.ts +++ b/app/src/transformations/commands/transformations/formatDuration.ts @@ -6,14 +6,39 @@ import type { Duration } from 'date-fns' * @returns string in format hh:mm:ss, e.g. 03:15:45 */ export function formatDuration(duration: Duration): string { - const { days, hours, minutes, seconds } = duration + const { hours, minutes, seconds } = timestampDetails(duration) - // edge case: protocol runs (or is paused) for over 24 hours - const hoursWithDays = days != null ? days * 24 + (hours ?? 0) : hours + return `${hours}:${minutes}:${seconds}` +} + +export function formatDurationLabeled(duration: Duration): string { + const { hours, minutes, seconds } = timestampDetails(duration, 1) + + return `${hours}h ${minutes}m ${seconds}s` +} + +function timestampDetails( + duration: Duration, + padHoursTo?: number +): { hours: string; minutes: string; seconds: string } { + const paddingWithDefault = padHoursTo ?? 2 + const days = duration?.days ?? 0 + const hours = duration?.hours ?? 0 + const minutes = duration?.minutes ?? 0 + const seconds = duration?.seconds ?? 0 + + const totalSeconds = seconds + minutes * 60 + hours * 3600 + days * 24 * 3600 - const paddedHours = padStart(hoursWithDays?.toString(), 2, '0') - const paddedMinutes = padStart(minutes?.toString(), 2, '0') - const paddedSeconds = padStart(seconds?.toString(), 2, '0') + const normalizedHours = Math.floor(totalSeconds / 3600) + const normalizedMinutes = Math.floor((totalSeconds % 3600) / 60) + const normalizedSeconds = totalSeconds % 60 - return `${paddedHours}:${paddedMinutes}:${paddedSeconds}` + const paddedHours = padStart( + normalizedHours.toString(), + paddingWithDefault, + '0' + ) + const paddedMinutes = padStart(normalizedMinutes.toString(), 2, '0') + const paddedSeconds = padStart(normalizedSeconds.toString(), 2, '0') + return { hours: paddedHours, minutes: paddedMinutes, seconds: paddedSeconds } } diff --git a/shared-data/command/schemas/10.json b/shared-data/command/schemas/10.json index 07afff241a1..6eb524b9a45 100644 --- a/shared-data/command/schemas/10.json +++ b/shared-data/command/schemas/10.json @@ -63,6 +63,7 @@ "thermocycler/openLid": "#/definitions/opentrons__protocol_engine__commands__thermocycler__open_lid__OpenLidCreate", "thermocycler/closeLid": "#/definitions/opentrons__protocol_engine__commands__thermocycler__close_lid__CloseLidCreate", "thermocycler/runProfile": "#/definitions/RunProfileCreate", + "thermocycler/runExtendedProfile": "#/definitions/RunExtendedProfileCreate", "absorbanceReader/closeLid": "#/definitions/opentrons__protocol_engine__commands__absorbance_reader__close_lid__CloseLidCreate", "absorbanceReader/openLid": "#/definitions/opentrons__protocol_engine__commands__absorbance_reader__open_lid__OpenLidCreate", "absorbanceReader/initialize": "#/definitions/InitializeCreate", @@ -253,6 +254,9 @@ { "$ref": "#/definitions/RunProfileCreate" }, + { + "$ref": "#/definitions/RunExtendedProfileCreate" + }, { "$ref": "#/definitions/opentrons__protocol_engine__commands__absorbance_reader__close_lid__CloseLidCreate" }, @@ -3911,6 +3915,108 @@ }, "required": ["params"] }, + "ProfileStep": { + "title": "ProfileStep", + "description": "An individual step in a Thermocycler extended profile.", + "type": "object", + "properties": { + "celsius": { + "title": "Celsius", + "description": "Target temperature in \u00b0C.", + "type": "number" + }, + "holdSeconds": { + "title": "Holdseconds", + "description": "Time to hold target temperature in seconds.", + "type": "number" + } + }, + "required": ["celsius", "holdSeconds"] + }, + "ProfileCycle": { + "title": "ProfileCycle", + "description": "An individual cycle in a Thermocycler extended profile.", + "type": "object", + "properties": { + "steps": { + "title": "Steps", + "description": "Steps to repeat.", + "type": "array", + "items": { + "$ref": "#/definitions/ProfileStep" + } + }, + "repetitions": { + "title": "Repetitions", + "description": "Number of times to repeat the steps.", + "type": "integer" + } + }, + "required": ["steps", "repetitions"] + }, + "RunExtendedProfileParams": { + "title": "RunExtendedProfileParams", + "description": "Input parameters for an individual Thermocycler profile step.", + "type": "object", + "properties": { + "moduleId": { + "title": "Moduleid", + "description": "Unique ID of the Thermocycler.", + "type": "string" + }, + "profileElements": { + "title": "Profileelements", + "description": "Elements of the profile. Each can be either a step or a cycle.", + "type": "array", + "items": { + "anyOf": [ + { + "$ref": "#/definitions/ProfileStep" + }, + { + "$ref": "#/definitions/ProfileCycle" + } + ] + } + }, + "blockMaxVolumeUl": { + "title": "Blockmaxvolumeul", + "description": "Amount of liquid in uL of the most-full well in labware loaded onto the thermocycler.", + "type": "number" + } + }, + "required": ["moduleId", "profileElements"] + }, + "RunExtendedProfileCreate": { + "title": "RunExtendedProfileCreate", + "description": "A request to execute a Thermocycler profile run.", + "type": "object", + "properties": { + "commandType": { + "title": "Commandtype", + "default": "thermocycler/runExtendedProfile", + "enum": ["thermocycler/runExtendedProfile"], + "type": "string" + }, + "params": { + "$ref": "#/definitions/RunExtendedProfileParams" + }, + "intent": { + "description": "The reason the command was added. If not specified or `protocol`, the command will be treated as part of the protocol run itself, and added to the end of the existing command queue.\n\nIf `setup`, the command will be treated as part of run setup. A setup command may only be enqueued if the run has not started.\n\nUse setup commands for activities like pre-run calibration checks and module setup, like pre-heating.", + "allOf": [ + { + "$ref": "#/definitions/CommandIntent" + } + ] + }, + "key": { + "title": "Key", + "description": "A key value, unique in this run, that can be used to track the same logical command across multiple runs of the same protocol. If a value is not provided, one will be generated.", + "type": "string" + } + }, + "required": ["params"] + }, "opentrons__protocol_engine__commands__absorbance_reader__close_lid__CloseLidParams": { "title": "CloseLidParams", "description": "Input parameters to close the lid on an absorbance reading.", diff --git a/shared-data/command/types/module.ts b/shared-data/command/types/module.ts index ff2787bfa25..b0df1ae6b6b 100644 --- a/shared-data/command/types/module.ts +++ b/shared-data/command/types/module.ts @@ -15,6 +15,7 @@ export type ModuleRunTimeCommand = | TCDeactivateBlockRunTimeCommand | TCDeactivateLidRunTimeCommand | TCRunProfileRunTimeCommand + | TCRunExtendedProfileRunTimeCommand | TCAwaitProfileCompleteRunTimeCommand | HeaterShakerSetTargetTemperatureRunTimeCommand | HeaterShakerWaitForTemperatureRunTimeCommand @@ -39,6 +40,7 @@ export type ModuleCreateCommand = | TCDeactivateBlockCreateCommand | TCDeactivateLidCreateCommand | TCRunProfileCreateCommand + | TCRunExtendedProfileCreateCommand | TCAwaitProfileCompleteCreateCommand | HeaterShakerWaitForTemperatureCreateCommand | HeaterShakerSetAndWaitForShakeSpeedCreateCommand @@ -189,6 +191,16 @@ export interface TCRunProfileRunTimeCommand TCRunProfileCreateCommand { result?: any } +export interface TCRunExtendedProfileCreateCommand + extends CommonCommandCreateInfo { + commandType: 'thermocycler/runExtendedProfile' + params: TCExtendedProfileParams +} +export interface TCRunExtendedProfileRunTimeCommand + extends CommonCommandRunTimeInfo, + TCRunExtendedProfileCreateCommand { + result?: any +} export interface TCAwaitProfileCompleteCreateCommand extends CommonCommandCreateInfo { commandType: 'thermocycler/awaitProfileComplete' @@ -305,3 +317,14 @@ export interface ThermocyclerSetTargetBlockTemperatureParams { volume?: number holdTimeSeconds?: number } + +export interface TCProfileCycle { + steps: AtomicProfileStep[] + repetitions: number +} + +export interface TCExtendedProfileParams { + moduleId: string + profileElements: Array + blockMaxVolumeUl?: number +} From f8608fd3688bfd2906876e07418093e89a92abc9 Mon Sep 17 00:00:00 2001 From: Max Marrone Date: Tue, 8 Oct 2024 09:54:57 -0400 Subject: [PATCH 19/27] feat(api-client): Add bindings for `/errorRecovery/settings` endpoints (#16427) --- api-client/src/errorRecovery/index.ts | 1 + .../settings/getErrorRecoverySettings.ts | 16 +++++++++++++++ .../src/errorRecovery/settings/index.ts | 3 +++ .../src/errorRecovery/settings/types.ts | 9 +++++++++ .../settings/updateErrorRecoverySettings.ts | 20 +++++++++++++++++++ api-client/src/index.ts | 1 + 6 files changed, 50 insertions(+) create mode 100644 api-client/src/errorRecovery/index.ts create mode 100644 api-client/src/errorRecovery/settings/getErrorRecoverySettings.ts create mode 100644 api-client/src/errorRecovery/settings/index.ts create mode 100644 api-client/src/errorRecovery/settings/types.ts create mode 100644 api-client/src/errorRecovery/settings/updateErrorRecoverySettings.ts diff --git a/api-client/src/errorRecovery/index.ts b/api-client/src/errorRecovery/index.ts new file mode 100644 index 00000000000..eca32dd0aef --- /dev/null +++ b/api-client/src/errorRecovery/index.ts @@ -0,0 +1 @@ +export * from './settings' diff --git a/api-client/src/errorRecovery/settings/getErrorRecoverySettings.ts b/api-client/src/errorRecovery/settings/getErrorRecoverySettings.ts new file mode 100644 index 00000000000..30a3b9f6aa1 --- /dev/null +++ b/api-client/src/errorRecovery/settings/getErrorRecoverySettings.ts @@ -0,0 +1,16 @@ +import { GET, request } from '../../request' + +import type { ResponsePromise } from '../../request' +import type { HostConfig } from '../../types' +import type { ErrorRecoverySettingsResponse } from './types' + +export function getErrorRecoverySettings( + config: HostConfig +): ResponsePromise { + return request( + GET, + '/errorRecovery/settings', + null, + config + ) +} diff --git a/api-client/src/errorRecovery/settings/index.ts b/api-client/src/errorRecovery/settings/index.ts new file mode 100644 index 00000000000..7f33c4c0069 --- /dev/null +++ b/api-client/src/errorRecovery/settings/index.ts @@ -0,0 +1,3 @@ +export { getErrorRecoverySettings } from './getErrorRecoverySettings' +export { updateErrorRecoverySettings } from './updateErrorRecoverySettings' +export * from './types' diff --git a/api-client/src/errorRecovery/settings/types.ts b/api-client/src/errorRecovery/settings/types.ts new file mode 100644 index 00000000000..d427ab88714 --- /dev/null +++ b/api-client/src/errorRecovery/settings/types.ts @@ -0,0 +1,9 @@ +export interface ErrorRecoverySettingsResponse { + data: { + enabled: boolean + } +} + +export interface ErrorRecoverySettingsRequest { + data: Partial +} diff --git a/api-client/src/errorRecovery/settings/updateErrorRecoverySettings.ts b/api-client/src/errorRecovery/settings/updateErrorRecoverySettings.ts new file mode 100644 index 00000000000..e5d1acf29aa --- /dev/null +++ b/api-client/src/errorRecovery/settings/updateErrorRecoverySettings.ts @@ -0,0 +1,20 @@ +import { PATCH, request } from '../../request' + +import type { ResponsePromise } from '../../request' +import type { HostConfig } from '../../types' +import type { + ErrorRecoverySettingsRequest, + ErrorRecoverySettingsResponse, +} from './types' + +export function updateErrorRecoverySettings( + config: HostConfig, + settings: ErrorRecoverySettingsRequest +): ResponsePromise { + return request( + PATCH, + '/errorRecovery/settings', + settings, + config + ) +} diff --git a/api-client/src/index.ts b/api-client/src/index.ts index 858772034ab..ade46aeee7f 100644 --- a/api-client/src/index.ts +++ b/api-client/src/index.ts @@ -3,6 +3,7 @@ export * from './calibration' export * from './client_data' export * from './dataFiles' export * from './deck_configuration' +export * from './errorRecovery' export * from './health' export * from './instruments' export * from './maintenance_runs' From 44aa75786c0b3e7e44e75c3f8c12925c234dd902 Mon Sep 17 00:00:00 2001 From: Josh McVey Date: Tue, 8 Oct 2024 09:23:39 -0500 Subject: [PATCH 20/27] chore(abt): upgrade python to 3.13 and upgrade dependencies on analyses battery (#16430) # Overview Upgrade python and dependencies on the analysis battery test. ## Checks - [x] Works locally - [x] CI lint works - [x] CI test works --- .github/workflows/analyses-snapshot-lint.yaml | 2 +- .github/workflows/analyses-snapshot-test.yaml | 12 +- analyses-snapshot-testing/Pipfile | 24 +- analyses-snapshot-testing/Pipfile.lock | 657 +++++++++--------- analyses-snapshot-testing/pyproject.toml | 4 +- 5 files changed, 330 insertions(+), 369 deletions(-) diff --git a/.github/workflows/analyses-snapshot-lint.yaml b/.github/workflows/analyses-snapshot-lint.yaml index 90724f3c7a2..17e13e30868 100644 --- a/.github/workflows/analyses-snapshot-lint.yaml +++ b/.github/workflows/analyses-snapshot-lint.yaml @@ -27,7 +27,7 @@ jobs: - name: Setup Python uses: 'actions/setup-python@v5' with: - python-version: '3.12' + python-version: '3.13.0-rc.3' cache: 'pipenv' cache-dependency-path: analyses-snapshot-testing/Pipfile.lock - name: Setup diff --git a/.github/workflows/analyses-snapshot-test.yaml b/.github/workflows/analyses-snapshot-test.yaml index 26576899188..7770db0d286 100644 --- a/.github/workflows/analyses-snapshot-test.yaml +++ b/.github/workflows/analyses-snapshot-test.yaml @@ -48,8 +48,8 @@ jobs: ANALYSIS_REF: ${{ github.event.inputs.ANALYSIS_REF || github.head_ref || 'edge' }} SNAPSHOT_REF: ${{ github.event.inputs.SNAPSHOT_REF || github.head_ref || 'edge' }} # If we're running because of workflow_dispatch, use the user input to decide - # whether to open a PR on failure. Otherwise, there is no user input, so always - # open a PR on failure. + # whether to open a PR on failure. Otherwise, there is no user input, + # so we only open a PR if the PR has the label 'gen-analyses-snapshot-pr' OPEN_PR_ON_FAILURE: ${{ (github.event_name == 'workflow_dispatch' && github.events.inputs.OPEN_PR_ON_FAILURE) || ((github.event_name != 'workflow_dispatch') && (contains(github.event.pull_request.labels.*.name, 'gen-analyses-snapshot-pr'))) }} PR_TARGET_BRANCH: ${{ github.event.pull_request.base.ref || 'not a pr'}} steps: @@ -75,10 +75,10 @@ jobs: working-directory: analyses-snapshot-testing run: make build-opentrons-analysis - - name: Set up Python 3.12 + - name: Set up Python 3.13 uses: actions/setup-python@v5 with: - python-version: '3.12' + python-version: '3.13.0-rc.3' cache: 'pipenv' cache-dependency-path: analyses-snapshot-testing/Pipfile.lock @@ -107,7 +107,7 @@ jobs: - name: Create Snapshot update Request id: create_pull_request if: always() && steps.handle_failure.outcome == 'success' && env.OPEN_PR_ON_FAILURE == 'true' && github.event_name == 'pull_request' - uses: peter-evans/create-pull-request@v6 + uses: peter-evans/create-pull-request@v7 with: commit-message: 'fix(analyses-snapshot-testing): heal analyses snapshots' title: 'fix(analyses-snapshot-testing): heal ${{ env.ANALYSIS_REF }} snapshots' @@ -130,7 +130,7 @@ jobs: - name: Create Snapshot update Request on edge overnight failure if: always() && steps.handle_failure.outcome == 'success' && github.event_name == 'schedule' - uses: peter-evans/create-pull-request@v6 + uses: peter-evans/create-pull-request@v7 with: # scheduled run uses the default values for ANALYSIS_REF and SNAPSHOT_REF which are edge commit-message: 'fix(analyses-snapshot-testing): heal ${{ env.ANALYSIS_REF }} snapshots' title: 'fix(analyses-snapshot-testing): heal ${{ env.ANALYSIS_REF }} snapshots' diff --git a/analyses-snapshot-testing/Pipfile b/analyses-snapshot-testing/Pipfile index 43bb4dd2475..85a1d29c337 100644 --- a/analyses-snapshot-testing/Pipfile +++ b/analyses-snapshot-testing/Pipfile @@ -4,20 +4,18 @@ url = "https://pypi.org/simple" verify_ssl = true [packages] -pytest = "==8.1.1" -black = "==24.3.0" -selenium = "==4.19.0" -importlib-metadata = "==7.1.0" -requests = "==2.31.0" +pytest = "==8.3.3" +black = "==24.10.0" +importlib-metadata = "==8.5.0" +httpx = "==0.27.2" python-dotenv = "==1.0.1" -mypy = "==1.9.0" -types-requests = "==2.31.0.20240311" -rich = "==13.7.1" -pydantic = "==2.6.4" -ruff = "==0.3.4" -docker = "==7.0.0" -syrupy = "==4.6.1" +mypy = "==1.11.2" +rich = "==13.9.2" +pydantic = "==2.9.2" +ruff = "==0.6.9" +docker = "==7.1.0" +syrupy = "==4.7.2" pytest-html = "==4.1.1" [requires] -python_version = "3.12" +python_version = "3.13" diff --git a/analyses-snapshot-testing/Pipfile.lock b/analyses-snapshot-testing/Pipfile.lock index 0672556f9cd..648d065049c 100644 --- a/analyses-snapshot-testing/Pipfile.lock +++ b/analyses-snapshot-testing/Pipfile.lock @@ -1,11 +1,11 @@ { "_meta": { "hash": { - "sha256": "b7ac4510c6e3aa343c669e1bd838183e905abb6f1701c6efbfb1c22f20cfae44" + "sha256": "6657134003c472f3e25e7c91a6b1f46eb8231b4518c18c90c6353bcf2666923e" }, "pipfile-spec": 6, "requires": { - "python_version": "3.12" + "python_version": "3.13" }, "sources": [ { @@ -18,56 +18,56 @@ "default": { "annotated-types": { "hashes": [ - "sha256:0641064de18ba7a25dee8f96403ebc39113d0cb953a01429249d5c7564666a43", - "sha256:563339e807e53ffd9c267e99fc6d9ea23eb8443c08f112651963e24e22f84a5d" + "sha256:1f02e8b43a8fbbc3f3e0d4f0f4bfc8131bcb4eebe8849b8e5c773f3a1c582a53", + "sha256:aff07c09a53a08bc8cfccb9c85b05f1aa9a2a6f23728d790723543408344ce89" ], "markers": "python_version >= '3.8'", - "version": "==0.6.0" + "version": "==0.7.0" }, - "attrs": { + "anyio": { "hashes": [ - "sha256:935dc3b529c262f6cf76e50877d35a4bd3c1de194fd41f47a2b7ae8f19971f30", - "sha256:99b87a485a5820b23b879f04c2305b44b951b502fd64be915879d77a7e8fc6f1" + "sha256:137b4559cbb034c477165047febb6ff83f390fc3b20bf181c1fc0a728cb8beeb", + "sha256:c7d2e9d63e31599eeb636c8c5c03a7e108d73b345f064f1c19fdc87b79036a9a" ], - 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+target-version = ['py313'] [tool.ruff] # Like Black line-length = 140 # Like Black indent-width = 4 -target-version = "py312" +target-version = "py313" exclude = ["files"] src = ["*.py", "automation", "tests", "citools"] From 7e39d06092e166fad8dd1d3270a1d4f4b968bd9c Mon Sep 17 00:00:00 2001 From: koji Date: Tue, 8 Oct 2024 11:29:59 -0400 Subject: [PATCH 21/27] fix(protocol-designer): fix pipette info card in protocol overview (#16429) * fix(protocol-designer): fix pipette info card in protocol overview --- .../ProtocolOverview/InstrumentsInfo.tsx | 130 ++++++++++++++++++ .../__tests__/InstrumentsInfo.test.tsx | 106 ++++++++++++++ .../__tests__/ProtocolOverview.test.tsx | 16 ++- .../src/pages/ProtocolOverview/index.tsx | 83 ++--------- 4 files changed, 254 insertions(+), 81 deletions(-) create mode 100644 protocol-designer/src/pages/ProtocolOverview/InstrumentsInfo.tsx create mode 100644 protocol-designer/src/pages/ProtocolOverview/__tests__/InstrumentsInfo.test.tsx diff --git a/protocol-designer/src/pages/ProtocolOverview/InstrumentsInfo.tsx b/protocol-designer/src/pages/ProtocolOverview/InstrumentsInfo.tsx new file mode 100644 index 00000000000..e87b6550904 --- /dev/null +++ b/protocol-designer/src/pages/ProtocolOverview/InstrumentsInfo.tsx @@ -0,0 +1,130 @@ +import { useTranslation } from 'react-i18next' + +import { + Flex, + StyledText, + Btn, + DIRECTION_COLUMN, + SPACING, + JUSTIFY_SPACE_BETWEEN, + TYPOGRAPHY, + ListItem, + ListItemDescriptor, +} from '@opentrons/components' +import { getPipetteSpecsV2, FLEX_ROBOT_TYPE } from '@opentrons/shared-data' + +import { BUTTON_LINK_STYLE } from '../../atoms' + +import type { PipetteName, RobotType } from '@opentrons/shared-data' +import type { AdditionalEquipmentEntities } from '@opentrons/step-generation' +import type { PipetteOnDeck } from '../../step-forms' + +interface InstrumentsInfoProps { + robotType: RobotType + pipettesOnDeck: PipetteOnDeck[] + additionalEquipment: AdditionalEquipmentEntities + setShowEditInstrumentsModal: (showEditInstrumentsModal: boolean) => void +} + +export function InstrumentsInfo({ + robotType, + pipettesOnDeck, + additionalEquipment, + setShowEditInstrumentsModal, +}: InstrumentsInfoProps): JSX.Element { + const { t } = useTranslation(['protocol_overview', 'shared']) + const leftPipette = pipettesOnDeck.find(pipette => pipette.mount === 'left') + const rightPipette = pipettesOnDeck.find(pipette => pipette.mount === 'right') + const isGripperAttached = Object.values(additionalEquipment).some( + equipment => equipment?.name === 'gripper' + ) + + const pipetteInfo = (pipette?: PipetteOnDeck): JSX.Element | string => { + const pipetteName = + pipette != null + ? getPipetteSpecsV2(pipette.name as PipetteName)?.displayName + : t('na') + const tipsInfo = pipette?.tiprackLabwareDef + ? pipette.tiprackLabwareDef.map(labware => labware.metadata.displayName) + : t('na') + + if (pipetteName === t('na') || tipsInfo === t('na')) { + return t('na') + } + + return ( + + {pipetteName} + {pipette != null && pipette.tiprackLabwareDef.length > 0 + ? pipette?.tiprackLabwareDef.map(labware => ( + + {labware.metadata.displayName} + + )) + : null} + + ) + } + + return ( + + + + {t('instruments')} + + + { + setShowEditInstrumentsModal(true) + }} + css={BUTTON_LINK_STYLE} + > + + {t('edit')} + + + + + + + + + + + + + + + {robotType === FLEX_ROBOT_TYPE ? ( + + + + ) : null} + + + ) +} diff --git a/protocol-designer/src/pages/ProtocolOverview/__tests__/InstrumentsInfo.test.tsx b/protocol-designer/src/pages/ProtocolOverview/__tests__/InstrumentsInfo.test.tsx new file mode 100644 index 00000000000..d982027d9fc --- /dev/null +++ b/protocol-designer/src/pages/ProtocolOverview/__tests__/InstrumentsInfo.test.tsx @@ -0,0 +1,106 @@ +import { describe, it, vi, beforeEach, expect } from 'vitest' +import { fireEvent, screen } from '@testing-library/react' + +import { FLEX_ROBOT_TYPE } from '@opentrons/shared-data' + +import { renderWithProviders } from '../../../__testing-utils__' +import { i18n } from '../../../assets/localization' +import { InstrumentsInfo } from '../InstrumentsInfo' + +import type { ComponentProps } from 'react' +import type { AdditionalEquipmentEntities } from '@opentrons/step-generation' +import type { PipetteOnDeck } from '../../../step-forms' + +const mockSetShowEditInstrumentsModal = vi.fn() +const mockPipettes = [ + { + mount: 'left', + id: 'mock-left', + name: 'p50_single_flex', + tiprackDefURI: ['opentrons/opentrons_flex_96_tiprack_50ul/1'], + tiprackLabwareDef: [ + { + metadata: { + displayName: 'Opentrons Flex 96 Tip Rack 50 µL', + displayCategory: 'tipRack', + displayVolumeUnits: 'µL', + tags: [], + }, + } as any, + ], + } as PipetteOnDeck, + { + mount: 'right', + id: 'mock-right', + name: 'p50_multi_flex', + tiprackDefURI: ['opentrons/opentrons_flex_96_filtertiprack_50ul/1'], + tiprackLabwareDef: [ + { + metadata: { + displayName: 'Opentrons Flex 96 Filter Tip Rack 50 µL', + displayCategory: 'tipRack', + displayVolumeUnits: 'µL', + tags: [], + }, + } as any, + ], + } as PipetteOnDeck, +] + +const mockAdditionalEquipment = { + 'mock:gripper': { + name: 'gripper', + id: 'mock:gripper', + }, +} as AdditionalEquipmentEntities + +const render = (props: ComponentProps) => { + return renderWithProviders(, { + i18nInstance: i18n, + }) +} + +describe('InstrumentsInfo', () => { + let props: ComponentProps + + beforeEach(() => { + props = { + robotType: FLEX_ROBOT_TYPE, + pipettesOnDeck: [], + additionalEquipment: {}, + setShowEditInstrumentsModal: mockSetShowEditInstrumentsModal, + } + }) + + it('should render text', () => { + render(props) + screen.getByText('Instruments') + screen.getByText('Robot type') + screen.getAllByText('Opentrons Flex') + screen.getByText('Left pipette') + screen.getByText('Right pipette') + screen.getByText('Extension mount') + expect(screen.getAllByText('N/A').length).toBe(3) + }) + + it('should render instruments info', () => { + props = { + ...props, + pipettesOnDeck: mockPipettes, + additionalEquipment: mockAdditionalEquipment, + } + render(props) + + screen.getByText('Flex 1-Channel 50 μL') + screen.getByText('Opentrons Flex 96 Tip Rack 50 µL') + screen.getByText('Flex 8-Channel 50 μL') + screen.getByText('Opentrons Flex 96 Filter Tip Rack 50 µL') + screen.getByText('Opentrons Flex Gripper') + }) + + it('should call mock function when clicking edit text button', () => { + render(props) + fireEvent.click(screen.getByText('Edit')) + expect(mockSetShowEditInstrumentsModal).toHaveBeenCalled() + }) +}) diff --git a/protocol-designer/src/pages/ProtocolOverview/__tests__/ProtocolOverview.test.tsx b/protocol-designer/src/pages/ProtocolOverview/__tests__/ProtocolOverview.test.tsx index 471898802f6..1ee9718966b 100644 --- a/protocol-designer/src/pages/ProtocolOverview/__tests__/ProtocolOverview.test.tsx +++ b/protocol-designer/src/pages/ProtocolOverview/__tests__/ProtocolOverview.test.tsx @@ -16,6 +16,7 @@ import { selectors as labwareIngredSelectors } from '../../../labware-ingred/sel import { ProtocolOverview } from '../index' import { DeckThumbnail } from '../DeckThumbnail' import { OffDeckThumbnail } from '../OffdeckThumbnail' +import { InstrumentsInfo } from '../InstrumentsInfo' import { LiquidDefinitions } from '../LiquidDefinitions' import type { NavigateFunction } from 'react-router-dom' @@ -29,6 +30,7 @@ vi.mock('../../../labware-ingred/selectors') vi.mock('../../../organisms') vi.mock('../../../labware-ingred/selectors') vi.mock('../LiquidDefinitions') +vi.mock('../InstrumentsInfo') const mockNavigate = vi.fn() @@ -78,6 +80,7 @@ describe('ProtocolOverview', () => { vi.mocked(LiquidDefinitions).mockReturnValue(
    mock LiquidDefinitions
    ) + vi.mocked(InstrumentsInfo).mockReturnValue(
    mock InstrumentsInfo
    ) }) it('renders each section with text', () => { @@ -99,15 +102,13 @@ describe('ProtocolOverview', () => { screen.getByText('Last exported') screen.getByText('Required app version') screen.getByText('8.0.0 or higher') + // instruments - screen.getByText('Instruments') - screen.getByText('Robot type') - screen.getAllByText('Opentrons Flex') - screen.getByText('Left pipette') - screen.getByText('Right pipette') - screen.getByText('Extension mount') + screen.getByText('mock InstrumentsInfo') + // liquids screen.getByText('mock LiquidDefinitions') + // steps screen.getByText('Protocol steps') }) @@ -126,7 +127,8 @@ describe('ProtocolOverview', () => { description: undefined, }) render() - expect(screen.getAllByText('N/A').length).toBe(7) + // ToDo (kk: 2024/10/07) this part should be replaced + expect(screen.getAllByText('N/A').length).toBe(4) }) it('navigates to starting deck state', () => { diff --git a/protocol-designer/src/pages/ProtocolOverview/index.tsx b/protocol-designer/src/pages/ProtocolOverview/index.tsx index 0009f4cf624..9a8dd1b4f4b 100644 --- a/protocol-designer/src/pages/ProtocolOverview/index.tsx +++ b/protocol-designer/src/pages/ProtocolOverview/index.tsx @@ -27,11 +27,7 @@ import { ToggleGroup, TYPOGRAPHY, } from '@opentrons/components' -import { - getPipetteSpecsV2, - FLEX_ROBOT_TYPE, - OT2_ROBOT_TYPE, -} from '@opentrons/shared-data' +import { OT2_ROBOT_TYPE } from '@opentrons/shared-data' import { getAdditionalEquipmentEntities, @@ -57,9 +53,10 @@ import { import { DeckThumbnail } from './DeckThumbnail' import { OffDeckThumbnail } from './OffdeckThumbnail' import { getWarningContent } from './UnusedModalContent' +import { InstrumentsInfo } from './InstrumentsInfo' import { LiquidDefinitions } from './LiquidDefinitions' -import type { CreateCommand, PipetteName } from '@opentrons/shared-data' +import type { CreateCommand } from '@opentrons/shared-data' import type { DeckSlot } from '@opentrons/step-generation' import type { ThunkDispatch } from '../../types' @@ -181,8 +178,6 @@ export function ProtocolOverview(): JSX.Element { } const pipettesOnDeck = Object.values(pipettes) - const leftPip = pipettesOnDeck.find(pip => pip.mount === 'left') - const rightPip = pipettesOnDeck.find(pip => pip.mount === 'right') const { protocolName, description, @@ -384,72 +379,12 @@ export function ProtocolOverview(): JSX.Element { - - - - {t('instruments')} - - - { - setShowEditInstrumentsModal(true) - }} - css={BUTTON_LINK_STYLE} - > - - {t('edit')} - - - - - - - - - - - - - - - {robotType === FLEX_ROBOT_TYPE ? ( - - - - ) : null} - - + From 6869198be24f46608cb513b86204ea5cf213e870 Mon Sep 17 00:00:00 2001 From: Josh McVey Date: Tue, 8 Oct 2024 14:09:30 -0500 Subject: [PATCH 22/27] feat(abt): speed up analyses battery with async analysis (#16431) # Overview Remove cruft from `generate_analyses.py` and analyze against `n` containers in a ThreadPoolExecutor. - [x] Works locally - [x] Works in CI --- .../citools/generate_analyses.py | 312 ++++++------------ .../citools/write_failed_analysis.py | 0 2 files changed, 105 insertions(+), 207 deletions(-) delete mode 100644 analyses-snapshot-testing/citools/write_failed_analysis.py diff --git a/analyses-snapshot-testing/citools/generate_analyses.py b/analyses-snapshot-testing/citools/generate_analyses.py index f1335b102ae..f67d0394429 100644 --- a/analyses-snapshot-testing/citools/generate_analyses.py +++ b/analyses-snapshot-testing/citools/generate_analyses.py @@ -1,13 +1,13 @@ +import concurrent import json import os -import signal import time -from contextlib import contextmanager +from concurrent.futures import ThreadPoolExecutor from dataclasses import dataclass from datetime import datetime, timezone from enum import Enum, auto from pathlib import Path -from typing import Any, Dict, Generator, List, Optional +from typing import Any, Dict, List, Optional import docker # type: ignore from automation.data.protocol import Protocol @@ -15,31 +15,22 @@ from rich.traceback import install install(show_locals=True) -IMAGE = "opentrons-analysis" -CONTAINER_LABWARE = "/var/lib/ot" -HOST_LABWARE = Path(Path(__file__).parent.parent, "files", "labware") -HOST_PROTOCOLS_ROOT = Path(Path(__file__).parent.parent, "files", "protocols") -CONTAINER_PROTOCOLS_ROOT = "/var/lib/ot/protocols" -CONTAINER_RESULTS = "/var/lib/ot/analysis_results" -HOST_RESULTS = Path(Path(__file__).parent.parent, "analysis_results") -ANALYSIS_SUFFIX = "analysis.json" +IMAGE: str = "opentrons-analysis" +CONTAINER_LABWARE: str = "/var/lib/ot" +HOST_LABWARE: Path = Path(Path(__file__).parent.parent, "files", "labware") +HOST_PROTOCOLS_ROOT: Path = Path(Path(__file__).parent.parent, "files", "protocols") +CONTAINER_PROTOCOLS_ROOT: str = "/var/lib/ot/protocols" +CONTAINER_RESULTS: str = "/var/lib/ot/analysis_results" +HOST_RESULTS: Path = Path(Path(__file__).parent.parent, "analysis_results") +ANALYSIS_SUFFIX: str = "analysis.json" +ANALYSIS_TIMEOUT_SECONDS: int = 30 +ANALYSIS_CONTAINER_INSTANCES: int = 5 console = Console() -@contextmanager -def timeout(seconds: int) -> Generator[None, None, None]: - # Signal handler function - def raise_timeout(signum, frame) -> None: # type: ignore[no-untyped-def] - raise TimeoutError - - # Set the signal handler for the alarm signal - signal.signal(signal.SIGALRM, raise_timeout) - signal.alarm(seconds) # Set the alarm - try: - yield - finally: - signal.alarm(0) # Disable the alarm +def is_running_in_github_actions() -> bool: + return os.getenv("GITHUB_ACTIONS") == "true" class ProtocolType(Enum): @@ -48,7 +39,7 @@ class ProtocolType(Enum): @dataclass -class AnalyzedProtocol: +class TargetProtocol: host_protocol_file: Path container_protocol_file: Path host_analysis_file: Path @@ -111,7 +102,7 @@ def set_analysis_execution_time(self, analysis_execution_time: float) -> None: self.analysis_execution_time = analysis_execution_time -def stop_and_restart_container(image_name: str, timeout: int = 60) -> docker.models.containers.Container: +def start_containers(image_name: str, num_containers: int, timeout: int = 60) -> List[docker.models.containers.Container]: client = docker.from_env() volumes = { str(HOST_LABWARE): {"bind": CONTAINER_LABWARE, "mode": "rw"}, @@ -119,64 +110,55 @@ def stop_and_restart_container(image_name: str, timeout: int = 60) -> docker.mod str(HOST_PROTOCOLS_ROOT): {"bind": CONTAINER_PROTOCOLS_ROOT, "mode": "rw"}, } - # Find the running container using the specified image - containers = client.containers.list(filters={"ancestor": image_name, "status": "running"}) - + # Stop and remove existing containers + containers: List[docker.models.containers.Container] = client.containers.list(filters={"ancestor": image_name}) if containers: - console.print("Stopping the running container(s)...") + console.print("Stopping and removing existing container(s)...") for container in containers: container.stop(timeout=10) + container.remove() - # Start a new container with the specified volume - console.print("Starting a new container.") - container = client.containers.run(image_name, detach=True, volumes=volumes) + # Start new containers + console.print(f"Starting {num_containers} new container(s).") + containers = [] + for _ in range(num_containers): + container = client.containers.run(image_name, detach=True, volumes=volumes) + containers.append(container) - # Wait for the container to be ready if a readiness command is provided + # Wait for containers to be ready start_time = time.time() while time.time() - start_time < timeout: - exit_code, output = container.exec_run(f"ls -al {CONTAINER_LABWARE}") - if exit_code == 0: - console.print("Container is ready.") + all_ready = True + for container in containers: + exit_code, _ = container.exec_run(f"ls -al {CONTAINER_LABWARE}") + if exit_code != 0: + all_ready = False + break + if all_ready: + console.print("All containers are ready.") break else: - console.print("Waiting for container to be ready...") - time.sleep(5) + console.print("Waiting for containers to be ready...") + time.sleep(5) else: - console.print("Timeout waiting for container to be ready. Proceeding anyway.") - return container + console.print("Timeout waiting for containers to be ready. Proceeding anyway.") + return containers def stop_and_remove_containers(image_name: str) -> None: client = docker.from_env() - - # Find all containers created from the specified image containers = client.containers.list(all=True, filters={"ancestor": image_name}) - for container in containers: try: - # Stop the container if it's running if container.status == "running": console.print(f"Stopping container {container.short_id}...") container.stop(timeout=10) - - # Remove the container console.print(f"Removing container {container.short_id}...") container.remove() - except docker.errors.ContainerError as e: + except Exception as e: console.print(f"Error stopping/removing container {container.short_id}: {e}") -def has_designer_application(json_file_path: Path) -> bool: - try: - with open(json_file_path, "r", encoding="utf-8") as file: - data = json.load(file) - return "designerApplication" in data - except json.JSONDecodeError: - # Handle the exception if the file is not a valid JSON - console.print(f"Invalid JSON file: {json_file_path}") - return False - - def host_analysis_path(protocol_file: Path, tag: str) -> Path: return Path(HOST_RESULTS, f"{protocol_file.stem}_{tag}_{ANALYSIS_SUFFIX}") @@ -185,79 +167,6 @@ def container_analysis_path(protocol_file: Path, tag: str) -> Path: return Path(CONTAINER_RESULTS, f"{protocol_file.stem}_{tag}_{ANALYSIS_SUFFIX}") -def generate_protocols(tag: str) -> List[AnalyzedProtocol]: - - # Since we do not have the specification for which labware to use - # we will use all labware in the host labware directory - all_custom_labware_paths = [str(host_path.relative_to(CONTAINER_LABWARE)) for host_path in list(Path(HOST_LABWARE).rglob("*.json"))] - - def find_pd_protocols() -> List[AnalyzedProtocol]: - # Check if the provided path is a valid directory - if not HOST_PROTOCOLS_ROOT.is_dir(): - raise NotADirectoryError(f"The path {HOST_PROTOCOLS_ROOT} is not a valid directory.") - - nonlocal all_custom_labware_paths - - # Recursively find all .json files - json_files = list(HOST_PROTOCOLS_ROOT.rglob("*.json")) - filtered_json_files = [file for file in json_files if has_designer_application(file)] - pd_protocols: List[AnalyzedProtocol] = [] - for path in filtered_json_files: - relative_path = path.relative_to(HOST_PROTOCOLS_ROOT) - updated_path = Path(CONTAINER_PROTOCOLS_ROOT, relative_path) - pd_protocols.append( - AnalyzedProtocol( - host_protocol_file=path, - container_protocol_file=updated_path, - host_analysis_file=host_analysis_path(path, tag), - container_analysis_file=container_analysis_path(path, tag), - tag=tag, - custom_labware_paths=all_custom_labware_paths, - ) - ) - return pd_protocols - - def find_python_protocols() -> List[AnalyzedProtocol]: - # Check if the provided path is a valid directory - if not HOST_PROTOCOLS_ROOT.is_dir(): - raise NotADirectoryError(f"The path {HOST_PROTOCOLS_ROOT} is not a valid directory.") - - nonlocal all_custom_labware_paths - - # Recursively find all .py files - python_files = list(HOST_PROTOCOLS_ROOT.rglob("*.py")) - py_protocols: List[AnalyzedProtocol] = [] - - for path in python_files: - relative_path = path.relative_to(HOST_PROTOCOLS_ROOT) - container_path = Path(CONTAINER_PROTOCOLS_ROOT, relative_path) - py_protocols.append( - AnalyzedProtocol( - host_protocol_file=path, - container_protocol_file=container_path, - host_analysis_file=host_analysis_path(path, tag), - container_analysis_file=container_analysis_path(path, tag), - tag=tag, - custom_labware_paths=all_custom_labware_paths, - ) - ) - return py_protocols - - return find_pd_protocols() + find_python_protocols() - - -def remove_all_files_in_directory(directory: Path) -> None: - for filename in os.listdir(directory): - file_path = os.path.join(directory, filename) - try: - if os.path.isfile(file_path) or os.path.islink(file_path): - os.unlink(file_path) - elif os.path.isdir(file_path): - pass # Currently, subdirectories are not removed - except Exception as e: - console.print(f"Failed to delete {file_path}. Reason: {e}") - - def protocol_custom_labware_paths_in_container(protocol: Protocol) -> List[str]: if not HOST_LABWARE.is_dir() or protocol.custom_labware is None: return [] @@ -269,98 +178,87 @@ def protocol_custom_labware_paths_in_container(protocol: Protocol) -> List[str]: ] -def analyze(protocol: AnalyzedProtocol, container: docker.models.containers.Container) -> bool: - # Run the analyze command - command = f"python -I -m opentrons.cli analyze --json-output {protocol.container_analysis_file} {protocol.container_protocol_file} {' '.join(protocol.custom_labware_paths)}" # noqa: E501 +def analyze(protocol: TargetProtocol, container: docker.models.containers.Container) -> bool: + command = ( + f"python -I -m opentrons.cli analyze --json-output {protocol.container_analysis_file} " + f"{protocol.container_protocol_file} {' '.join(protocol.custom_labware_paths)}" + ) start_time = time.time() - timeout_duration = 30 # seconds + result = None + exit_code = None try: - with timeout(timeout_duration): - command_result = container.exec_run(cmd=command) - exit_code = command_result.exit_code - result = command_result.output - protocol.command_output = result.decode("utf-8") - protocol.command_exit_code = exit_code - protocol.set_analysis() - protocol.set_analysis_execution_time(time.time() - start_time) - return True - except TimeoutError: - console.print(f"Command execution exceeded {timeout_duration} seconds and was aborted.") - logs = container.logs() - # Decode and print the logs - console.print(f"container logs{logs.decode('utf-8')}") - except KeyboardInterrupt: - console.print("Execution was interrupted by the user.") - raise + command_result = container.exec_run(cmd=command) + exit_code = command_result.exit_code + result = command_result.output + protocol.command_output = result.decode("utf-8") if result else "" + protocol.command_exit_code = exit_code + protocol.set_analysis() + return True except Exception as e: console.print(f"An unexpected error occurred: {e}") - protocol.command_output = result.decode("utf-8") - console.print(f"Command output: {protocol.command_output}") - protocol.command_exit_code = exit_code - console.print(f"Exit code: {protocol.command_exit_code}") + protocol.command_output = result.decode("utf-8") if result else str(e) + protocol.command_exit_code = exit_code if exit_code is not None else -1 protocol.set_analysis() return False - protocol.command_output = None - protocol.command_exit_code = None - protocol.analysis = None - protocol.set_analysis_execution_time(time.time() - start_time) - return False - + finally: + protocol.set_analysis_execution_time(time.time() - start_time) + console.print(f"Analysis of {protocol.host_protocol_file.name} completed in {protocol.analysis_execution_time:.2f} seconds.") + + +def analyze_many(protocol_files: List[TargetProtocol], containers: List[docker.models.containers.Container]) -> None: + num_containers = len(containers) + with ThreadPoolExecutor(max_workers=num_containers) as executor: + futures = [] + for i, protocol in enumerate(protocol_files): + container = containers[i % num_containers] + future = executor.submit(analyze, protocol, container) + futures.append((future, protocol)) + for future, protocol in futures: + try: + future.result(timeout=ANALYSIS_TIMEOUT_SECONDS) + except concurrent.futures.TimeoutError: + console.print(f"Analysis of {protocol.host_protocol_file} exceeded {ANALYSIS_TIMEOUT_SECONDS} seconds and was aborted.") + # Handle timeout (e.g., mark as failed) + except Exception as e: + console.print(f"An error occurred during analysis: {e}") -def analyze_many(protocol_files: List[AnalyzedProtocol], container: docker.models.containers.Container) -> None: - for file in protocol_files: - analyze(file, container) accumulated_time = sum(protocol.analysis_execution_time for protocol in protocol_files if protocol.analysis_execution_time is not None) console.print(f"{len(protocol_files)} protocols with total analysis time of {accumulated_time:.2f} seconds.\n") -def analyze_against_image(tag: str) -> List[AnalyzedProtocol]: +def analyze_against_image(tag: str, protocols: List[TargetProtocol], num_containers: int = 1) -> List[TargetProtocol]: image_name = f"{IMAGE}:{tag}" - protocols = generate_protocols(tag) - protocols_to_process = protocols - # protocols_to_process = protocols[:1] # For testing try: - console.print(f"Analyzing {len(protocols_to_process)} protocol(s) against {image_name}...") - container = stop_and_restart_container(image_name) - analyze_many(protocols_to_process, container) + console.print(f"\nAnalyzing {len(protocols)} protocol(s) against {image_name} using {num_containers} container(s)...") + containers = start_containers(image_name, num_containers) + analyze_many(protocols, containers) finally: - stop_and_remove_containers(image_name) - return protocols_to_process + if is_running_in_github_actions(): + pass # We don't need to stop and remove containers in CI + else: + stop_and_remove_containers(image_name) + return protocols def generate_analyses_from_test(tag: str, protocols: List[Protocol]) -> None: """Generate analyses from the tests.""" - try: - image_name = f"{IMAGE}:{tag}" - protocols_to_process: List[AnalyzedProtocol] = [] - # convert the protocols to AnalyzedProtocol - for test_protocol in protocols: - host_protocol_file = Path(test_protocol.file_path) - container_protocol_file = Path(CONTAINER_PROTOCOLS_ROOT, host_protocol_file.relative_to(HOST_PROTOCOLS_ROOT)) - host_analysis_file = host_analysis_path(host_protocol_file, tag) - container_analysis_file = container_analysis_path(host_protocol_file, tag) - protocols_to_process.append( - AnalyzedProtocol( - host_protocol_file, - container_protocol_file, - host_analysis_file, - container_analysis_file, - tag, - protocol_custom_labware_paths_in_container(test_protocol), - ) + start_time = time.time() + protocols_to_process: List[TargetProtocol] = [] + for test_protocol in protocols: + host_protocol_file = Path(test_protocol.file_path) + container_protocol_file = Path(CONTAINER_PROTOCOLS_ROOT, host_protocol_file.relative_to(HOST_PROTOCOLS_ROOT)) + host_analysis_file = host_analysis_path(host_protocol_file, tag) + container_analysis_file = container_analysis_path(host_protocol_file, tag) + protocols_to_process.append( + TargetProtocol( + host_protocol_file, + container_protocol_file, + host_analysis_file, + container_analysis_file, + tag, + protocol_custom_labware_paths_in_container(test_protocol), ) - console.print(f"Analyzing {len(protocols_to_process)} protocol(s) against {tag}...") - container = stop_and_restart_container(image_name) - # Analyze the protocols - for protocol_to_analyze in protocols_to_process: - console.print(f"Analyzing {protocol_to_analyze.host_protocol_file}...") - analyzed = analyze(protocol_to_analyze, container) - if not analyzed: # Fail fast - console.print("Analysis failed. Exiting.") - stop_and_remove_containers(image_name) - accumulated_time = sum( - protocol.analysis_execution_time for protocol in protocols_to_process if protocol.analysis_execution_time is not None ) - console.print(f"{len(protocols_to_process)} protocols with total analysis time of {accumulated_time:.2f} seconds.\n") - finally: - stop_and_remove_containers(image_name) + analyze_against_image(tag, protocols_to_process, ANALYSIS_CONTAINER_INSTANCES) + end_time = time.time() + console.print(f"Clock time to generate analyses: {end_time - start_time:.2f} seconds.") diff --git a/analyses-snapshot-testing/citools/write_failed_analysis.py b/analyses-snapshot-testing/citools/write_failed_analysis.py deleted file mode 100644 index e69de29bb2d..00000000000 From 9ea27a20f4b86ea6f46a6605509dd670875d570a Mon Sep 17 00:00:00 2001 From: Josh McVey Date: Tue, 8 Oct 2024 14:40:18 -0500 Subject: [PATCH 23/27] feat(ai-server): improved logging (#16435) # Overview Redo logging for this API ## Test Plan and Hands on Testing - [x] local logging output in the container is JSON - [x] local logging output with local environment is text Once merged and auto-deployed to staging, we will look at the output in DataDog ## Risk assessment - medium - we are not getting what we need in DataDog to build filters and alerts and so we must evolve with this this - there is also a risk with the middleware stacking, so we will test a lot in staging --- opentrons-ai-server/Dockerfile | 9 +- opentrons-ai-server/Makefile | 2 +- opentrons-ai-server/Pipfile | 3 +- opentrons-ai-server/Pipfile.lock | 767 ++++++++++-------- .../api/domain/openai_predict.py | 11 +- opentrons-ai-server/api/domain/prompts.py | 8 +- .../api/handler/custom_logging.py | 133 +++ opentrons-ai-server/api/handler/fast.py | 82 +- opentrons-ai-server/api/handler/local_run.py | 13 +- .../api/handler/logging_config.py | 39 - opentrons-ai-server/api/integration/auth.py | 17 +- opentrons-ai-server/api/settings.py | 17 +- .../api/uvicorn_disable_logging.json | 36 + .../tests/helpers/huggingface_client.py | 1 + 14 files changed, 736 insertions(+), 402 deletions(-) create mode 100644 opentrons-ai-server/api/handler/custom_logging.py delete mode 100644 opentrons-ai-server/api/handler/logging_config.py create mode 100644 opentrons-ai-server/api/uvicorn_disable_logging.json diff --git a/opentrons-ai-server/Dockerfile b/opentrons-ai-server/Dockerfile index ddd19bb88c7..7a9a696145b 100644 --- a/opentrons-ai-server/Dockerfile +++ b/opentrons-ai-server/Dockerfile @@ -1,7 +1,8 @@ -FROM --platform=linux/amd64 python:3.12-slim +ARG PLATFORM=linux/amd64 +FROM --platform=$PLATFORM python:3.12-slim -ENV PYTHONUNBUFFERED True -ENV DOCKER_RUNNING True +ENV PYTHONUNBUFFERED=True +ENV DOCKER_RUNNING=True WORKDIR /code @@ -15,4 +16,4 @@ COPY ./api /code/api EXPOSE 8000 -CMD ["ddtrace-run", "uvicorn", "api.handler.fast:app", "--proxy-headers", "--host", "0.0.0.0", "--port", "8000", "--timeout-keep-alive", "190", "--workers", "3"] +CMD ["ddtrace-run", "uvicorn", "api.handler.fast:app", "--proxy-headers", "--host", "0.0.0.0", "--port", "8000", "--timeout-keep-alive", "190", "--log-config", "/code/api/uvicorn_disable_logging.json", "--workers", "3"] diff --git a/opentrons-ai-server/Makefile b/opentrons-ai-server/Makefile index e3f678606e1..60eba38a312 100644 --- a/opentrons-ai-server/Makefile +++ b/opentrons-ai-server/Makefile @@ -115,7 +115,7 @@ run: docker logs -f $(CONTAINER_NAME) .PHONY: clean -clean: +clean: gen-requirements docker stop $(CONTAINER_NAME) || true docker rm $(CONTAINER_NAME) || true diff --git a/opentrons-ai-server/Pipfile b/opentrons-ai-server/Pipfile index a6ee65a0160..34b0b8d32dd 100644 --- a/opentrons-ai-server/Pipfile +++ b/opentrons-ai-server/Pipfile @@ -13,9 +13,10 @@ fastapi = "==0.111.0" ddtrace = "==2.9.2" pydantic-settings = "==2.3.4" pyjwt = {extras = ["crypto"], version = "*"} -python-json-logger = "==2.0.7" beautifulsoup4 = "==4.12.3" markdownify = "==0.13.1" +structlog = "==24.4.0" +asgi-correlation-id = "==4.3.3" [dev-packages] docker = "==7.1.0" diff --git a/opentrons-ai-server/Pipfile.lock b/opentrons-ai-server/Pipfile.lock index 8861f152e8e..55811db04cf 100644 --- a/opentrons-ai-server/Pipfile.lock +++ b/opentrons-ai-server/Pipfile.lock @@ -1,7 +1,7 @@ { "_meta": { "hash": { - "sha256": "7526bc1898bd03e19a277baf44f56d6f1287870288af558c8d8b719118af3389" + "sha256": "20b9e324d809f68cb0465d5e3d98467ceb5860f583fddc347ade1e5ad6a3b6ab" }, "pipfile-spec": 6, "requires": { @@ -18,108 +18,108 @@ "default": { "aiohappyeyeballs": { "hashes": [ - "sha256:55a1714f084e63d49639800f95716da97a1f173d46a16dfcfda0016abb93b6b2", - "sha256:7ce92076e249169a13c2f49320d1967425eaf1f407522d707d59cac7628d62bd" + "sha256:75cf88a15106a5002a8eb1dab212525c00d1f4c0fa96e551c9fbe6f09a621586", + "sha256:8a7a83727b2756f394ab2895ea0765a0a8c475e3c71e98d43d76f22b4b435572" ], "markers": "python_version >= '3.8'", - "version": "==2.4.0" + "version": "==2.4.3" }, "aiohttp": { 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"sha256:fc2c80bc87fba076e6cbb926216c27fba274dae7100a7b9a0983b53132dd99f2", + "sha256:fe4d2536c827f508348d7b40c08767e8c7071614250927233bf0c92170451c0a" + ], + "markers": "python_version >= '3.8'", + "version": "==1.14.0" }, "zipp": { "hashes": [ @@ -2563,11 +2672,11 @@ }, "botocore-stubs": { "hashes": [ - "sha256:1184dcb19d833041cfadc3c533c8cb7ae246a9ab9b974b33b42fe209f54f551b", - "sha256:acb1c77d422c9bf51161c98a2912fd0b4abb4efe9578d7f4c851c77d30fc754a" + "sha256:b1aebecdfa4f4fc02b0a68a5e438877034b195168809a7202ee32b42245d3ece", + "sha256:d79a408dfc503a1a0389d10cd29ad22a01450d0d53902ea216815e2ba98913ba" ], "markers": "python_version >= '3.8'", - "version": "==1.35.26" + "version": "==1.35.35" }, "certifi": { "hashes": [ @@ -2952,11 +3061,11 @@ }, "rich": { "hashes": [ - "sha256:1760a3c0848469b97b558fc61c85233e3dafb69c7a071b4d60c38099d3cd4c06", - "sha256:8260cda28e3db6bf04d2d1ef4dbc03ba80a824c88b0e7668a0f23126a424844a" + "sha256:51a2c62057461aaf7152b4d611168f93a9fc73068f8ded2790f29fe2b5366d0c", + "sha256:8c82a3d3f8dcfe9e734771313e606b39d8247bb6b826e196f4914b333b743cf1" ], - "markers": "python_full_version >= '3.7.0'", - "version": "==13.8.1" + "markers": "python_full_version >= '3.8.0'", + "version": "==13.9.2" }, "ruff": { "hashes": [ @@ -3000,11 +3109,11 @@ }, "types-awscrt": { "hashes": [ - "sha256:117ff2b1bb657f09d01b7e0ce3fe3fa6e039be12d30b826896182725c9ce85b1", - "sha256:9f7f47de68799cb2bcb9e486f48d77b9f58962b92fba43cb8860da70b3c57d1b" + "sha256:67a660c90bad360c339f6a79310cc17094d12472042c7ca5a41450aaf5fc9a54", + "sha256:b2c196bbd3226bab42d80fae13c34548de9ddc195f5a366d79c15d18e5897aa9" ], "markers": "python_version >= '3.8'", - "version": "==0.21.5" + "version": "==0.22.0" }, "types-beautifulsoup4": { "hashes": [ diff --git a/opentrons-ai-server/api/domain/openai_predict.py b/opentrons-ai-server/api/domain/openai_predict.py index c9733614458..71b34cff12b 100644 --- a/opentrons-ai-server/api/domain/openai_predict.py +++ b/opentrons-ai-server/api/domain/openai_predict.py @@ -1,7 +1,8 @@ -import logging from pathlib import Path from typing import List, Tuple +import structlog +from ddtrace import tracer from llama_index.core import Settings as li_settings from llama_index.core import StorageContext, load_index_from_storage from llama_index.embeddings.openai import OpenAIEmbedding @@ -25,8 +26,8 @@ from api.domain.utils import refine_characters from api.settings import Settings -logger = logging.getLogger(__name__) - +settings: Settings = Settings() +logger = structlog.stdlib.get_logger(settings.logger_name) ROOT_PATH: Path = Path(Path(__file__)).parent.parent.parent @@ -38,6 +39,7 @@ def __init__(self, settings: Settings) -> None: model_name="text-embedding-3-large", api_key=self.settings.openai_api_key.get_secret_value() ) + @tracer.wrap() def get_docs_all(self, query: str) -> Tuple[str, str, str]: commands = self.extract_atomic_description(query) logger.info("Commands", extra={"commands": commands}) @@ -85,6 +87,7 @@ def get_docs_all(self, query: str) -> Tuple[str, str, str]: return example_commands, docs + docs_ref, standard_api_names + @tracer.wrap() def extract_atomic_description(self, protocol_description: str) -> List[str]: class atomic_descr(BaseModel): """ @@ -106,6 +109,7 @@ class atomic_descr(BaseModel): descriptions.append(x) return descriptions + @tracer.wrap() def refine_response(self, assistant_message: str) -> str: if assistant_message is None: return "" @@ -129,6 +133,7 @@ def refine_response(self, assistant_message: str) -> str: return response.choices[0].message.content if response.choices[0].message.content is not None else "" + @tracer.wrap() def predict(self, prompt: str, chat_completion_message_params: List[ChatCompletionMessageParam] | None = None) -> None | str: prompt = refine_characters(prompt) diff --git a/opentrons-ai-server/api/domain/prompts.py b/opentrons-ai-server/api/domain/prompts.py index 582bd1565ea..8d335b65227 100644 --- a/opentrons-ai-server/api/domain/prompts.py +++ b/opentrons-ai-server/api/domain/prompts.py @@ -1,15 +1,16 @@ import json -import logging import uuid from typing import Any, Dict, Iterable import requests +import structlog +from ddtrace import tracer from openai.types.chat import ChatCompletionToolParam from api.settings import Settings settings: Settings = Settings() -logger = logging.getLogger(__name__) +logger = structlog.stdlib.get_logger(settings.logger_name) def generate_unique_name() -> str: @@ -17,13 +18,14 @@ def generate_unique_name() -> str: return unique_name +@tracer.wrap() def send_post_request(payload: str) -> str: url = "https://Opentrons-simulator.hf.space/protocol" protocol_name: str = generate_unique_name() data = {"name": protocol_name, "content": payload} hf_token: str = settings.huggingface_api_key.get_secret_value() headers = {"Content-Type": "application/json", "Authorization": "Bearer {}".format(hf_token)} - + logger.info("Sending POST request to the simulate API", extra={"url": url, "protocolName": data["name"]}) response = requests.post(url, json=data, headers=headers) if response.status_code != 200: diff --git a/opentrons-ai-server/api/handler/custom_logging.py b/opentrons-ai-server/api/handler/custom_logging.py new file mode 100644 index 00000000000..a062528f803 --- /dev/null +++ b/opentrons-ai-server/api/handler/custom_logging.py @@ -0,0 +1,133 @@ +# Taken directly from https://gist.github.com/nymous/f138c7f06062b7c43c060bf03759c29e +import logging +import sys + +import ddtrace +import structlog +from ddtrace import tracer +from structlog.types import EventDict, Processor + + +# https://github.com/hynek/structlog/issues/35#issuecomment-591321744 +def rename_event_key(_, __, event_dict: EventDict) -> EventDict: # type: ignore[no-untyped-def] + """ + Log entries keep the text message in the `event` field, but Datadog + uses the `message` field. This processor moves the value from one field to + the other. + See https://github.com/hynek/structlog/issues/35#issuecomment-591321744 + """ + event_dict["message"] = event_dict.pop("event") + return event_dict + + +def drop_color_message_key(_, __, event_dict: EventDict) -> EventDict: # type: ignore[no-untyped-def] + """ + Uvicorn logs the message a second time in the extra `color_message`, but we don't + need it. This processor drops the key from the event dict if it exists. + """ + event_dict.pop("color_message", None) + return event_dict + + +def tracer_injection(_, __, event_dict: EventDict) -> EventDict: # type: ignore[no-untyped-def] + # get correlation ids from current tracer context + span = tracer.current_span() + trace_id, span_id = (str((1 << 64) - 1 & span.trace_id), span.span_id) if span else (None, None) + + # add ids to structlog event dictionary + event_dict["dd.trace_id"] = str(trace_id or 0) + event_dict["dd.span_id"] = str(span_id or 0) + + # add the env, service, and version configured for the tracer + event_dict["dd.env"] = ddtrace.config.env or "" + event_dict["dd.service"] = ddtrace.config.service or "" + event_dict["dd.version"] = ddtrace.config.version or "" + + return event_dict + + +def setup_logging(json_logs: bool = False, log_level: str = "INFO") -> None: + timestamper = structlog.processors.TimeStamper(fmt="iso") + + shared_processors: list[Processor] = [ + structlog.contextvars.merge_contextvars, + structlog.stdlib.add_logger_name, + structlog.stdlib.add_log_level, + structlog.stdlib.PositionalArgumentsFormatter(), + structlog.stdlib.ExtraAdder(), + drop_color_message_key, + tracer_injection, + timestamper, + structlog.processors.StackInfoRenderer(), + ] + + if json_logs: + # We rename the `event` key to `message` only in JSON logs, as Datadog looks for the + # `message` key but the pretty ConsoleRenderer looks for `event` + shared_processors.append(rename_event_key) + # Format the exception only for JSON logs, as we want to pretty-print them when + # using the ConsoleRenderer + shared_processors.append(structlog.processors.format_exc_info) + + structlog.configure( + processors=shared_processors + + [ + # Prepare event dict for `ProcessorFormatter`. + structlog.stdlib.ProcessorFormatter.wrap_for_formatter, + ], + logger_factory=structlog.stdlib.LoggerFactory(), + cache_logger_on_first_use=True, + ) + + log_renderer: structlog.types.Processor + if json_logs: + log_renderer = structlog.processors.JSONRenderer() + else: + log_renderer = structlog.dev.ConsoleRenderer() + + formatter = structlog.stdlib.ProcessorFormatter( + # These run ONLY on `logging` entries that do NOT originate within + # structlog. + foreign_pre_chain=shared_processors, + # These run on ALL entries after the pre_chain is done. + processors=[ + # Remove _record & _from_structlog. + structlog.stdlib.ProcessorFormatter.remove_processors_meta, + log_renderer, + ], + ) + + handler = logging.StreamHandler() + # Use OUR `ProcessorFormatter` to format all `logging` entries. + handler.setFormatter(formatter) + root_logger = logging.getLogger() + root_logger.addHandler(handler) + root_logger.setLevel(log_level.upper()) + + for _log in ["uvicorn", "uvicorn.error"]: + # Clear the log handlers for uvicorn loggers, and enable propagation + # so the messages are caught by our root logger and formatted correctly + # by structlog + logging.getLogger(_log).handlers.clear() + logging.getLogger(_log).propagate = True + + # Since we re-create the access logs ourselves, to add all information + # in the structured log (see the `logging_middleware` in main.py), we clear + # the handlers and prevent the logs to propagate to a logger higher up in the + # hierarchy (effectively rendering them silent). + logging.getLogger("uvicorn.access").handlers.clear() + logging.getLogger("uvicorn.access").propagate = False + + def handle_exception(exc_type, exc_value, exc_traceback): # type: ignore[no-untyped-def] + """ + Log any uncaught exception instead of letting it be printed by Python + (but leave KeyboardInterrupt untouched to allow users to Ctrl+C to stop) + See https://stackoverflow.com/a/16993115/3641865 + """ + if issubclass(exc_type, KeyboardInterrupt): + sys.__excepthook__(exc_type, exc_value, exc_traceback) + return + + root_logger.error("Uncaught exception", exc_info=(exc_type, exc_value, exc_traceback)) + + sys.excepthook = handle_exception diff --git a/opentrons-ai-server/api/handler/fast.py b/opentrons-ai-server/api/handler/fast.py index 3c88e08a1a2..8e5572d0c15 100644 --- a/opentrons-ai-server/api/handler/fast.py +++ b/opentrons-ai-server/api/handler/fast.py @@ -1,9 +1,13 @@ import asyncio import os +import time from typing import Any, Awaitable, Callable, List, Literal, Union -import ddtrace +import structlog +from asgi_correlation_id import CorrelationIdMiddleware +from asgi_correlation_id.context import correlation_id from ddtrace import tracer +from ddtrace.contrib.asgi.middleware import TraceMiddleware from fastapi import FastAPI, HTTPException, Query, Request, Response, Security, status from fastapi.exceptions import RequestValidationError from fastapi.middleware.cors import CORSMiddleware @@ -11,9 +15,10 @@ from fastapi.responses import HTMLResponse, JSONResponse from pydantic import BaseModel, Field, conint from starlette.middleware.base import BaseHTTPMiddleware +from uvicorn.protocols.utils import get_path_with_query_string from api.domain.openai_predict import OpenAIPredict -from api.handler.logging_config import get_logger, setup_logging +from api.handler.custom_logging import setup_logging from api.integration.auth import VerifyToken from api.models.chat_request import ChatRequest from api.models.chat_response import ChatResponse @@ -21,10 +26,12 @@ from api.models.internal_server_error import InternalServerError from api.settings import Settings -setup_logging() -logger = get_logger(__name__) -ddtrace.patch(logging=True) settings: Settings = Settings() +setup_logging(json_logs=settings.json_logging, log_level=settings.log_level.upper()) + +access_logger = structlog.stdlib.get_logger("api.access") +logger = structlog.stdlib.get_logger(settings.logger_name) + auth: VerifyToken = VerifyToken() openai: OpenAIPredict = OpenAIPredict(settings) @@ -75,6 +82,61 @@ async def dispatch(self, request: Request, call_next: Any) -> JSONResponse | Any app.add_middleware(TimeoutMiddleware, timeout_s=178) +@app.middleware("http") +async def logging_middleware(request: Request, call_next) -> Response: # type: ignore[no-untyped-def] + structlog.contextvars.clear_contextvars() + # These context vars will be added to all log entries emitted during the request + request_id = correlation_id.get() + structlog.contextvars.bind_contextvars(request_id=request_id) + + start_time = time.perf_counter_ns() + # If the call_next raises an error, we still want to return our own 500 response, + # so we can add headers to it (process time, request ID...) + response = Response(status_code=500) + try: + response = await call_next(request) + except Exception: + structlog.stdlib.get_logger("api.error").exception("Uncaught exception") + raise + finally: + process_time = time.perf_counter_ns() - start_time + status_code = response.status_code + url = get_path_with_query_string(request.scope) # type: ignore[arg-type] + client_host = request.client.host if request.client and request.client.host else "unknown" + client_port = request.client.port if request.client and request.client.port else "unknown" + http_method = request.method if request.method else "unknown" + http_version = request.scope["http_version"] + # Recreate the Uvicorn access log format, but add all parameters as structured information + access_logger.info( + f"""{client_host}:{client_port} - "{http_method} {url} HTTP/{http_version}" {status_code}""", + http={ + "url": str(request.url), + "status_code": status_code, + "method": http_method, + "request_id": request_id, + "version": http_version, + }, + network={"client": {"ip": client_host, "port": client_port}}, + duration=process_time, + ) + response.headers["X-Process-Time"] = str(process_time / 10**9) + return response + + +# This middleware must be placed after the logging, to populate the context with the request ID +# NOTE: Why last?? +# Answer: middlewares are applied in the reverse order of when they are added (you can verify this +# by debugging `app.middleware_stack` and recursively drilling down the `app` property). +app.add_middleware(CorrelationIdMiddleware) + +tracing_middleware = next((m for m in app.user_middleware if m.cls == TraceMiddleware), None) +if tracing_middleware is not None: + app.user_middleware = [m for m in app.user_middleware if m.cls != TraceMiddleware] + structlog.stdlib.get_logger("api.datadog_patch").info("Patching Datadog tracing middleware to be the outermost middleware...") + app.user_middleware.insert(0, tracing_middleware) + app.middleware_stack = app.build_middleware_stack() + + # Models class Status(BaseModel): status: Literal["ok", "error"] @@ -134,7 +196,7 @@ async def create_chat_completion( return ChatResponse(reply=response, fake=body.fake) except Exception as e: - logger.exception(e) + logger.exception("Error processing chat completion") raise HTTPException( status_code=status.HTTP_500_INTERNAL_SERVER_ERROR, detail=InternalServerError(exception_object=e).model_dump() ) from e @@ -143,7 +205,7 @@ async def create_chat_completion( @app.get( "/health", response_model=Status, - summary="LB Health Check", + summary="Load Balancer Health Check", description="Check the health and version of the API.", include_in_schema=False, ) @@ -154,10 +216,14 @@ async def get_health(request: Request) -> Status: - **returns**: A Status containing the version of the API. """ - logger.debug(f"{request.method} {request.url.path}") + if request.url.path == "/health": + pass # This is a health check from the load balancer + else: + logger.info(f"{request.method} {request.url.path}", extra={"requestMethod": request.method, "requestPath": request.url.path}) return Status(status="ok", version=settings.dd_version) +@tracer.wrap() @app.get("/api/timeout", response_model=TimeoutResponse) async def timeout_endpoint(request: Request, seconds: conint(ge=1, le=300) = Query(..., description="Number of seconds to wait")): # type: ignore # noqa: B008 """ diff --git a/opentrons-ai-server/api/handler/local_run.py b/opentrons-ai-server/api/handler/local_run.py index 0b82fae7e41..e9bbcc6f151 100644 --- a/opentrons-ai-server/api/handler/local_run.py +++ b/opentrons-ai-server/api/handler/local_run.py @@ -1,9 +1,12 @@ # run.py import uvicorn -from api.handler.logging_config import setup_logging - -setup_logging() - if __name__ == "__main__": - uvicorn.run("api.handler.fast:app", host="localhost", port=8000, timeout_keep_alive=190, reload=True) + uvicorn.run( + "api.handler.fast:app", + host="localhost", + port=8000, + timeout_keep_alive=190, + reload=True, + log_config=None, + ) diff --git a/opentrons-ai-server/api/handler/logging_config.py b/opentrons-ai-server/api/handler/logging_config.py deleted file mode 100644 index fc576b6ad80..00000000000 --- a/opentrons-ai-server/api/handler/logging_config.py +++ /dev/null @@ -1,39 +0,0 @@ -# logging_config.py -import logging - -from pythonjsonlogger import jsonlogger - -from api.settings import Settings - -FORMAT = ( - "%(asctime)s %(levelname)s [%(name)s] [%(filename)s:%(lineno)d] " - "[dd.service=%(dd.service)s dd.env=%(dd.env)s dd.version=%(dd.version)s dd.trace_id=%(dd.trace_id)s dd.span_id=%(dd.span_id)s] " - "- %(message)s" -) - -LOCAL_FORMAT = "%(asctime)s %(levelname)s [%(name)s] [%(filename)s:%(lineno)d] - %(message)s" - - -def setup_logging() -> None: - settings = Settings() - log_handler = logging.StreamHandler() - - if settings.environment == "local": - formatter = logging.Formatter(LOCAL_FORMAT) - else: - formatter = jsonlogger.JsonFormatter(FORMAT) # type: ignore - - log_handler.setFormatter(formatter) - - logging.basicConfig( - level=settings.log_level.upper(), - handlers=[log_handler], - ) - - -# Call this function to initialize logging -setup_logging() - - -def get_logger(name: str) -> logging.Logger: - return logging.getLogger(name) diff --git a/opentrons-ai-server/api/integration/auth.py b/opentrons-ai-server/api/integration/auth.py index c3cf4b8d163..12e8b2a4a9e 100644 --- a/opentrons-ai-server/api/integration/auth.py +++ b/opentrons-ai-server/api/integration/auth.py @@ -1,13 +1,14 @@ -import logging from typing import Any, Optional import jwt +import structlog from fastapi import HTTPException, Security, status from fastapi.security import HTTPAuthorizationCredentials, HTTPBearer, SecurityScopes from api.settings import Settings -logger = logging.getLogger(__name__) +settings: Settings = Settings() +logger = structlog.stdlib.get_logger(settings.logger_name) class UnauthenticatedException(HTTPException): @@ -35,10 +36,10 @@ async def verify( try: signing_key = self.jwks_client.get_signing_key_from_jwt(credentials.credentials).key except jwt.PyJWKClientError as error: - logger.error(error, extra={"credentials": credentials}) + logger.error("Client Error", extra={"credentials": credentials}, exc_info=True) raise UnauthenticatedException() from error except jwt.exceptions.DecodeError as error: - logger.error(error, extra={"credentials": credentials}) + logger.error("Decode Error", extra={"credentials": credentials}, exc_info=True) raise UnauthenticatedException() from error try: @@ -51,10 +52,10 @@ async def verify( ) logger.info("Decoded token", extra={"token": payload}) return payload - except jwt.ExpiredSignatureError as error: - logger.error(error, extra={"credentials": credentials}) + except jwt.ExpiredSignatureError: + logger.error("Expired Signature", extra={"credentials": credentials}, exc_info=True) # Handle token expiration, e.g., refresh token, re-authenticate, etc. - except jwt.PyJWTError as error: - logger.error(error, extra={"credentials": credentials}) + except jwt.PyJWTError: + logger.error("General JWT Error", extra={"credentials": credentials}, exc_info=True) # Handle other JWT errors raise UnauthenticatedException() diff --git a/opentrons-ai-server/api/settings.py b/opentrons-ai-server/api/settings.py index c29f44aface..c59a25c33de 100644 --- a/opentrons-ai-server/api/settings.py +++ b/opentrons-ai-server/api/settings.py @@ -1,3 +1,4 @@ +import os from pathlib import Path from pydantic import SecretStr @@ -6,6 +7,10 @@ ENV_PATH: Path = Path(Path(__file__).parent.parent, ".env") +def is_running_in_docker() -> bool: + return os.path.exists("/.dockerenv") + + class Settings(BaseSettings): """ If the env_file file exists: It will read the configurations from the env_file file (local execution) @@ -26,7 +31,7 @@ class Settings(BaseSettings): auth0_algorithms: str = "RS256" dd_version: str = "hardcoded_default_from_settings" allowed_origins: str = "*" - dd_logs_injection: str = "true" + dd_trace_enabled: str = "false" cpu: str = "1028" memory: str = "2048" @@ -35,6 +40,16 @@ class Settings(BaseSettings): openai_api_key: SecretStr = SecretStr("default_openai_api_key") huggingface_api_key: SecretStr = SecretStr("default_huggingface_api_key") + @property + def json_logging(self) -> bool: + if self.environment == "local" and not is_running_in_docker(): + return False + return True + + @property + def logger_name(self) -> str: + return "app.logger" + def get_settings_from_json(json_str: str) -> Settings: """ diff --git a/opentrons-ai-server/api/uvicorn_disable_logging.json b/opentrons-ai-server/api/uvicorn_disable_logging.json new file mode 100644 index 00000000000..e2f06cb503f --- /dev/null +++ b/opentrons-ai-server/api/uvicorn_disable_logging.json @@ -0,0 +1,36 @@ +{ + "version": 1, + "disable_existing_loggers": false, + "formatters": { + "default": { + "()": "uvicorn.logging.DefaultFormatter", + "format": "%(asctime)s - %(name)s - %(levelname)s - %(message)s" + }, + "access": { + "()": "uvicorn.logging.AccessFormatter", + "format": "%(asctime)s - %(name)s - %(levelname)s - %(message)s" + } + }, + "handlers": { + "default": { + "formatter": "default", + "class": "logging.NullHandler" + }, + "access": { + "formatter": "access", + "class": "logging.NullHandler" + } + }, + "loggers": { + "uvicorn.error": { + "level": "INFO", + "handlers": ["default"], + "propagate": false + }, + "uvicorn.access": { + "level": "INFO", + "handlers": ["access"], + "propagate": false + } + } +} diff --git a/opentrons-ai-server/tests/helpers/huggingface_client.py b/opentrons-ai-server/tests/helpers/huggingface_client.py index 7b66fd61674..a55792d2fb7 100644 --- a/opentrons-ai-server/tests/helpers/huggingface_client.py +++ b/opentrons-ai-server/tests/helpers/huggingface_client.py @@ -39,6 +39,7 @@ def get_auth_headers(self, token_override: str | None = None) -> dict[str, str]: return {"Authorization": f"Bearer {self.settings.HF_API_KEY}"} def post_simulate_protocol(self, protocol: Protocol) -> Response: + console.print(self.auth_headers) return self.httpx.post("https://opentrons-simulator.hf.space/protocol", headers=self.standard_headers, json=protocol.model_dump()) From 6c8c5835a3eedd98887177369c15527a65c26500 Mon Sep 17 00:00:00 2001 From: Anthony Ngumah <68346382+AnthonyNASC20@users.noreply.github.com> Date: Wed, 9 Oct 2024 09:35:11 -0400 Subject: [PATCH 24/27] feat(hardware-testing): Abr Asair Script update (#16440) # Overview ## Test Plan and Hands on Testing ## Changelog ## Review requests --- abr-testing/protocol_simulation/__init__.py | 1 + .../protocol_simulation/simulation_metrics.py | 353 ++++++++++++++++++ .../hardware_testing/drivers/__init__.py | 35 +- .../scripts/abr_asair_sensor.py | 2 +- 4 files changed, 370 insertions(+), 21 deletions(-) create mode 100644 abr-testing/protocol_simulation/__init__.py create mode 100644 abr-testing/protocol_simulation/simulation_metrics.py diff --git a/abr-testing/protocol_simulation/__init__.py b/abr-testing/protocol_simulation/__init__.py new file mode 100644 index 00000000000..157c21fd93e --- /dev/null +++ b/abr-testing/protocol_simulation/__init__.py @@ -0,0 +1 @@ +"""The package holding code for simulating protocols.""" \ No newline at end of file diff --git a/abr-testing/protocol_simulation/simulation_metrics.py b/abr-testing/protocol_simulation/simulation_metrics.py new file mode 100644 index 00000000000..544bc3fb4bc --- /dev/null +++ b/abr-testing/protocol_simulation/simulation_metrics.py @@ -0,0 +1,353 @@ +import re +import sys +import os +from pathlib import Path +from click import Context +from opentrons.cli import analyze +import json +import argparse +from datetime import datetime +from abr_testing.automation import google_sheets_tool +from abr_testing.data_collection import read_robot_logs +from typing import Set, Dict, Any, Tuple, List, Union +from abr_testing.tools import plate_reader + +def look_for_air_gaps(protocol_file_path: str) -> int: + instances = 0 + try: + with open(protocol_file_path, "r") as open_file: + protocol_lines = open_file.readlines() + for line in protocol_lines: + if "air_gap" in line: + print(line) + instances += 1 + print(f'Found {instances} instance(s) of the air gap function') + open_file.close() + except Exception as error: + print("Error reading protocol:", error.with_traceback()) + return instances + +def set_api_level(protocol_file_path) -> None: + with open(protocol_file_path, "r") as file: + file_contents = file.readlines() + # Look for current'apiLevel:' + for i, line in enumerate(file_contents): + print(line) + if 'apiLevel' in line: + print(f"The current API level of this protocol is: {line}") + change = input("Would you like to simulate with a different API level? (Y/N) ").strip().upper() + + if change == "Y": + api_level = input("Protocol API Level to Simulate with: ") + # Update new API level + file_contents[i] = f'apiLevel: {api_level}\n' + print(f"Updated line: {file_contents[i]}") + break + with open(protocol_file_path, "w") as file: + file.writelines(file_contents) + print("File updated successfully.") + +original_exit = sys.exit + +def mock_exit(code=None) -> None: + print(f"sys.exit() called with code: {code}") + raise SystemExit(code) + +def get_labware_name(id: str, object_dict: dict, json_data: dict) -> str: + slot = "" + for obj in object_dict: + if obj['id'] == id: + try: + # Try to get the slotName from the location + slot = obj['location']['slotName'] + return " SLOT: " + slot + except KeyError: + location = obj.get('location', {}) + + # Check if location contains 'moduleId' + if 'moduleId' in location: + return get_labware_name(location['moduleId'], json_data['modules'], json_data) + + # Check if location contains 'labwareId' + elif 'labwareId' in location: + return get_labware_name(location['labwareId'], json_data['labware'], json_data) + + return " Labware not found" + +def parse_results_volume(json_data_file: str) -> Tuple[ + List[str], List[str], List[str], List[str], + List[str], List[str], List[str], List[str], + List[str], List[str], List[str] + ]: + json_data = [] + with open(json_data_file, "r") as json_file: + json_data = json.load(json_file) + commands = json_data.get("commands", []) + start_time = datetime.fromisoformat(commands[0]["createdAt"]) + end_time = datetime.fromisoformat(commands[len(commands)-1]["completedAt"]) + header = ["", "Protocol Name", "Date", "Time"] + header_fill_row = ["", protocol_name, str(file_date.date()), str(file_date.time())] + labware_names_row =["Labware Name"] + volume_dispensed_row =["Total Volume Dispensed uL"] + volume_aspirated_row =["Total Volume Aspirated uL"] + change_in_volume_row = ["Total Change in Volume uL"] + start_time_row = ["Start Time"] + end_time_row = ["End Time"] + total_time_row = ["Total Time of Execution"] + metrics_row = [ + "Metric", + "Heatershaker # of Latch Open/Close", + "Heatershaker # of Homes", + "Heatershaker # of Rotations", + "Heatershaker Temp On Time (sec)", + "Temp Module # of Temp Changes", + "Temp Module Temp On Time (sec)", + "Temp Mod Time to 4C (sec)", + "Thermocycler # of Lid Open/Close", + "Thermocycler Block # of Temp Changes", + "Thermocycler Block Temp On Time (sec)", + "Thermocycler Block Time to 4C (sec)", + "Thermocycler Lid # of Temp Changes", + "Thermocycler Lid Temp On Time (sec)", + "Thermocycler Lid Time to 105C (sec)", + "Plate Reader # of Reads", + "Plate Reader Avg Read Time (sec)", + "Plate Reader # of Initializations", + "Plate Reader Avg Initialize Time (sec)", + "Plate Reader # of Lid Movements", + "Plate Reader Result", + "Left Pipette Total Tip Pick Up(s)", + "Left Pipette Total Aspirates", + "Left Pipette Total Dispenses", + "Right Pipette Total Tip Pick Up(s)", + "Right Pipette Total Aspirates", + "Right Pipette Total Dispenses", + "Gripper Pick Ups", + "Total Liquid Probes", + "Average Liquid Probe Time (sec)", + ] + values_row = ["Value"] + labware_well_dict = {} + hs_dict, temp_module_dict, thermo_cycler_dict, plate_reader_dict, instrument_dict = {}, {}, {}, {}, {} + try: + hs_dict = read_robot_logs.hs_commands(json_data) + temp_module_dict = read_robot_logs.temperature_module_commands(json_data) + thermo_cycler_dict = read_robot_logs.thermocycler_commands(json_data) + plate_reader_dict = read_robot_logs.plate_reader_commands(json_data, hellma_plate_standards) + instrument_dict = read_robot_logs.instrument_commands(json_data) + except: + pass + + metrics = [hs_dict, temp_module_dict, thermo_cycler_dict, plate_reader_dict, instrument_dict] + + # Iterate through all the commands executed in the protocol run log + for x, command in enumerate(commands): + if x != 0: + prev_command = commands[x-1] + if command["commandType"] == "aspirate": + if not (prev_command["commandType"] == "comment" and (prev_command['params']['message'] == "AIR GAP" or prev_command['params']['message'] == "MIXING")): + labware_id = command["params"]["labwareId"] + labware_name = "" + for labware in json_data.get("labware"): + if labware["id"] == labware_id: + labware_name = (labware["loadName"]) + get_labware_name(labware["id"], json_data["labware"], json_data) + well_name = command["params"]["wellName"] + + if labware_id not in labware_well_dict: + labware_well_dict[labware_id] = {} + + if well_name not in labware_well_dict[labware_id]: + labware_well_dict[labware_id][well_name] = (labware_name, 0, 0, "") + + vol = int(command["params"]["volume"]) + + labware_name, added_volumes, subtracted_volumes, log = labware_well_dict[labware_id][well_name] + + subtracted_volumes += vol + log+=(f"aspirated {vol} ") + labware_well_dict[labware_id][well_name] = (labware_name, added_volumes, subtracted_volumes, log) + elif command["commandType"] == "dispense": + if not (prev_command["commandType"] == "comment" and (prev_command['params']['message'] == "MIXING")): + labware_id = command["params"]["labwareId"] + labware_name = "" + for labware in json_data.get("labware"): + if labware["id"] == labware_id: + labware_name = (labware["loadName"]) + get_labware_name(labware["id"], json_data["labware"], json_data) + well_name = command["params"]["wellName"] + + if labware_id not in labware_well_dict: + labware_well_dict[labware_id] = {} + + if well_name not in labware_well_dict[labware_id]: + labware_well_dict[labware_id][well_name] = (labware_name, 0, 0, "") + + vol = int(command["params"]["volume"]) + labware_name, added_volumes, subtracted_volumes, log = labware_well_dict[labware_id][well_name] + added_volumes += vol + log+=(f"dispensed {vol} ") + labware_well_dict[labware_id][well_name] = (labware_name, added_volumes, subtracted_volumes, log) + # file_date_formatted = file_date.strftime("%Y-%m-%d_%H-%M-%S") + with open(f"{os.path.dirname(json_data_file)}\\{protocol_name}_well_volumes_{file_date_formatted}.json", "w") as output_file: + json.dump(labware_well_dict, output_file) + output_file.close() + + # populate row lists + for labware_id in labware_well_dict.keys(): + volume_added = 0 + volume_subtracted = 0 + labware_name ="" + for well in labware_well_dict[labware_id].keys(): + labware_name, added_volumes, subtracted_volumes, log = labware_well_dict[labware_id][well] + volume_added += added_volumes + volume_subtracted += subtracted_volumes + labware_names_row.append(labware_name) + volume_dispensed_row.append(str(volume_added)) + volume_aspirated_row.append(str(volume_subtracted)) + change_in_volume_row.append(str(volume_added - volume_subtracted)) + start_time_row.append(str(start_time.time())) + end_time_row.append(str(end_time.time())) + total_time_row.append(str(end_time - start_time)) + + for metric in metrics: + for cmd in metric.keys(): + values_row.append(str(metric[cmd])) + return( + header, + header_fill_row, + labware_names_row, + volume_dispensed_row, + volume_aspirated_row, + change_in_volume_row, + start_time_row, + end_time_row, + total_time_row, + metrics_row, + values_row) + +def main(storage_directory, google_sheet_name, protocol_file_path): + sys.exit = mock_exit + + # Read file path from arguments + protocol_file_path = Path(protocol_file_path) + global protocol_name + protocol_name = protocol_file_path.stem + print("Simulating", protocol_name) + global file_date + file_date = datetime.now() + global file_date_formatted + file_date_formatted = file_date.strftime("%Y-%m-%d_%H-%M-%S") + # Prepare output file + json_file_path = f"{storage_directory}\\{protocol_name}_{file_date_formatted}.json" + json_file_output = open(json_file_path, "wb+") + error_output = f"{storage_directory}\\error_log" + # Run protocol simulation + try: + with Context(analyze) as ctx: + ctx.invoke( + analyze, + files=[protocol_file_path], + json_output=json_file_output, + human_json_output=None, + log_output=error_output, + log_level="ERROR", + check=False + ) + except SystemExit as e: + print(f"SystemExit caught with code: {e}") + finally: + sys.exit = original_exit + json_file_output.close() + with open(error_output, "r") as open_file: + try: + errors = open_file.readlines() + if not errors: pass + else: + print(errors) + sys.exit(1) + except: + print("error simulating ...") + sys.exit() + + try: + credentials_path = os.path.join(storage_directory, "credentials.json") + print(credentials_path) + except FileNotFoundError: + print(f"Add credentials.json file to: {storage_directory}.") + sys.exit() + + global hellma_plate_standards + + try: + hellma_plate_standards = plate_reader.read_hellma_plate_files(storage_directory, 101934) + except: + print(f"Add helma plate standard files to {storage_directory}.") + sys.exit() + + google_sheet = google_sheets_tool.google_sheet( + credentials_path, google_sheet_name, 0 + ) + + google_sheet.write_to_row([]) + + for row in parse_results_volume(json_file_path): + print("Writing results to", google_sheet_name) + print(str(row)) + google_sheet.write_to_row(row) + +if __name__ == "__main__": + CLEAN_PROTOCOL = True + parser = argparse.ArgumentParser(description="Read run logs on google drive.") + parser.add_argument( + "storage_directory", + metavar="STORAGE_DIRECTORY", + type=str, + nargs=1, + help="Path to long term storage directory for run logs.", + ) + parser.add_argument( + "sheet_name", + metavar="SHEETNAME", + type=str, + nargs=1, + help="Name of sheet to upload results to", + ) + parser.add_argument( + "protocol_file_path", + metavar="PROTOCOL_FILE_PATH", + type=str, + nargs=1, + help="Path to protocol file" + + ) + args = parser.parse_args() + storage_directory = args.storage_directory[0] + sheet_name = args.sheet_name[0] + protocol_file_path = args.protocol_file_path[0] + + SETUP = True + while(SETUP): + print("This current version cannot properly handle air gap calls.\nThese may cause simulation results to be inaccurate") + air_gaps = look_for_air_gaps(protocol_file_path) + if air_gaps > 0: + choice = "" + while not choice: + choice = input("This protocol contains air gaps, results may be innacurate, would you like to continue? (Y/N): ") + if choice.upper() == "Y": + SETUP = False + CLEAN_PROTOCOL = True + elif choice.upper() == "N": + CLEAN_PROTOCOL = False + SETUP = False + print("Please remove air gaps then re-run") + else: + choice = "" + print("Please enter a valid response.") + SETUP = False + + if CLEAN_PROTOCOL: + main( + storage_directory, + sheet_name, + protocol_file_path, + ) + else: sys.exit(0) \ No newline at end of file diff --git a/hardware-testing/hardware_testing/drivers/__init__.py b/hardware-testing/hardware_testing/drivers/__init__.py index fde7e228d9b..f1b4c991e2c 100644 --- a/hardware-testing/hardware_testing/drivers/__init__.py +++ b/hardware-testing/hardware_testing/drivers/__init__.py @@ -15,28 +15,23 @@ def list_ports_and_select(device_name: str = "", port_substr: str = None) -> str idx_str = "" for i, p in enumerate(ports): print(f"\t{i + 1}) {p.device}") - if port_substr: - for i, p in enumerate(ports): - if port_substr in p.device: - idx = i + 1 - break - else: - idx_str = input( - f"\nenter number next to {device_name} port (or ENTER to re-scan): " - ) - if not idx_str: - return list_ports_and_select(device_name) - if not device_name: - device_name = "desired" - - try: + if port_substr: + for i, p in enumerate(ports): + if port_substr in p.device: + return p.device + + while True: + idx_str = input( + f"\nEnter number next to {device_name} port (or ENTER to re-scan): " + ) + if not idx_str: + return list_ports_and_select(device_name, port_substr) + try: idx = int(idx_str.strip()) - except TypeError: - pass - return ports[idx - 1].device - except (ValueError, IndexError): - return list_ports_and_select() + return ports[idx - 1].device + except (ValueError, IndexError): + print("Invalid selection. Please try again.") def find_port(vid: int, pid: int) -> str: diff --git a/hardware-testing/hardware_testing/scripts/abr_asair_sensor.py b/hardware-testing/hardware_testing/scripts/abr_asair_sensor.py index f2c00e015d3..1e8fca0358c 100644 --- a/hardware-testing/hardware_testing/scripts/abr_asair_sensor.py +++ b/hardware-testing/hardware_testing/scripts/abr_asair_sensor.py @@ -26,7 +26,7 @@ def __init__(self, robot: str, duration: int, frequency: int) -> None: test_name = "ABR-Environment-Monitoring" run_id = data.create_run_id() file_name = data.create_file_name(test_name, run_id, robot) - sensor = asair_sensor.BuildAsairSensor(False, False, "USB") + sensor = asair_sensor.BuildAsairSensor(False, False, "USB0") print(sensor) env_data = sensor.get_reading() header = [ From e9dc78a40ce0bca5857c3e130915454923c88784 Mon Sep 17 00:00:00 2001 From: Anthony Ngumah <68346382+AnthonyNASC20@users.noreply.github.com> Date: Wed, 9 Oct 2024 09:35:42 -0400 Subject: [PATCH 25/27] feat(abr-testing): Protocol simulator, utilizes opentrons CLI to simulate and record information regarding a protocol. (#16433) # Overview Utilizes Opentrons CLI to simulate protocols and get information including; expected change in volume, deck labware, and module usage insights. ## Test Plan and Hands on Testing Tested tool using all abr protocols in the test-protocols folder as well as self made test-protocols to verify the accuracy of the results. ## Changelog Protocol will now comment if an aspiration belongs to air gap, to indicate that the volume should not change ## Risk assessment Low risk, this protocol simulation tool is still in it's beta, and does not change overall functionality of its dependencies. From 1f50f1d2fb5701dd346515283ed61de8ae380a60 Mon Sep 17 00:00:00 2001 From: Josh McVey Date: Wed, 9 Oct 2024 11:09:09 -0500 Subject: [PATCH 26/27] fix(abt): move to 3.13 stable (#16442) # Overview Moved to `3.13.0-rc.3` yesterday, today the stable is available in the runners. I speculate this will solve the issues with python not being mapped in https://github.com/Opentrons/opentrons/actions/runs/11243746409/job/31260344370?pr=16439 --- .github/workflows/analyses-snapshot-lint.yaml | 2 +- .github/workflows/analyses-snapshot-test.yaml | 2 +- analyses-snapshot-testing/mypy.ini | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/analyses-snapshot-lint.yaml b/.github/workflows/analyses-snapshot-lint.yaml index 17e13e30868..7a51a5e976a 100644 --- a/.github/workflows/analyses-snapshot-lint.yaml +++ b/.github/workflows/analyses-snapshot-lint.yaml @@ -27,7 +27,7 @@ jobs: - name: Setup Python uses: 'actions/setup-python@v5' with: - python-version: '3.13.0-rc.3' + python-version: '3.13.0' cache: 'pipenv' cache-dependency-path: analyses-snapshot-testing/Pipfile.lock - name: Setup diff --git a/.github/workflows/analyses-snapshot-test.yaml b/.github/workflows/analyses-snapshot-test.yaml index 7770db0d286..09539d873e9 100644 --- a/.github/workflows/analyses-snapshot-test.yaml +++ b/.github/workflows/analyses-snapshot-test.yaml @@ -78,7 +78,7 @@ jobs: - name: Set up Python 3.13 uses: actions/setup-python@v5 with: - python-version: '3.13.0-rc.3' + python-version: '3.13.0' cache: 'pipenv' cache-dependency-path: analyses-snapshot-testing/Pipfile.lock diff --git a/analyses-snapshot-testing/mypy.ini b/analyses-snapshot-testing/mypy.ini index cab126eb42d..d5e1e97f945 100644 --- a/analyses-snapshot-testing/mypy.ini +++ b/analyses-snapshot-testing/mypy.ini @@ -7,7 +7,7 @@ disallow_any_generics = true check_untyped_defs = true no_implicit_reexport = true exclude = "__init__.py" -python_version = 3.12 +python_version = 3.13 plugins = pydantic.mypy [pydantic-mypy] From 50d3208120b5b94b08805a81ab24aa4309e9c921 Mon Sep 17 00:00:00 2001 From: Max Marrone Date: Wed, 9 Oct 2024 13:52:11 -0400 Subject: [PATCH 27/27] docs(robot-server): Fix labware router response bodies (#16444) ## Overview The `GET /runs/{id}/loaded_labware_definitions` and `POST /runs/{id}/labware_definitions` endpoints were accidentally documented in OpenAPI as returning the *run,* not the labware definition. This fixes that. ## Review requests * Documented return types match actual return types? * OK with the `SimpleBody[list[...]]` thing? ## Risk assessment Low. --- .../robot_server/runs/router/labware_router.py | 10 ++++------ robot-server/robot_server/service/json_api/__init__.py | 2 -- robot-server/robot_server/service/json_api/response.py | 6 ------ robot-server/tests/runs/router/test_labware_router.py | 2 +- 4 files changed, 5 insertions(+), 15 deletions(-) diff --git a/robot-server/robot_server/runs/router/labware_router.py b/robot-server/robot_server/runs/router/labware_router.py index 7eba96afa0e..16924fd4ae8 100644 --- a/robot-server/robot_server/runs/router/labware_router.py +++ b/robot-server/robot_server/runs/router/labware_router.py @@ -16,7 +16,6 @@ RequestModel, SimpleBody, PydanticResponse, - ResponseList, ) from ..run_models import Run, LabwareDefinitionSummary @@ -86,7 +85,7 @@ async def add_labware_offset( ), status_code=status.HTTP_201_CREATED, responses={ - status.HTTP_201_CREATED: {"model": SimpleBody[Run]}, + status.HTTP_201_CREATED: {"model": SimpleBody[LabwareDefinitionSummary]}, status.HTTP_404_NOT_FOUND: {"model": ErrorBody[RunNotFound]}, status.HTTP_409_CONFLICT: {"model": ErrorBody[Union[RunStopped, RunNotIdle]]}, }, @@ -134,14 +133,14 @@ async def add_labware_definition( " Repeated definitions will be deduplicated." ), responses={ - status.HTTP_200_OK: {"model": SimpleBody[Run]}, + status.HTTP_200_OK: {"model": SimpleBody[list[SD_LabwareDefinition]]}, status.HTTP_409_CONFLICT: {"model": ErrorBody[RunStopped]}, }, ) async def get_run_loaded_labware_definitions( runId: str, run_data_manager: Annotated[RunDataManager, Depends(get_run_data_manager)], -) -> PydanticResponse[SimpleBody[ResponseList[SD_LabwareDefinition]]]: +) -> PydanticResponse[SimpleBody[list[SD_LabwareDefinition]]]: """Get a run's loaded labware definition by the run ID. Args: @@ -155,8 +154,7 @@ async def get_run_loaded_labware_definitions( except RunNotCurrentError as e: raise RunStopped(detail=str(e)).as_error(status.HTTP_409_CONFLICT) from e - labware_definitions_result = ResponseList.construct(__root__=labware_definitions) return await PydanticResponse.create( - content=SimpleBody.construct(data=labware_definitions_result), + content=SimpleBody.construct(data=labware_definitions), status_code=status.HTTP_200_OK, ) diff --git a/robot-server/robot_server/service/json_api/__init__.py b/robot-server/robot_server/service/json_api/__init__.py index 2680c99049f..78a9deeaa4d 100644 --- a/robot-server/robot_server/service/json_api/__init__.py +++ b/robot-server/robot_server/service/json_api/__init__.py @@ -14,7 +14,6 @@ DeprecatedResponseDataModel, ResourceModel, PydanticResponse, - ResponseList, NotifyRefetchBody, NotifyUnsubscribeBody, ) @@ -44,7 +43,6 @@ "DeprecatedResponseDataModel", "DeprecatedResponseModel", "DeprecatedMultiResponseModel", - "ResponseList", # notify models "NotifyRefetchBody", "NotifyUnsubscribeBody", diff --git a/robot-server/robot_server/service/json_api/response.py b/robot-server/robot_server/service/json_api/response.py index e1e422f255c..8764d8edd53 100644 --- a/robot-server/robot_server/service/json_api/response.py +++ b/robot-server/robot_server/service/json_api/response.py @@ -278,12 +278,6 @@ class DeprecatedMultiResponseModel( ) -class ResponseList(BaseModel, Generic[ResponseDataT]): - """A response that returns a list resource.""" - - __root__: List[ResponseDataT] - - class NotifyRefetchBody(BaseResponseBody): """A notification response that returns a flag for refetching via HTTP.""" diff --git a/robot-server/tests/runs/router/test_labware_router.py b/robot-server/tests/runs/router/test_labware_router.py index 9a38ce6cd0f..1e3b929446d 100644 --- a/robot-server/tests/runs/router/test_labware_router.py +++ b/robot-server/tests/runs/router/test_labware_router.py @@ -169,7 +169,7 @@ async def test_get_run_labware_definition( runId="run-id", run_data_manager=mock_run_data_manager ) - assert result.content.data.__root__ == [ + assert result.content.data == [ SD_LabwareDefinition.construct(namespace="test_1"), # type: ignore[call-arg] SD_LabwareDefinition.construct(namespace="test_2"), # type: ignore[call-arg] ]