From 72bad58e50c21982ef04babc637c6fdfd147283a Mon Sep 17 00:00:00 2001 From: Seth Foster Date: Mon, 13 Nov 2023 16:51:20 -0500 Subject: [PATCH 1/6] chore(app-shell): Fix internal release updates (#13966) Since ac0304a5c61462c2c31174308f88eed5404cfda8 we were not properly setting the folder-part of the app update flow in internal-releases which meant the app couldn't update. Closes RQA-1882 --- .github/workflows/app-test-build-deploy.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/app-test-build-deploy.yaml b/.github/workflows/app-test-build-deploy.yaml index f50e4c0ad9e..dc93eae9c9a 100644 --- a/.github/workflows/app-test-build-deploy.yaml +++ b/.github/workflows/app-test-build-deploy.yaml @@ -230,7 +230,7 @@ jobs: echo "Configuring project, bucket, and folder for ot3" echo "project=ot3" >> $GITHUB_OUTPUT echo "bucket=${{env._APP_DEPLOY_BUCKET_OT3}}" >> $GITHUB_OUTPUT - echo "folder=${{env._APP_DEPLOY_BUCKET_OT3}}" >> $GITHUB_OUTPUT + echo "folder=${{env._APP_DEPLOY_FOLDER_OT3}}" >> $GITHUB_OUTPUT fi - uses: 'actions/checkout@v3' with: From be2ac8e55139d9945bfff277f9758dc0add14a47 Mon Sep 17 00:00:00 2001 From: Seth Foster Date: Mon, 13 Nov 2023 17:19:13 -0500 Subject: [PATCH 2/6] chore: update internal release notes (#13967) --- api/release-notes-internal.md | 47 +++-------------------- app-shell/build/release-notes-internal.md | 18 +++------ 2 files changed, 11 insertions(+), 54 deletions(-) diff --git a/api/release-notes-internal.md b/api/release-notes-internal.md index 07c68ac4749..426958f061b 100644 --- a/api/release-notes-internal.md +++ b/api/release-notes-internal.md @@ -4,52 +4,17 @@ For more details about this release, please see the full [technical change log][ --- -# Internal Release 0.14.0 +# Internal Release 1.0.0 ## New Stuff In This Release -- Return tip heights and some other pipette behaviors are now properly executed based on the kind of tip being used -- Release Flex robot software builds are now cryptographically signed. If you run a release build, you can only install other properly signed release builds. Note that if the robot was previously on a non-release build this won't latch; remove the update server config file at ``/var/lib/otupdate/config.json`` to go back to signed builds only. -- Error handling has been overhauled; all errors now display with an error code for easier reporting. Many of those error codes are the 4000 catchall still but this will improve over time. -- If there's an error during the post-run cleanup steps, where the robot homes and drops tips, the run should no longer get stuck in a permanent "finishing" state. It should get marked as failed. -- Further updates to Flex motion control parameters from hardware testing for both gantry and plunger speeds and acceleration -- Pipette overpressure detection is now integrated. -- All instrument flows should now show errors if they occur instead of skipping a step -- Fixes to several incorrect status displays in ODD (i.e. protocols skipping the full-color outcome splash) -- Robot can now handle json protocol v7 -- Support for PVT (v1.1) grippers -- Update progress should get displayed after restart for firmware updates -- Removed `use_pick_up_location_lpc_offset` and `use_drop_location_lpc_offset` from `protocol_context.move_labware` arguments. So they should be removed from any protocols that used them. This change also requires resetting the protocol run database on the robot. -- Added 'contextual' gripper offsets to deck, labware and module definitions. So, any labware movement offsets that were previously being specified in the protocol should now be removed or adjusted or they will get added twice. +- Fixed an issue where the robot wasn't actually checking for updates; you will now correctly get prompted to update your robot from the settings tab of the ODD when an update is available, including during onboarding +- You can update the robot by putting a system update (ot3-system.zip) on a flash drive and plugging it in the front USB port, then going to robot settings +- Support for 96-channel pipettes in protocols +- Early provisional support for deck configuration and trash chutes in protocols ## Big Things That Don't Work Yet So Don't Report Bugs About Them ### Robot Control -- Pipette pressure sensing for liquid-level sensing purposes -- Labware pick up failure with gripper -- E-stop integrated handling especially with modules - -## Big Things That Do Work Please Do Report Bugs About Them -### Robot Control -- Protocol behavior -- Labware movement between slots/modules, both manual and with gripper, from python protocols -- Labware drop/gripper crash errors, but they're very insensitive -- Pipette and gripper automated offset calibration -- Network connectivity and discoverability -- Firmware update for all devices -- Cancelling a protocol run. We're even more sure we fixed this so definitely tell us if it's not. -- USB connectivity -- Stall detection firing basically ever unless you clearly ran into something - -### ODD -- Protocol execution including end-of-protocol screen -- Protocol run monitoring -- Attach and calibrate -- Network connection management, including viewing IP addresses and connecting to wifi networks -- Automatic updates of robot software when new internal releases are created -- Chrome remote devtools - if you enable them and then use Chrome to go to robotip:9223 you'll get devtools -- After a while, the ODD should go into idle; if you touch it, it will come back online - - - +- Pipette partial tip pickup is present but not fully validated or developed yet. Partial tip pickup on 96 channel pipettes will not use correct motion parameters; using the front channel of a pipette in partial tip pickup does not work. diff --git a/app-shell/build/release-notes-internal.md b/app-shell/build/release-notes-internal.md index 08663572808..3c53342b57c 100644 --- a/app-shell/build/release-notes-internal.md +++ b/app-shell/build/release-notes-internal.md @@ -3,26 +3,18 @@ For more details about this release, please see the full [technical changelog][] --- -# Internal Release 0.14.0 +# Internal Release 1.0.0 -This is 0.14.0, an internal release for the app supporting the Opentrons Flex. +This is 1.0.0, an internal release for the app supporting the Opentrons Flex. This is still pretty early in the process, so some things are known not to work, and are listed below. Some things that may surprise you do work, and are also listed below. There may also be some littler things of note, and those are at the bottom. ## New Stuff In This Release -- All instrument flows should display errors properly now -- Update robot flows don't say OT-2s anymore -- There should be fewer surprise scroll bars on Windows -- The configuration of the on-device display can be factory-reset, which lets you go back to the first-time setup flow +- Support for running labware position check using the calibration adapter for added accuracy (note: not an automated flow, just uses the adapter instead of a tip) +- Support for 96-channel pipettes in protocols +- Early provisional support for deck configuration and trash chutes in protocols -## Big Things That Do Work Please Do Report Bugs About Them -- Connecting to a Flex, including via USB -- Running protocols on those Flexs including simulate, play/pause, labware position check - - Except for gripper; no LPC for gripper -- Attach, detach, and calibration flows for pipettes and gripper when started from the device page -- Automatic updates of app and robot when new internal-releases are created - From 1b3d68027a5a769d11689166fde06f16983bab24 Mon Sep 17 00:00:00 2001 From: Sarah Breen Date: Wed, 15 Nov 2023 10:59:48 -0500 Subject: [PATCH 3/6] feat(shared-data, app): add configureNozzleLayout command type in run log (#13961) * feat(shared-data, app): add configureNozzleLayout command type and run log support --- .../en/protocol_command_text.json | 3 +- .../CommandText/PipettingCommandText.tsx | 16 ++++++- .../__tests__/CommandText.test.tsx | 2 +- app/src/organisms/CommandText/index.tsx | 19 ++++++++ .../CommandText/utils/getWellRange.ts | 46 +++++++++++++++++++ app/src/organisms/CommandText/utils/index.ts | 1 + shared-data/command/types/setup.ts | 37 +++++++++++++++ 7 files changed, 121 insertions(+), 3 deletions(-) create mode 100644 app/src/organisms/CommandText/utils/getWellRange.ts diff --git a/app/src/assets/localization/en/protocol_command_text.json b/app/src/assets/localization/en/protocol_command_text.json index 8d84b9e341f..fddc61a345e 100644 --- a/app/src/assets/localization/en/protocol_command_text.json +++ b/app/src/assets/localization/en/protocol_command_text.json @@ -6,6 +6,7 @@ "closing_tc_lid": "Closing Thermocycler lid", "comment": "Comment", "configure_for_volume": "Configure {{pipette}} to aspirate {{volume}} µL", + "configure_nozzle_layout": "Configure {{pipette}} to use {{amount}} nozzles", "confirm_and_resume": "Confirm and resume", "deactivate_hs_shake": "Deactivating shaker", "deactivate_temperature_module": "Deactivating Temperature Module", @@ -37,7 +38,7 @@ "opening_tc_lid": "Opening Thermocycler lid", "pause_on": "Pause on {{robot_name}}", "pause": "Pause", - "pickup_tip": "Picking up tip from {{well_name}} of {{labware}} in {{labware_location}}", + "pickup_tip": "Picking up tip(s) from {{well_range}} of {{labware}} in {{labware_location}}", "prepare_to_aspirate": "Preparing {{pipette}} to aspirate", "return_tip": "Returning tip to {{well_name}} of {{labware}} in {{labware_location}}", "save_position": "Saving position", diff --git a/app/src/organisms/CommandText/PipettingCommandText.tsx b/app/src/organisms/CommandText/PipettingCommandText.tsx index 8aff25b4da3..7285195c994 100644 --- a/app/src/organisms/CommandText/PipettingCommandText.tsx +++ b/app/src/organisms/CommandText/PipettingCommandText.tsx @@ -16,7 +16,9 @@ import { getLabwareName, getLabwareDisplayLocation, getFinalLabwareLocation, + getWellRange, } from './utils' +import type { PipetteName } from '@opentrons/shared-data' type PipettingRunTimeCommmand = | AspirateRunTimeCommand @@ -122,8 +124,20 @@ export const PipettingCommandText = ({ }) } case 'pickUpTip': { + const pipetteId = command.params.pipetteId + const pipetteName: + | PipetteName + | undefined = robotSideAnalysis.pipettes.find( + pip => pip.id === pipetteId + )?.pipetteName + return t('pickup_tip', { - well_name: wellName, + well_range: getWellRange( + pipetteId, + allPreviousCommands, + wellName, + pipetteName + ), labware: getLabwareName(robotSideAnalysis, labwareId), labware_location: displayLocation, }) diff --git a/app/src/organisms/CommandText/__tests__/CommandText.test.tsx b/app/src/organisms/CommandText/__tests__/CommandText.test.tsx index 28ef08f940f..0ce3a0e6ded 100644 --- a/app/src/organisms/CommandText/__tests__/CommandText.test.tsx +++ b/app/src/organisms/CommandText/__tests__/CommandText.test.tsx @@ -219,7 +219,7 @@ describe('CommandText', () => { { i18nInstance: i18n } )[0] getByText( - 'Picking up tip from A1 of Opentrons 96 Tip Rack 300 µL in Slot 9' + 'Picking up tip(s) from A1 of Opentrons 96 Tip Rack 300 µL in Slot 9' ) } }) diff --git a/app/src/organisms/CommandText/index.tsx b/app/src/organisms/CommandText/index.tsx index 67e76526ab1..8ce1605f5fa 100644 --- a/app/src/organisms/CommandText/index.tsx +++ b/app/src/organisms/CommandText/index.tsx @@ -165,6 +165,25 @@ export function CommandText(props: Props): JSX.Element | null { ) } + case 'configureNozzleLayout': { + const { configuration_params, pipetteId } = command.params + const pipetteName = robotSideAnalysis.pipettes.find( + pip => pip.id === pipetteId + )?.pipetteName + + // TODO (sb, 11/9/23): Add support for other configurations when needed + return ( + + {t('configure_nozzle_layout', { + amount: configuration_params.style === 'COLUMN' ? '8' : 'all', + pipette: + pipetteName != null + ? getPipetteNameSpecs(pipetteName)?.displayName + : '', + })} + + ) + } case 'prepareToAspirate': { const { pipetteId } = command.params const pipetteName = robotSideAnalysis.pipettes.find( diff --git a/app/src/organisms/CommandText/utils/getWellRange.ts b/app/src/organisms/CommandText/utils/getWellRange.ts new file mode 100644 index 00000000000..8baa6c0b709 --- /dev/null +++ b/app/src/organisms/CommandText/utils/getWellRange.ts @@ -0,0 +1,46 @@ +import { + getPipetteNameSpecs, + PipetteName, + RunTimeCommand, +} from '@opentrons/shared-data' + +/** + * @param pipetteName name of pipette being used + * @param commands list of commands to search within + * @param wellName the target well for pickup tip + * @returns WellRange string of wells pipette will pickup tips from + */ +export function getWellRange( + pipetteId: string, + commands: RunTimeCommand[], + wellName: string, + pipetteName?: PipetteName +): string { + const pipetteChannels = pipetteName + ? getPipetteNameSpecs(pipetteName)?.channels ?? 1 + : 1 + let usedChannels = pipetteChannels + if (pipetteChannels === 96) { + for (const c of commands.reverse()) { + if ( + c.commandType === 'configureNozzleLayout' && + c.params?.pipetteId === pipetteId + ) { + // TODO(sb, 11/9/23): add support for quadrant and row configurations when needed + if (c.params.configuration_params.style === 'SINGLE') { + usedChannels = 1 + } else if (c.params.configuration_params.style === 'COLUMN') { + usedChannels = 8 + } + break + } + } + } + if (usedChannels === 96) { + return 'A1 - H12' + } else if (usedChannels === 8) { + const column = wellName.substr(1) + return `A${column} - H${column}` + } + return wellName +} diff --git a/app/src/organisms/CommandText/utils/index.ts b/app/src/organisms/CommandText/utils/index.ts index 0b7a5c24124..5435a292d11 100644 --- a/app/src/organisms/CommandText/utils/index.ts +++ b/app/src/organisms/CommandText/utils/index.ts @@ -5,3 +5,4 @@ export * from './getModuleDisplayLocation' export * from './getLiquidDisplayName' export * from './getLabwareDisplayLocation' export * from './getFinalLabwareLocation' +export * from './getWellRange' diff --git a/shared-data/command/types/setup.ts b/shared-data/command/types/setup.ts index f8fb78752e5..e5b3184241d 100644 --- a/shared-data/command/types/setup.ts +++ b/shared-data/command/types/setup.ts @@ -71,7 +71,20 @@ export interface LoadFixtureRunTimeCommand result?: LoadLabwareResult } +export interface ConfigureNozzleLayoutCreateCommand + extends CommonCommandCreateInfo { + commandType: 'configureNozzleLayout' + params: ConfigureNozzleLayoutParams +} + +export interface ConfigureNozzleLayoutRunTimeCommand + extends CommonCommandRunTimeInfo, + ConfigureNozzleLayoutCreateCommand { + result?: {} +} + export type SetupRunTimeCommand = + | ConfigureNozzleLayoutRunTimeCommand | LoadPipetteRunTimeCommand | LoadLabwareRunTimeCommand | LoadFixtureRunTimeCommand @@ -80,6 +93,7 @@ export type SetupRunTimeCommand = | MoveLabwareRunTimeCommand export type SetupCreateCommand = + | ConfigureNozzleLayoutCreateCommand | LoadPipetteCreateCommand | LoadLabwareCreateCommand | LoadFixtureCreateCommand @@ -161,3 +175,26 @@ interface LoadFixtureParams { loadName: FixtureLoadName fixtureId?: string } + +const COLUMN = 'COLUMN' +const SINGLE = 'SINGLE' +const ROW = 'ROW' +const QUADRANT = 'QUADRANT' +const EMPTY = 'EMPTY' + +export type NozzleConfigurationStyle = + | typeof COLUMN + | typeof SINGLE + | typeof ROW + | typeof QUADRANT + | typeof EMPTY + +interface NozzleConfigurationParams { + primary_nozzle: string + style: NozzleConfigurationStyle +} + +interface ConfigureNozzleLayoutParams { + pipetteId: string + configuration_params: NozzleConfigurationParams +} From 53dbd31efee9aa7e0155f76c5693d5a8196ba2c8 Mon Sep 17 00:00:00 2001 From: Seth Foster Date: Wed, 15 Nov 2023 12:37:39 -0500 Subject: [PATCH 4/6] fix(app): do not require probe presence on 96 (#13986) The 96 channel pipette is not capable of continuously checking for the presence of a tip (or indeed a calibration probe). It needs to run a special routing, exposed through ot3api.get_tip_presence_status() or ot3api.verify_tip_presence(), to check for a tip. This happens automatically in most of the places we use tips - aka inside other protocol engine commands - but it does not happen automatically and all the time. This is usually fine, but when we're doing calibration we do it through a protocol engine maintenance run where the way we interact with the robot is dispatching PE commands - and we don't ever dispatch a PE command that implicitly causes a tip check. That means that the 96 can't be relied on to get the presence of a tip. The long term fix for this is to add a checkTipPresence command to the engine, at least as a maintenance command; in the short term, we can disable the presence check for 96 channel pipettes to unblock testing. Closes RQA-1892 --- app/src/organisms/LabwarePositionCheck/AttachProbe.tsx | 3 ++- app/src/organisms/PipetteWizardFlows/AttachProbe.tsx | 2 +- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/app/src/organisms/LabwarePositionCheck/AttachProbe.tsx b/app/src/organisms/LabwarePositionCheck/AttachProbe.tsx index f54032e48f1..48f9353147e 100644 --- a/app/src/organisms/LabwarePositionCheck/AttachProbe.tsx +++ b/app/src/organisms/LabwarePositionCheck/AttachProbe.tsx @@ -78,6 +78,7 @@ export const AttachProbe = (props: AttachProbeProps): JSX.Element | null => { (instrument): instrument is PipetteData => instrument.ok && instrument.mount === pipetteMount ) + const is96Channel = attachedPipette?.data.channels === 96 React.useEffect(() => { // move into correct position for probe attach on mount @@ -103,7 +104,7 @@ export const AttachProbe = (props: AttachProbeProps): JSX.Element | null => { setIsPending(true) refetch() .then(() => { - if (attachedPipette?.state?.tipDetected) { + if (is96Channel || attachedPipette?.state?.tipDetected) { chainRunCommands( [ { commandType: 'home', params: { axes: [pipetteZMotorAxis] } }, diff --git a/app/src/organisms/PipetteWizardFlows/AttachProbe.tsx b/app/src/organisms/PipetteWizardFlows/AttachProbe.tsx index f12c7065661..388b6420fae 100644 --- a/app/src/organisms/PipetteWizardFlows/AttachProbe.tsx +++ b/app/src/organisms/PipetteWizardFlows/AttachProbe.tsx @@ -81,7 +81,7 @@ export const AttachProbe = (props: AttachProbeProps): JSX.Element | null => { setIsPending(true) refetch() .then(() => { - if (attachedPipette?.state?.tipDetected) { + if (is96Channel || attachedPipette?.state?.tipDetected) { chainRunCommands?.( [ { From 67d3c55acbe2c71646b4dac275f148fdde3be77b Mon Sep 17 00:00:00 2001 From: Seth Foster Date: Wed, 15 Nov 2023 15:58:17 -0500 Subject: [PATCH 5/6] chore: update update-from-usb fake release notes (#13984) * chore: update update-from-usb fake release notes * Flex --- app-shell-odd/src/system-update/index.ts | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/app-shell-odd/src/system-update/index.ts b/app-shell-odd/src/system-update/index.ts index c0ea2f49ee3..15f64186e0d 100644 --- a/app-shell-odd/src/system-update/index.ts +++ b/app-shell-odd/src/system-update/index.ts @@ -212,7 +212,9 @@ const getVersionFromZipIfValid = (path: string): Promise => const fakeReleaseNotesForMassStorage = (version: string): string => ` # Opentrons Robot Software Version ${version} -This update is from a USB mass storage device connected to your flex, and release notes cannot be shown. +This update is from a USB mass storage device connected to your Flex, and release notes cannot be shown. + +Don't remove the USB mass storage device while the update is in progress. ` export const getLatestMassStorageUpdateFiles = ( From c80798dca9b8d435a0d5c342a9ef7e81525a8438 Mon Sep 17 00:00:00 2001 From: Alise Au <20424172+ahiuchingau@users.noreply.github.com> Date: Wed, 15 Nov 2023 17:48:40 -0500 Subject: [PATCH 6/6] refactor(shared-data): update 96-channel liquid handling functions (#13993) Updates from hardware for 96 channel ul/mm --------- Co-authored-by: Seth Foster --- .../ninety_six_channel/p1000/default/1_0.json | 328 +++++------------- .../ninety_six_channel/p1000/default/3_0.json | 328 +++++------------- .../ninety_six_channel/p1000/default/3_3.json | 328 +++++------------- .../ninety_six_channel/p1000/default/3_4.json | 328 +++++------------- .../ninety_six_channel/p1000/default/3_5.json | 328 +++++------------- 5 files changed, 400 insertions(+), 1240 deletions(-) diff --git a/shared-data/pipette/definitions/2/liquid/ninety_six_channel/p1000/default/1_0.json b/shared-data/pipette/definitions/2/liquid/ninety_six_channel/p1000/default/1_0.json index a3794ba520e..8ca9dc4ece4 100644 --- a/shared-data/pipette/definitions/2/liquid/ninety_six_channel/p1000/default/1_0.json +++ b/shared-data/pipette/definitions/2/liquid/ninety_six_channel/p1000/default/1_0.json @@ -20,96 +20,36 @@ "aspirate": { "default": { "1": [ - [0.4148, -1705.1015, 20.5455], - [0.4476, -80.633, 47.2788], - [0.5512, -1.5936, 11.9026], - [0.6027, -18.9998, 21.4972], - [0.6503, -15.8781, 19.6156], - [0.7733, 3.0612, 7.2993], - [0.8391, -5.2227, 13.7056], - [0.9736, 3.0706, 6.7467], - [1.16, -0.374, 10.1005], - [1.3964, 1.3004, 8.1582], - [1.5815, -0.4837, 10.6494], - [1.8306, 1.1464, 8.0714], - [2.0345, 0.0132, 10.1459], - [2.6221, 0.5374, 9.0794], - [2.9655, -1.7582, 15.0986], - [3.5124, 0.2754, 9.0681], - [4.6591, 1.406, 5.097], - [5.367, 0.394, 9.8123], - [6.0839, 0.3365, 10.1205], - [6.8312, 0.3379, 10.1121], - [7.5676, 0.2611, 10.637], - [8.2397, 0.095, 11.8939], - [8.9776, 0.2015, 11.0165], - [10.413, 0.1332, 11.6294], - [11.8539, 0.1074, 11.8979], - [13.3655, 0.1286, 11.6464], - [14.8236, 0.0758, 12.3519], - [16.3203, 0.083, 12.2457], - [17.7915, 0.0581, 12.6515], - [19.2145, 0.0273, 13.1995], - [20.6718, 0.0388, 12.9792], - [22.1333, 0.0357, 13.044], - [25.0761, 0.0332, 13.0977], - [28.0339, 0.029, 13.2035], - [30.967, 0.0201, 13.4538], - [33.8727, 0.013, 13.6737], - [36.8273, 0.0172, 13.5324], - [39.7594, 0.0121, 13.7191], - [42.6721, 0.0083, 13.8687], - [45.5964, 0.0085, 13.8618], - [48.5297, 0.0084, 13.8668], - [51.4512, 0.0064, 13.9651] + [1.933333, 2.844459, 4.750159], + [2.833333, 1.12901, 8.066694], + [3.603333, 0.254744, 10.543779], + [4.836667, 1.101839, 7.491414], + [5.755, 0.277649, 11.47775], + [6.643333, 0.14813, 12.223126], + [7.548333, 0.145635, 12.239705], + [8.475, 0.15097, 12.199433], + [13.02, 0.071736, 12.870946], + [22.318333, 0.042305, 13.254131], + [36.463333, 0.021195, 13.725284], + [54.82, 0.001805, 14.43229] ] } }, "dispense": { "default": { "1": [ - [0.4148, -1705.1015, 20.5455], - [0.4476, -80.633, 47.2788], - [0.5512, -1.5936, 11.9026], - [0.6027, -18.9998, 21.4972], - [0.6503, -15.8781, 19.6156], - [0.7733, 3.0612, 7.2993], - [0.8391, -5.2227, 13.7056], - [0.9736, 3.0706, 6.7467], - [1.16, -0.374, 10.1005], - [1.3964, 1.3004, 8.1582], - [1.5815, -0.4837, 10.6494], - [1.8306, 1.1464, 8.0714], - 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