fix(api): restrict the labware that can be moved to the plate reader + validate wavelengths. #16649

vegano1 · 2024-10-30T23:04:48Z

Overview

This pull request restricts labware that can be loaded or moved onto a plate reader slot

Contains 96 wells exactly
Is below a certain height restriction (16 mm)

This also restricts the wavelengths that can be used

Closes: PLAT-541 PLAT-581

Test Plan and Hands on Testing

Load and move labware on a plate reader with a height 15mm or less
Make sure we raise LabwareMovementNotAllowedError if the labware is not 96 wells or the height is > 15mm
Make sure we only accept wavelengths in the range of 350 - 1000 nm or throw analysis error otherwise
Make sure we only accept 1 wavelength in single mode and 1-6 wavelengths in multi-mode or throw analysis error otherwise.

Changelog

add raise_if_labware_incompatible_with_plate_reader that checks labware compatibility with the plate reader
use raise_if_labware_incompatible_with_plate_reader in LoadModule and MoveLabware commands.
Add checks to absorbance reader PAPI commands so we fail during analysis if we have invalid wavelengths

Review requests

is the labware.py module the correct location for raise_if_labware_incompatible_with_plate_reader

Risk assessment

low

…reader.

CaseyBatten

Looks great, should do what we need. Just a question below about clarifying our final pick for the max height restriction.

CaseyBatten · 2024-10-31T18:23:53Z

api/src/opentrons/protocol_engine/state/labware.py

+    def raise_if_labware_incompatible_with_plate_reader(
+        self,
+        labware_id: str,
+    ) -> None:
+        """Raise an error if the labware is not compatible with the plate reader."""


Solid, the two cases in here should cover us pretty well.

CaseyBatten · 2024-10-31T18:23:59Z

api/src/opentrons/protocol_engine/state/labware.py

@@ -81,6 +81,10 @@
 }


+# The max height of the labware that can fit in a plate reader
+_PLATE_READER_MAX_LABWARE_Z_MM = 15


Are we sure we want the limit to be 15mm? Inner dimension of the plate reader lid was measured to approximately 16mm.

yeah, just as a margin of error.

This would rule out the Tough PCR plate, which has a definition height of 16.00 mm. I think we definitely want to allow it.

@ecormany
good call out, fixed it.

…reader.

…ub.com/Opentrons/opentrons into PLAT-541-restrict-plate-reader-labware

ecormany · 2024-11-01T18:09:13Z

I'm getting simulation/analysis errors just trying to load a plate reader on this branch. Is this something wrong with my setup?

Protocol (truncated, but it fails on line 23, the one that starts pr =)


requirements = {"robotType": "Flex", "apiLevel": "2.21"}

def run(protocol: protocol_api.ProtocolContext):
    # load tip rack
    tiprack = protocol.load_labware(
        load_name="opentrons_flex_96_tiprack_1000ul", location="C3"
    )
    # attach pipette to left mount
    pipette = protocol.load_instrument(
        instrument_name="flex_1channel_1000",
        mount="left",
        tip_racks=[tiprack]
    )
    # load well plate in deck slot D2
    plate = protocol.load_labware(
        load_name="corning_96_wellplate_360ul_flat", location="D2"
    )
    # load trash bin
    trash = protocol.load_trash_bin("A3")

    pr = protocol.load_module(
        module_name="absorbanceReaderV1",
        location="D3"
    )

Result

ProtocolCommandFailedError [line 23]: Error 4000 GENERAL_ERROR (ProtocolCommandFailedError): LabwareNotLoadedError: Labware 87f8d4f8-4a13-4351-aab3-87d991554d43 not found.
Caught exception: {'message': 'Task was destroyed but it is pending!', 'task': <Task pending name='Task-17' coro=<Poller._poll_forever() done, defined at /Users/edwardcormany/opentrons/api/src/opentrons/hardware_control/poller.py:76> wait_for=<Future pending cb=[Task.task_wakeup()]>>}

vegano1 · 2024-11-01T19:35:42Z

I'm getting simulation/analysis errors just trying to load a plate reader on this branch. Is this something wrong with my setup?

Protocol (truncated, but it fails on line 23, the one that starts pr =)


requirements = {"robotType": "Flex", "apiLevel": "2.21"}

def run(protocol: protocol_api.ProtocolContext):
    # load tip rack
    tiprack = protocol.load_labware(
        load_name="opentrons_flex_96_tiprack_1000ul", location="C3"
    )
    # attach pipette to left mount
    pipette = protocol.load_instrument(
        instrument_name="flex_1channel_1000",
        mount="left",
        tip_racks=[tiprack]
    )
    # load well plate in deck slot D2
    plate = protocol.load_labware(
        load_name="corning_96_wellplate_360ul_flat", location="D2"
    )
    # load trash bin
    trash = protocol.load_trash_bin("A3")

    pr = protocol.load_module(
        module_name="absorbanceReaderV1",
        location="D3"
    )

Result

ProtocolCommandFailedError [line 23]: Error 4000 GENERAL_ERROR (ProtocolCommandFailedError): LabwareNotLoadedError: Labware 87f8d4f8-4a13-4351-aab3-87d991554d43 not found.
Caught exception: {'message': 'Task was destroyed but it is pending!', 'task': <Task pending name='Task-17' coro=<Poller._poll_forever() done, defined at /Users/edwardcormany/opentrons/api/src/opentrons/hardware_control/poller.py:76> wait_for=<Future pending cb=[Task.task_wakeup()]>>}

Yeah there was a bug, should be fixed now.

ecormany · 2024-11-01T20:14:45Z

It loads and the restrictions on wavelengths are working now too! Fantastic.

One question: do we care to distinguish between loading and moving oversize labware to the reader? Currently they both raise the same error:

    reservoir = pr.load_labware(
        name="usascientific_12_reservoir_22ml",
    )

ProtocolCommandFailedError [line 29]: Error 4000 GENERAL_ERROR (ProtocolCommandFailedError): LabwareMovementNotAllowedError: Cannot move 'usascientific_12_reservoir_22ml' into plate reader because the labware contains 12 wells where 96 wells is expected.

codecov · 2024-11-01T21:21:47Z

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@@                  Coverage Diff                   @@
##             chore_release-8.2.0   #16649   +/-   ##
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validate wavelengths for analysis update max height to 16mm and clean up

sfoster1

Looks good but maybe make the wavelength limits a constant?

sfoster1 · 2024-11-05T14:44:33Z

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

+            )
+
+        if reference_wavelength is not None and (
+            reference_wavelength < 350 or reference_wavelength > 1000


can we maybe get these as consts

vegano1 requested a review from a team as a code owner October 30, 2024 23:04

vegano1 requested a review from CaseyBatten October 30, 2024 23:05

fix(api): restrict the labware that can be loaded/moved to the plate …

4c2831e

…reader.

vegano1 force-pushed the PLAT-541-restrict-plate-reader-labware branch from f32ce9d to 4c2831e Compare October 31, 2024 11:54

vegano1 requested a review from a team as a code owner October 31, 2024 11:54

vegano1 requested review from smb2268 and removed request for a team October 31, 2024 11:54

vegano1 changed the base branch from edge to chore_release-8.2.0 October 31, 2024 11:54

CaseyBatten approved these changes Oct 31, 2024

View reviewed changes

vegano1 added 2 commits November 1, 2024 08:51

fix(api): restrict the labware that can be loaded/moved to the plate …

5e890df

…reader.

Merge branch 'PLAT-541-restrict-plate-reader-labware' of https://gith…

f05e9ba

…ub.com/Opentrons/opentrons into PLAT-541-restrict-plate-reader-labware

vegano1 requested a review from a team as a code owner November 1, 2024 19:33

vegano1 changed the title ~~fix(api): restrict the labware that can be loaded/moved to the plate reader.~~ fix(api): restrict the labware that can be moved to the plate reader. Nov 1, 2024

vegano1 force-pushed the PLAT-541-restrict-plate-reader-labware branch from 369c920 to e25402a Compare November 1, 2024 19:40

vegano1 requested a review from ecormany November 1, 2024 19:50

vegano1 force-pushed the PLAT-541-restrict-plate-reader-labware branch from 5b86acb to 6fc53da Compare November 1, 2024 20:02

vegano1 force-pushed the PLAT-541-restrict-plate-reader-labware branch from 04b0cc8 to a950f15 Compare November 1, 2024 21:24

use LabwareDefinition instead of labware id

3129f05

validate wavelengths for analysis update max height to 16mm and clean up

vegano1 force-pushed the PLAT-541-restrict-plate-reader-labware branch from a950f15 to 3129f05 Compare November 3, 2024 22:01

vegano1 changed the title ~~fix(api): restrict the labware that can be moved to the plate reader.~~ fix(api): restrict the labware that can be moved to the plate reader + validate wavelengths. Nov 3, 2024

sfoster1 approved these changes Nov 5, 2024

View reviewed changes

add abs wavelength min/max constants

842edda

vegano1 merged commit 01c06d5 into chore_release-8.2.0 Nov 5, 2024
21 checks passed

vegano1 deleted the PLAT-541-restrict-plate-reader-labware branch November 5, 2024 18:25

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fix(api): restrict the labware that can be moved to the plate reader + validate wavelengths. #16649

fix(api): restrict the labware that can be moved to the plate reader + validate wavelengths. #16649

vegano1 commented Oct 30, 2024 •

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fix(api): restrict the labware that can be moved to the plate reader + validate wavelengths. #16649

fix(api): restrict the labware that can be moved to the plate reader + validate wavelengths. #16649

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vegano1 commented Oct 30, 2024 • edited by jira bot Loading

Overview

Test Plan and Hands on Testing

Changelog

Review requests

Risk assessment

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