feat(protocol-engine): absorbance plate reader engine load behavior and lid movement command #15599

ahiuchingau · 2024-07-08T20:38:15Z

Overview

Covers PLAT-447 PLAT-381 PLAT-210 PLAT-209 PLAT-204 PLAT-205 PLAT-206 PLAT-215 PLAT-193 PLAT-194 PLAT-397 PLAT-398 PLAT-406 PLAT-407
This PR introduces the fundamental load module and labware presence behavior for the plate reader and it's associated lid.
This PR implements the open_lid and close_lid commands for the plate reader.

Changelog

add plate reader lid definition as a labware
add lid dock addressable areas to the deck definition
add plate reader lid definition as legacyFixture to be loaded as deck fixed labware
update deck fixed labware logic to account for deck configuration, addressable areas, etc
load the module lid labware when the protocol engine is created so long as a plate reader exists in the deck configuration
load the module lid in for analysis whenever a load module command occurs for the plate reader
add protocol engine action AddAbsorbanceReaderLidAction to pass the lid's labware id to the absorbance plate reader substate in the case of analysis and virtualized modules
add open_lid and close_lid protocol engine command

Tests

Ensure plate reader lid is loaded into protocol engine on start, and references to opening and closing pass analysis
Ensure that open and close lid remove and replace the lid of the plate reader as expected during a run
Ensure the Deck Configuration provides the addressable areas needed for referencing the two primary locations on the plate reader

ahiuchingau · 2024-07-09T18:43:11Z

shared-data/labware/definitions/2/opentrons_flex_lid_absorbance_plate_reader_module/1.json

+  ],
+  "parameters": {
+    "format": "irregular",
+    "quirks": [],


add a new quirk: unloadable_by_user
Add engine logic to check the quirk

…ds and bump required version to 2.21

…e commands and bump required version to 2.21

… ensure addressable areas used exclusively

github-actions · 2024-07-24T20:42:33Z

A PR has been opened to address analyses snapshot changes. Please review the changes here: https://github.com/Opentrons/opentrons/pull/

CaseyBatten · 2024-07-24T20:50:18Z

Some notes on behavior changes in this latest commit:

I have added the Plate Reader Lid to the legacyFixtures of the ot3_standard.json v5 file with their "slots" aligning to the addressable area of the Reader they are physically associated with
DeckFixedLabware has had it's location parameter update to accept any labware location, not just deck slot locations
When create_protocol_engine handles deck fixed labware, it now can account for these kinds of "addressable area" based labware items, and will only load them if the deck configuration provides a fixture that matches
The Modules state store is now passed deck fixed labware as well
When a plate reader module is loaded, and the state store initializes it's substate, the plate reader will now assign it's lid labware id based on which lids are available in the deck fixed labware list that match the modules expected mounting position
When in analysis, the Protocol Core API will manually load a plate reader lid labware onto the newly loaded plate reader module, allowing us to perform with the same behavior as a run even with the absence of the deck configuration
Module behavior for the Plate Readers now exclusively utilizes the plate reader addressable areas, as opposed to slots D3 and D4
Open and Close lid functions also operate exclusively on addressable areas

After exploring a series of implementation methods to get us where we want to be with this, this series of changes made the most sense. Let us know your thoughts on this and if any apparent problems would arise from these refactors.

codecov · 2024-07-25T15:06:00Z

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 63.31%. Comparing base (61d23fc) to head (9c26a9a).
Report is 2 commits behind head on edge.

Additional details and impacted files

@@           Coverage Diff           @@
##             edge   #15599   +/-   ##
=======================================
  Coverage   63.31%   63.31%           
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  Files         300      300           
  Lines       15773    15773           
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  Hits         9986     9986           
  Misses       5787     5787

Flag	Coverage Δ
g-code-testing	`92.43% <ø> (ø)`
shared-data	`73.40% <ø> (ø)`

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github-actions · 2024-07-25T15:11:36Z

A PR has been opened to address analyses snapshot changes. Please review the changes here: https://github.com/Opentrons/opentrons/pull/

this was set to 2 21 for testing but should remain at 2 20

ecormany · 2024-07-25T16:00:19Z

Took a quick look at docstrings and they're good for now! We can make any edits this fall when we write a full documentation page for the reader (RTC-488).

vegano1 · 2024-08-06T19:39:32Z

api/src/opentrons/protocol_engine/commands/absorbance_reader/close_lid.py

+    pickUpOffset: Optional[LabwareOffsetVector] = Field(
+        None,
+        description="Offset to use when picking up labware. "
+        "Experimental param, subject to change",
+    )
+    dropOffset: Optional[LabwareOffsetVector] = Field(
+        None,
+        description="Offset to use when dropping off labware. "
+        "Experimental param, subject to change",
+    )


@CaseyBatten
Do we still need this?, since we know the exact location of the lid per the definition?

We utilized this previously for D3/D4 movement estimations (third column in general) before the addressable area hookups were in place, can definitely be removed now.

vegano1 · 2024-08-06T19:41:23Z

api/src/opentrons/protocol_engine/commands/absorbance_reader/close_lid.py

+        # TODO (AA): we probably don't need this, but let's keep it until we're sure
+        user_offset_data = LabwareMovementOffsetData(
+            pickUpOffset=params.pickUpOffset or LabwareOffsetVector(x=0, y=0, z=0),
+            dropOffset=params.dropOffset or LabwareOffsetVector(x=0, y=0, z=0),
+        )


What do we still need this for?

Same reasoning as stated above, can be removed now.

vegano1 · 2024-08-06T19:42:18Z

api/src/opentrons/protocol_engine/commands/absorbance_reader/open_lid.py

+        # TODO (AA): we probably don't need this, but let's keep it until we're sure
+        user_offset_data = LabwareMovementOffsetData(
+            pickUpOffset=params.pickUpOffset or LabwareOffsetVector(x=0, y=0, z=0),
+            dropOffset=params.dropOffset or LabwareOffsetVector(x=0, y=0, z=0),
+        )


same, not sure if needed anymore?

vegano1 · 2024-08-06T19:45:13Z

api/src/opentrons/protocol_engine/commands/absorbance_reader/read.py

@@ -63,32 +61,32 @@ async def execute(
        if abs_reader is not None:
            result = await abs_reader.start_measure(wavelength=params.sampleWavelength)


Are we guaranteed to be initialized by the time we get here? or do we need to raise some error otherwise?

Do we want to check the plate presence here before beginning a read? since we cant read if there's no plate.

This will be covered in a separate PR related to the Read behavior live data hookups, engine validations, etc.

vegano1 · 2024-08-06T20:05:08Z

@CaseyBatten

This is great, thank you for getting this over the edge!

Left a few comments on

removing pickUpOffset and dropOffset from open/close lid protocol engine commands
Additional validation is needed before measuring like initializing + checking plate presence.

vegano1 · 2024-08-08T20:09:51Z

@CaseyBatten
The changes look good,
let's remove the no longer used pickUpOffset/dropOffset + fix merge conflicts and get this sucker merged :)

… params

vegano1 · 2024-08-09T13:00:20Z

@CaseyBatten

This looks good, thank you for making the changes and fixing the merge conflicts.

The front-end tests failing seems unrelated to the changes made
We will need to update the API command-schema snapshot as the test_command_schema_has_not_changed test is failing

CaseyBatten

These fundamental engine behaviors as well as the framework for Plate Reader interaction allow the use of the plate reader in a protocol and ensure the handling of the lid as an object with trackable state in the context of engine behavior.

CaseyBatten · 2024-08-09T17:32:10Z

api/src/opentrons/protocol_engine/resources/deck_data_provider.py

+                        labware.append(
+                            DeckFixedLabware(
+                                labware_id=labware_id,
+                                definition=definition,
+                                location=addressable_area_location,
+                            )


The addition of the lids to the fixed labware loading mechanism is how we manage to ensure a lid exists within the engine context before an explicit load module command has occurred, utilizing the deck configuration.

CaseyBatten · 2024-08-09T17:35:34Z

shared-data/deck/definitions/5/ot3_standard.json

+      {
+        "id": "absorbanceReaderV1LidA3",
+        "slot": "absorbanceReaderV1A3",
+        "labware": "opentrons_flex_lid_absorbance_plate_reader_module",
+        "displayName": "Plate Reader Lid"
+      },


The addition of this (and all similar plate reader lids) ensures a lid "fixture" labware is tagged via the addressable areas loaded onto the deck. This mechanism gives us the tools to inject labware into the engine context without explicit load commands given only the provided configuration of the deck itself.

CaseyBatten · 2024-08-09T17:38:10Z

api/src/opentrons/protocol_engine/commands/absorbance_reader/open_lid.py

+        new_location = self._state_view.modules.absorbance_reader_dock_location(
+            mod_substate.module_id
+        )


Ensure we handle the Lid dock as an addressable area, resolved via the module which created it.

CaseyBatten · 2024-08-09T17:39:01Z

api/src/opentrons/protocol_engine/commands/absorbance_reader/close_lid.py

+            addressableAreaName=self._state_view.modules.ensure_and_convert_module_fixture_location(
+                deck_slot=self._state_view.modules.get_location(
+                    params.moduleId
+                ).slotName,
+                deck_type=self._state_view.config.deck_type,
+                model=absorbance_model,
+            )
+        )


Ensure we handle the module reader slot as an addressable area, resolved through the module and location in which the module was loaded.

…nd lid movement command (#15599) Covers PLAT-447 PLAT-381 PLAT-210 PLAT-209 PLAT-215 Introduces the fundamental load module and labware presence behavior for the plate reader and it's associated lid, includes the `open_lid` and `close_lid` commands for the plate reader.

ahiuchingau force-pushed the abs96_move-lid-command branch from 439e88f to c46bd3a Compare July 9, 2024 17:06

ahiuchingau commented Jul 9, 2024

View reviewed changes

ahiuchingau added 13 commits July 10, 2024 13:52

PLAT-397 add module lid definition

f694335

PLAT-398 add module lid dock addressable area

ed13f7c

squash! PLAT-397 add module lid definition

957f246

fixup async byonoy library get_plate_presence()

6051392

PLAT-215 load lid in lid dock when module is loaded

29d0418

PLAT-209 & PLAT-210 add open_lid and close_lid protocol engine comman…

7935c4f

…ds and bump required version to 2.21

some changes required to get the app working

d6200b6

squash! PLAT-209 & PLAT-210 add open_lid and close_lid protocol engin…

0e2b885

…e commands and bump required version to 2.21

update absorbance module offset in definition

febc1d2

add a protocol engine error

d656112

error handling

262cdf2

update setup-py

eb053b1

format

fece1e7

ahiuchingau force-pushed the abs96_move-lid-command branch from b34f5bd to fece1e7 Compare July 10, 2024 19:09

ahiuchingau and others added 4 commits July 10, 2024 18:05

AddAbsorbanceReaderLidAction to add lid id as module substate

58ace2d

fix linter errors

cda987a

simplified protocol commmands

772d913

streamline engine logic include plate reader lid as fixed labware and…

6371d4d

… ensure addressable areas used exclusively

CaseyBatten marked this pull request as ready for review July 24, 2024 20:50

CaseyBatten requested review from a team as code owners July 24, 2024 20:50

CaseyBatten requested review from mjhuff and removed request for a team July 24, 2024 20:50

CaseyBatten changed the title ~~feat(protocol-engine): absorbance plate reader lid movement command~~ feat(protocol-engine): absorbance plate reader engine load behavior and lid movement command Jul 24, 2024

labware fixture correction for app tests

f1ff265

CaseyBatten added 2 commits July 25, 2024 10:59

remove lid from app view

dbb5792

Merge branch 'edge' into abs96_move-lid-command

051e1bd

correct max api version

4ceef15

this was set to 2 21 for testing but should remain at 2 20

analysis validation fix accounting for reader lid as fixture

93176e3

CaseyBatten requested a review from jbleon95 July 26, 2024 20:37

vegano1 approved these changes Aug 6, 2024

View reviewed changes

CaseyBatten added 3 commits August 8, 2024 17:08

Removal of hard coded pickup and drop offsets from open and close lid…

acabc45

… params

Merge branch 'edge' into abs96_move-lid-command

7f70a80

linting fixes

9c26a9a

CaseyBatten added 3 commits August 9, 2024 10:30

command schema v9 fix

9639e28

schema lint

c77522e

compatible labware pipette fix

83fd7d0

CaseyBatten approved these changes Aug 9, 2024

View reviewed changes

CaseyBatten merged commit 58a7d19 into edge Aug 9, 2024
59 checks passed

vegano1 deleted the abs96_move-lid-command branch August 9, 2024 17:43

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feat(protocol-engine): absorbance plate reader engine load behavior and lid movement command #15599

feat(protocol-engine): absorbance plate reader engine load behavior and lid movement command #15599

ahiuchingau commented Jul 8, 2024 •

edited by vegano1

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CaseyBatten Aug 9, 2024

		@@ -63,32 +61,32 @@ async def execute(
		if abs_reader is not None:
		result = await abs_reader.start_measure(wavelength=params.sampleWavelength)

feat(protocol-engine): absorbance plate reader engine load behavior and lid movement command #15599

feat(protocol-engine): absorbance plate reader engine load behavior and lid movement command #15599

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ahiuchingau commented Jul 8, 2024 • edited by vegano1 Loading

Overview

Changelog

Tests

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ahiuchingau commented Jul 8, 2024 •

edited by vegano1

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