DPL-903 Bioscan - Add automatic library prep submissions

[andrewsparkes]

Closes #1381

Changes proposed in this pull request

Modifies Bioscan configuration to allow automatic library prep submissions.
Adds a new submission presenter and statemachine.

[codecov]

Codecov Report

Attention: Patch coverage is 92.64706% with 5 lines in your changes missing coverage. Please review.

Project coverage is 81.76%. Comparing base (981e98d) to head (c16ed6e).

Files with missing lines	Patch %	Lines
...encescape/api/v2/shared/has_workline_identifier.rb	33.33%	4 Missing ⚠️
...esenters/submission_when_passed_plate_presenter.rb	87.50%	1 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #2377      +/-   ##
===========================================
+ Coverage    81.72%   81.76%   +0.04%     
===========================================
  Files          494      496       +2     
  Lines        19248    19313      +65     
  Branches       362      362              
===========================================
+ Hits         15731    15792      +61     
- Misses        3515     3519       +4     
  Partials         2        2              

Flag	Coverage Δ
javascript	75.55% <ø> (ø)
pull_request	81.76% <92.64%> (+0.04%)	⬆️
push	81.76% <92.64%> (+0.04%)	⬆️
ruby	91.86% <92.64%> (+0.01%)	⬆️

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[Copilot]

Pull Request Overview

This pull request introduces automatic library prep submissions for Bioscan by updating configuration settings, adding a new submission presenter, and implementing relevant state machine behavior. Key changes include test specs for the new presenter, configuration updates in YAML and robots files, and adjustments to the workline identifier methods to support arrays.

Reviewed Changes

Copilot reviewed 9 out of 9 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
spec/models/presenters/submission_when_passed_plate_presenter_spec.rb	Adds tests for the new SubmissionWhenPassedPlatePresenter with various submission contexts
spec/models/labels/plate_384_single_label_spec.rb	Adds tests for first_of_configured_purpose including array support for alternative workline identifiers
config/robots.rb	Updates robot configuration comment and purpose values to include both Lysate and Lysate Input
config/purposes/bioscan.yml	Updates plate configuration for submission options and alternative workline identifiers
config/pipelines/high_throughput_bioscan.yml	Adjusts pipeline relationships to include Lysate Input
app/sequencescape/sequencescape/api/v2/shared/has_workline_identifier.rb	Modifies workline_reference to support array config values for alternative workline identifiers
app/models/presenters/submission_when_passed_plate_presenter.rb	Introduces a new presenter for handling submissions when a plate passes
app/models/labels/plate_384_single_label.rb	Updates the method to resolve the first matching ancestor based on alternative workline identifiers
app/models/concerns/presenters/statemachine/submission_when_passed.rb	Implements a state machine for submission behavior on plates

[StephenHulme]

Couple comments, but looks good

[yoldas]

I can't fully remember the randomised controls and lysate negative discussion to check a few more points but overall this PR looks very good.

[KatyTaylor]

Couple of comments but basically seems good I think!

[KatyTaylor]

Just wondering if this file actually needed any code changes -

ancestors.where(purpose_name: alternative_workline_identifier_purpose).last

'where' works with arrays as well as single items, doesn't it?

I expect something blew up though, since you're changing it!