Y24-268 - Create a presenter for automated submission for WGS branch on Adp Lig plate #1982

StephenHulme · 2024-10-08T13:10:49Z

Closes sanger/sequencescape#4290

Changes proposed in this pull request

Refactors sidebar rendering
Adds a new PermissiveSubmissionPlatePresenter adding elements of the PermissivePlatePresenter to the SubmissionPlatePresenter
Adds a new permissive submission state machine
Rewords workflow message
Prevents new submissions from being created if any are currently active for a plate

Current issues

Pooling affects availability of Add an empty ___ plate button - I think this is expected?

Current screenshots

Previous screenshots

Instructions for Reviewers

[All PRs] - Confirm PR template filled
[Feature Branches] - Review code
[Production Merges to main]
- Check story numbers included
- Check for debug code
- Check version

codecov · 2024-10-08T13:18:22Z

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 78.18%. Comparing base (0c7e26e) to head (44817ff).
Report is 37 commits behind head on develop.

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #1982      +/-   ##
===========================================
+ Coverage    77.97%   78.18%   +0.21%     
===========================================
  Files          459      466       +7     
  Lines        17699    17989     +290     
  Branches       225      225              
===========================================
+ Hits         13800    14065     +265     
- Misses        3897     3922      +25     
  Partials         2        2

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javascript	`69.69% <ø> (ø)`
pull_request	`78.05% <100.00%> (+0.08%)`	⬆️
push	`78.04% <100.00%> (+0.07%)`	⬆️
ruby	`91.16% <100.00%> (+<0.01%)`	⬆️

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StephenHulme · 2024-10-11T13:35:05Z

app/models/concerns/presenters/statemachine/permissive_submission.rb

+ state :passed do
+ include StateAllowsChildCreation
+ include DoesNotAllowLibraryPassing
+
+ def sidebar_partial
+ 'submission_default'
+ end
+ end


'submission_default' shows the newly combined sidebar

StephenHulme · 2024-10-11T13:37:38Z

app/models/presenters/submission_plate_presenter.rb

- include Presenters::StateChangeless
+ # TODO: confirm Presenters::StateChangeless is not required here


This is almost certainly incorrect, but as StateChangeless says "Include in presenters that suppress state changes under all circumstances", this feels like a good start. If State Changes are prevented the Manual Transfer button is not displayed (and I'm assuming the plate cannot enter passed state).
I suspect the way forward is to specify under what circumstances the state may change or not.

Solved by creating a new SubmissionBehaviour in d15c05e that can be used where required

StephenHulme · 2024-10-11T13:41:17Z

@yoldas @KatyTaylor @andrewsparkes thanks for the conversation this morning - it gave me a much better idea of what we are trying to achieve, the various ways of doing so, and why.
Would you please have a look at this PR to confirm I'm on the correct track? I've highlighted some areas of interest in the comments.

StephenHulme · 2024-10-14T14:54:02Z

app/views/plates/_choose_workflow.html.erb

+ <%# TODO: confirm that this is a suitable check and does not disrupt workflows besides LCMT WGS branch %>
+ <% if not presenter.labware.any_complete_requests? %>


How can I check and confirm this?

I don't see any checking of requests working on a labware created via permissive presenters, because I think that labware will be in pending state and have no aliquots/samples or requests because nothing has been transferred into it yet.
(we discussed this the other day, but I forget the conclusion! am I wrong?)

In theory a plate in a pipeline could have both completed and active requests. e.g. Bespoke chromium splits into 3 library preps each with a different submission and requests. So, including the closed request for the DNA prep part of the pipeline that ends with creation of the branch point plate, the branch plate could have 3 more to make 4 in total, e.g. 2 completed sets of library prep requests per well plus a third set of library prep requests still active (3 different library types). (NB. that one does not have automated submissions)

- Potential multiple workflows will be evident from multiple buttons - Active workflows/submissions will be visible above this message

StephenHulme · 2024-10-15T15:21:00Z

From issue story:

We should restrict submission button to only display if there’s not already an active submission of configured type

Addressed in a154da1

codeclimate · 2024-10-15T15:26:06Z

Code Climate has analyzed commit 44817ff and detected 0 issues on this pull request.

The test coverage on the diff in this pull request is 100.0% (50% is the threshold).

This pull request will bring the total coverage in the repository to 91.2% (0.1% change).

View more on Code Climate.

andrewsparkes

Looks good to me. Just check Submission values for WGS.

andrewsparkes · 2024-10-21T08:44:14Z

config/purposes/lcm_triomics.wip.yml

+ template_name: 'Limber-Htp - LCM Triomics WGS'
+ allowed_extra_barcodes: false
+ request_options:
+ # TODO: replace with the correct request options


Assume you've asked Scott about those fragment sizes?

StephenHulme added 2 commits October 1, 2024 09:42

feat: add wgs branch initial plate purpose

d8c4a08

Merge branch 'develop' into y24-268-adp-lig-plate-automated-submission

db07ab5

StephenHulme added 6 commits October 10, 2024 15:04

wip: lcmt

9e5cf02

refactor: allow combining of sidebar elements using a parent container

3478941

fix: change choose-workflow message when there is an active workflow

856acef

feat: create a new PermissiveSubmissionPlatePresenter and state machine

1823148

fix: allow plates to be passed in PermissiveSubmissionPlatePresenter

fc0507b

style: clean-up comments

9ffc791

StephenHulme marked this pull request as draft October 11, 2024 13:30

style: clean-up another comment

531230d

StephenHulme requested review from yoldas and andrewsparkes October 11, 2024 13:33

StephenHulme assigned KatyTaylor and unassigned KatyTaylor Oct 11, 2024

StephenHulme requested a review from KatyTaylor October 11, 2024 13:33

StephenHulme commented Oct 11, 2024

View reviewed changes

StephenHulme added 9 commits October 14, 2024 12:44

fix: add temporary request options

2f2b8a2

refactor: pull out submission behviour into a separate module

d15c05e

fix: allow new presenter to be independent of SubmissionPlatePresenter

9d5ad09

tests: add tests for PermissiveSubmissionPlatePresenter

25c46ff

style: lint

06a88de

Merge branch 'develop' into y24-268-adp-lig-plate-automated-submission

29150e1

style: remove old comment

13bb548

style: update documentation comments

a132f2d

tests: it_behaves_like a stock presenter becomes it allows state change

af888f7

StephenHulme commented Oct 14, 2024

View reviewed changes

StephenHulme marked this pull request as ready for review October 14, 2024 15:01

StephenHulme added 3 commits October 15, 2024 15:45

fix: only allow a new submission if none are currently active or pending

a154da1

fix: clean up display of existing submissions card

dd447a1

fix: keep it simple by generalising the workflows message

44817ff

- Potential multiple workflows will be evident from multiple buttons - Active workflows/submissions will be visible above this message

StephenHulme requested review from andrewsparkes and KatyTaylor and removed request for andrewsparkes and KatyTaylor October 16, 2024 10:15

andrewsparkes approved these changes Oct 21, 2024

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Y24-268 - Create a presenter for automated submission for WGS branch on Adp Lig plate #1982

Y24-268 - Create a presenter for automated submission for WGS branch on Adp Lig plate #1982

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andrewsparkes Oct 21, 2024

		include Presenters::StateChangeless
		# TODO: confirm Presenters::StateChangeless is not required here

		<%# TODO: confirm that this is a suitable check and does not disrupt workflows besides LCMT WGS branch %>
		<% if not presenter.labware.any_complete_requests? %>

Y24-268 - Create a presenter for automated submission for WGS branch on Adp Lig plate #1982

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Y24-268 - Create a presenter for automated submission for WGS branch on Adp Lig plate #1982

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