Y24-099 plate split to racks #2028

andrewsparkes · 2024-10-25T11:19:07Z

Closes #1696

Changes proposed in this pull request

Adds specific tube rack and tube creation for scRNA

…99-plate-split-to-racks

KatyTaylor

Haven't looked at the big one yet - the labware creator - but have left some comments on the smaller changes.

KatyTaylor · 2024-10-25T13:27:22Z

app/frontend/stylesheets/limber/screen.scss

@@ -280,6 +282,7 @@ nav.robots-list {
  .work-completion-button,
  .create-plate-button,
  .create-tube-button,
+  .create-tube_rack-button,


Seems like some of this stuff could just be generic, like .create-labware-button or params[:limber_labware_id] in the above file. Let's not add refactoring to the scope of the story though!

Agree, assuming the buttons don't have to have different text or some other difference.

Plus the suggested action Add button now looks like 'Add tube_rack' with an underscore which looks odd (works for tube and plate as they are single word classes).

KatyTaylor · 2024-10-25T13:28:20Z

app/helpers/page_helper.rb

@@ -53,6 +53,7 @@ def jumbotron(jumbotron_id = nil, options = {}, &)
  # eg. state_badge('pending')
  # <span class="state-badge-pending">Pending</span>
  def state_badge(state)
+    return if state.blank?


What happens if this returns nil? The state badge is not shown?

This was temporary to get past the fact that the tube rack didn't have a state. And yes it doesn't show the state badge on the page.

Can be removed once state for TubeRacks is fixed by another story.

KatyTaylor · 2024-10-25T13:32:18Z

app/models/concerns/presenters/creation_behaviour.rb

+  def compatible_tube_rack_purposes
+    construct_buttons(purposes_of_type('tube_rack'))
+  end
+


Feels like this wants to be refactored to:

def compatible_labware_purposes(labware_type) construct_buttons(purposes_of_type(labware_type)) end

But again, maybe we can save up refactoring ideas for another story to try to draw a line under this story! Will keep commenting them if I notice and we can decide what to do.

Yeah. I think this is building the 'other actions' grey buttons. That could do with some better ordering/structuring in any case.

app/models/state_changers.rb

app/sequencescape/sequencescape/api/v2.rb

app/sequencescape/sequencescape/api/v2/aliquot.rb

app/sequencescape/sequencescape/api/v2/tube_rack.rb

KatyTaylor · 2024-10-25T13:53:46Z

config/purposes/scrna_core_cell_extraction.yml

-  :presenter_class: Presenters::SimpleTubePresenter
-  :state_changer_class: StateChangers::AutomaticTubeStateChanger
+      child_spare_tube_rack_purpose_name: TR LRC Bank Spare
+      child_tube_rack_metadata_key: 'tube_rack_barcode'


We want this key to be the same EVERYWHERE, right? It's part of Abdullah's design doc?
So it doesn't feel quite right here against a specific purpose.

How do I reference something like a TubeRack class constant from within a yml file?

I think it should be an app-wide configuration setting on the Sequencescape side.

if it will ALWAYS be the same key then there is no need for Limber to know what it is or include it in the purpose config. instead of passing it through for each tube rack in the attributes, I can pull it out of a tuberack constants initializer file like I made in the other story on the SS side.

Yes exactly

config/routes.rb

…he tuberack, used for fetching active requests

codecov · 2024-11-01T11:04:59Z

Codecov Report

Attention: Patch coverage is 88.23529% with 18 lines in your changes missing coverage. Please review.

Project coverage is 78.11%. Comparing base (e338692) to head (f4eca57).
Report is 25 commits behind head on y24-088-tuberacks-epic.

Files with missing lines	Patch %	Lines
app/models/limber/tube_rack.rb	55.55%	4 Missing ⚠️
...dels/labware_creators/plate_split_to_tube_racks.rb	96.10%	3 Missing ⚠️
app/sequencescape/sequencescape/api/v2.rb	50.00%	3 Missing ⚠️
app/models/state_changers.rb	84.61%	2 Missing ⚠️
app/models/labware_creators.rb	0.00%	1 Missing ⚠️
app/models/limber/multiplexed_library_tube.rb	50.00%	1 Missing ⚠️
app/models/limber/plate.rb	50.00%	1 Missing ⚠️
app/models/limber/tube.rb	50.00%	1 Missing ⚠️
app/sequencescape/sequencescape/api/v2/asset.rb	50.00%	1 Missing ⚠️
app/sequencescape/sequencescape/api/v2/labware.rb	66.66%	1 Missing ⚠️

Additional details and impacted files

@@                    Coverage Diff                     @@
##           y24-088-tuberacks-epic    #2028      +/-   ##
==========================================================
+ Coverage                   78.08%   78.11%   +0.02%     
==========================================================
  Files                         478      480       +2     
  Lines                       18069    18155      +86     
  Branches                      262      262              
==========================================================
+ Hits                        14110    14182      +72     
- Misses                       3957     3971      +14     
  Partials                        2        2

Flag	Coverage Δ
javascript	`69.89% <ø> (ø)`
pull_request	`78.11% <88.23%> (?)`
push	`78.11% <88.23%> (+0.02%)`	⬆️
ruby	`91.16% <88.23%> (-0.10%)`	⬇️

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KatyTaylor · 2024-11-12T14:53:02Z

app/models/labware_creators/plate_split_to_tube_racks.rb

@@ -71,6 +71,9 @@ class PlateSplitToTubeRacks < Base

    PARENT_PLATE_INCLUDES =
      'wells.aliquots,wells.aliquots.sample,wells.downstream_tubes,wells.downstream_tubes.custom_metadatum_collection'
+    SEQ_TUBE_RACK_NAME = 'SEQ Tube Rack'
+    SPR_TUBE_RACK_NAME = 'SPR Tube Rack'
+    DEFAULT_TUBE_RACK_SIZE = '96'


Where is this used?

KatyTaylor · 2024-11-12T14:58:59Z

app/models/labware_creators/plate_split_to_tube_racks.rb

      parent
    end

-    # Display the children tab in the plate view so we see the child tubes listed.
+    # We will want to see the list of tubes in the rack
+    # TODO: as these are racked_tubes and not child tubes, does the tube rack presenter have a relatives tab?


Is the 'anchor' the tab it lands on, on the destination plate? If so, we're landing on the parent plate (not a tube rack), so the relatives tab is normal and should (hopefully) show us a list of child tube racks.

KatyTaylor · 2024-11-20T13:43:49Z

app/models/state_changers.rb

+      return nil unless FILTER_FAILS_ON.include?(target_state)
+
+      # determine list of tubes requiring the state change
+      tubes_locations_filtered = labware.tubes.reject { |t| t.state == 'failed' }.map(&:racked_tube.coordinate)


Discussed whether we should be filtering out 'cancelled' tubes here too? Have this - https://github.com/sanger/limber/pull/2034/files

Also need to test failing and cancelling at the tube rack level.

Think about whether to create a new story for any of these things.

andrewsparkes added 9 commits October 2, 2024 10:25

fix typo in comment

b581f0d

added purpose config fields and tube rack relationships

b84e321

Added tube rack purpose v2 resource

909255e

Merge branch 'y24-099-tube-rack-banking-sequencescape-api' into y24-0…

85b10fd

…99-plate-split-to-racks

Merge branch 'y24-088-tuberacks-epic' into y24-099-plate-split-to-racks

b8bc954

checks added to prevent casting inappropriate values

3f85856

added specific tube rack creation and related api changes

ae959c0

added check for blank

2fa7b50

changed redirect to return to parent plate

b394822

KatyTaylor reviewed Oct 25, 2024

View reviewed changes

andrewsparkes added 8 commits October 28, 2024 16:43

added check for tube rack false

f64c55b

added cached relationship for request type to factory

eb600c6

added methods to fetch aliquots and requests_as_source for tubes in t…

e29762a

…he tuberack, used for fetching active requests

removed unneeded comment

4e5b29c

put WellHelpers include back as breaking tests

f2bf2d4

fixed tests for labware creator

5708619

reverted has_one to belongs_to as breaking tests

e934d73

add WellHelpers back into tube rack as using coordinate methods

bdd0c77

added additional unit tests

f414945

andrewsparkes linked an issue Nov 1, 2024 that may be closed by this pull request

Y24-099 Tube Rack Banking Sequencescape API #1696

Closed

4 tasks

andrewsparkes added 3 commits November 1, 2024 15:20

fixed typo

2c74086

fixed test for private method

715c7ea

added comments and added tests for contents_for in TubeRackStateChanger

456d986

andrewsparkes requested review from yoldas and KatyTaylor November 6, 2024 09:38

KatyTaylor reviewed Nov 12, 2024

View reviewed changes

StephenHulme mentioned this pull request Nov 15, 2024

Y24-396 - [BUG] Cancelling a PBMC tube #2002

Open

KatyTaylor reviewed Nov 20, 2024

View reviewed changes

Merged develop

c5bb206

andrewsparkes and others added 2 commits November 20, 2024 16:45

removed references to tube rack barcode metadata key

4a329b2

Merge branch 'y24-088-tuberacks-epic' into y24-099-plate-split-to-racks

f4eca57

andrewsparkes merged commit c2b9761 into y24-088-tuberacks-epic Nov 27, 2024
14 checks passed

andrewsparkes deleted the y24-099-plate-split-to-racks branch November 27, 2024 10:35

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Y24-099 plate split to racks #2028

Y24-099 plate split to racks #2028

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Y24-099 plate split to racks #2028

Y24-099 plate split to racks #2028

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andrewsparkes commented Oct 25, 2024

Changes proposed in this pull request

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