Y26-012 - Automating buffer addition - wireframes

[KatyTaylor]

Description
Bit of research into the parent story to enable a better size estimate, and check customer expectations of how the feature will look.

Acceptance Criteria
The following outputs from the research are produced:

• Create quick wireframes (any method) showing the places in the UI that will change for the parent story - show to the customer for feedback
• Create description (English, or pseudo-code) of how the cherrypicking algorithm and/or Tecan file generation will need to change for the parent story
• Split the parent story into subtasks, if it seems appropriate

Who the primary contacts are for this work
Katy, Lynda

Additional context or information
In case helpful for getting orientated, here are recent(ish) stories done on the cherrypicking code:

• Y25-447 - Modify Structure of Tecan Cherry-picking Worklists to Reuse Tips for Buffer Addition Steps #5101 (Tecan file generation)
• Y24-383 - Cherrypicking improvements (minimum volume) #4413 (Changes to the cherrypicking algorithm, never merged)

[yoldas]

Screenshots

UI changes

I have asked the questions about the following changes by email.

Q1. Input Field) [Updated based on feedback]

I propose the following for entering the option for the buffer volume for empty plates. There will be an additional section in Cherrypicking options called “Additional options”, in which there will be a text field “Buffer volume for empty wells (µl)” after other inputs. The story Y25-680 specifies the volume as 120 (µl) but given there can be different plate types with different maximum volumes, I would like to collect the value explicitly if required. Filling this box means, the robot file will contain additional buffer steps, and the robot will automatically add buffer to the empty wells on the plate using the amount specified. What do you think about this new field in the user interface? For example, changing it to read “Automatic buffer volume for empty wells (µl)” to avoid confusion.

Feedback:
is it possible to have this as a check-box that says “automatic buffer addition for empty wells required?” and then if we select that, the default volume listed is 120ul, but we can change this? Like we have in the “pick by volume” in the example below? Don’t worry if this would be difficult, but I think this would be the most user-friendly (and reduce the risk for errors) for the SSR team.

Update: Implemented checkbox

Q2 and Q3. Worksheet) [Updated based on feedback]
If the buffer volume for empty wells (µl) is specified, the worksheet will include a line after the chart as shown (attachment: worksheet.png) If the option is not specified, there will not be such a line.

It also uses a similar notation on the chart to show empty buffers, “e” rather than “b”. It has also a legend at the bottom to show what it means. Note that we will add these “e” numbers only when the option is specified.

Code changes

To generate the screenshots, see the next comment, Local setup.

For implementing the parent, see the PR of this story (Branch: y26-012-automating-buffer-addition), which provides a working implementation but it misses tests.

What is left for the parent story and what can be checked?

• The PR has no unit tests - the changes in PR works when running in SS locally.
• It is not tested with a non-standard "Plate Template" option and it may not work, but it may be irrelevant for the process.
• Another test with partial destination plates would be useful.
• It is not tested with "Control plate & placement type" option.

[yoldas]

Notes

Example for the original data_object structure in the Tecan driver file generators:

[1] pry(#<Robot::Generator::TecanV2>)> data_object
=> {"destination" =>
  {"SQPD-9101" =>
    {"name" => "ABgene 0765",
     "plate_size" => 96,
     "control" => false,
     "mapping" =>
      [{"src_well" => ["SQPD-9089", "A1"], "dst_well" => "A1", "volume" => 100.0, "buffer_volume" => 0.0},
       {"src_well" => ["SQPD-9089", "A2"], "dst_well" => "B1", "volume" => 100.0, "buffer_volume" => 0.0},
       {"src_well" => ["SQPD-9089", "A3"], "dst_well" => "C1", "volume" => 100.0, "buffer_volume" => 0.0},
       {"src_well" => ["SQPD-9090", "A1"], "dst_well" => "D1", "volume" => 100.0, "buffer_volume" => 0.0},
       {"src_well" => ["SQPD-9090", "A2"], "dst_well" => "E1", "volume" => 100.0, "buffer_volume" => 0.0},
       {"src_well" => ["SQPD-9090", "A3"], "dst_well" => "F1", "volume" => 100.0, "buffer_volume" => 0.0}]}},
 "source" =>
  {"SQPD-9089" => {"name" => "ABgene 0800", "plate_size" => 96, "control" => false},
   "SQPD-9090" => {"name" => "ABgene 0800", "plate_size" => 96, "control" => false}},
 "time" => Thu, 19 Feb 2026 15:20:20.785717000 GMT +00:00,
 "user" => "admin"}

Local setup

Run SS

bundle exec rake application:post_deploy
bundle exec rails s

Run Jobs

bundle exec rake jobs:work

Run Labwhere at port 3200

bundle exec rails s -p3200

In Sequencescape,
UAT actions, Generate 2 stock plates
Submissions, Cherrypick submission on the plates on a few wells, e.g. A1,B1,C1
Labwhere Reception, scan plates to postmanpat
Pipelines, Cherrypick, create a batch using the scanned labware
Go to the batch page, Actions, Select Plate Template, set volume options for UI for input
Release the batch to see worksheet and driver file changes

[andrewsparkes]

Follow the readme to set up labware locally, esp part about renaming the bunny and database yml files to remove 'example'.
For the postmanpat location I had to edit the location barcode in my DB to be just 'postmanpat' rather than lw-postmanpat-123 or similar that you get when you 'create location'