Y26 031 labware location report by retention instructions by wendyyang · Pull Request #5637 · sanger/sequencescape

wendyyang · 2026-03-23T19:08:11Z

Closes #

Changes proposed in this pull request

add retention instruction column in location report table
add filter by retention instruction on the return record

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codecov · 2026-03-27T09:19:45Z

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 87.25%. Comparing base (a71005e) to head (7e4e26f).

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #5637      +/-   ##
===========================================
+ Coverage    87.22%   87.25%   +0.02%     
===========================================
  Files         1461     1461              
  Lines        33022    33032      +10     
  Branches      3475     3476       +1     
===========================================
+ Hits         28805    28822      +17     
+ Misses        4196     4189       -7     
  Partials        21       21

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Pull request overview

Adds retention-instruction support to Location Reports so users can filter returned labware by retention instruction, while persisting the selected instructions on the report record.

Changes:

Add retention_instructions (serialized array) to LocationReport and persist it via a new DB column.
Extend the selection form + controller strong params to allow multi-select retention instructions.
Filter selected labware by retention instruction and add an RSpec scenario for it.

Reviewed changes

Copilot reviewed 7 out of 7 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
spec/models/location_report_spec.rb	Adds coverage for filtering by retention instruction.
db/schema.rb	Updates schema with the new `location_reports.retention_instructions` column.
db/migrate/20260325134057_add_retention_instructions_to_lcation_reports.rb	Introduces the migration adding the new column.
app/views/location_reports/_location_labware_selection_form.html.erb	Adds a multi-select retention instruction filter UI.
app/models/location_report/location_report_form.rb	Passes `retention_instructions` from the form into the model.
app/models/location_report.rb	Serializes `retention_instructions` and filters labware results accordingly.
app/controllers/location_reports_controller.rb	Permits `retention_instructions` as an array param.

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Copilot · 2026-03-27T13:25:45Z

app/models/location_report.rb

+  def validate_result_size(params)
    count = Labware.search_for_count_of_labware(params)
    if count > configatron.fetch(:location_reports_fetch_count_max, 25000)
      errors.add(:base, I18n.t('location_reports.errors.too_many_labwares_found', count:))
-      return []
+      []
    end
-    # Only plates and tubes are currently supported by this report
-    Labware.search_for_labware(params).filter { |labware| labware.is_a?(Plate) || labware.is_a?(Tube) }
  end


validate_result_size currently adds an error and returns [], but does not explicitly halt callers (and returns nil on success). Consider making this method return a boolean (eg true/false) or raising/returning consistently so callers can reliably short-circuit when the limit is exceeded.

db/migrate/20260325134057_add_retention_instructions_to_lcation_reports.rb

Copilot · 2026-03-27T13:25:46Z

app/controllers/location_reports_controller.rb

      :barcodes,
      :barcodes_text,


location_report_params permits :barcodes and :barcodes_text twice. This duplication is redundant and can confuse future edits; remove the duplicates so each permitted key appears only once.

Suggested change

:barcodes,

:barcodes_text,

Copilot · 2026-03-27T13:25:46Z

app/models/location_report.rb

  def search_for_labware_by_selection
-    params = { faculty_sponsor_ids:, study_id:, start_date:, end_date:, plate_purpose_ids:, barcodes: }
+    params = { faculty_sponsor_ids:, study_id:, start_date:, end_date:, plate_purpose_ids:, barcodes:,
+               retention_instructions: }
+    validate_result_size(params)
+
+    # Only plates and tubes are currently supported by this report
+    labwares = Labware.search_for_labware(params).filter { |labware| labware.is_a?(Plate) || labware.is_a?(Tube) }
+
+    filter_labware_by_retention_instructions(labwares)


validate_result_size(params) returns an empty array when the result set is too large, but its return value is ignored here. That means the code will still execute Labware.search_for_labware(params) even after adding the too_many_labwares_found error, defeating the safeguard and potentially loading a very large dataset. Short-circuit the method (eg return [] immediately) when the validation fails.

BenTopping

Couple questions about whether we need to support multiple retention_instructions.

N.B. Haven't tested locally.

BenTopping · 2026-03-31T09:06:19Z

app/models/location_report.rb

+    # Only plates and tubes are currently supported by this report
+    labwares = Labware.search_for_labware(params).filter { |labware| labware.is_a?(Plate) || labware.is_a?(Tube) }
+
+    filter_labware_by_retention_instructions(labwares)


I think this filter should be moved into the search_for_labware function as a new scope. This would keep it consistent with the behaviour of the other fields in this selection form.

BenTopping · 2026-03-31T09:13:02Z

app/views/location_reports/_location_labware_selection_form.html.erb


+  <div class='form-group'>
+    <%= f.label 'retention_instructions', 'Retention instructions' %>
+    <%= f.select :retention_instructions, options_for_select(retention_instruction_option_for_select, location_report_form.retention_instructions), { include_hidden: false }, { class: 'form-control select2', :multiple => true } %>


Do we want users to be able to select multiple at once?

We should be able to change the options here so the labels are the readable versions (Long term storage) but the option values are the normalised long_term_storage. This would prevent us having to format them here https://github.com/sanger/sequencescape/pull/5637/changes#diff-96a48d35086a071258b6b8210f00ccf6a1092d9a4443c8c46d5c1a8765548a5aR228

BenTopping · 2026-03-31T09:19:02Z

db/migrate/20260325134057_add_retention_instructions_to_location_reports.rb

+# frozen_string_literal: true
+class AddRetentionInstructionsToLocationReports < ActiveRecord::Migration[7.2]
+  def change
+    add_column :location_reports, :retention_instructions, :text


I think string should be fine here as its a small column. If we are only allowing filter by one retention_instruction we could change this to retention_instruction (no 's') and change to an enum.

BenTopping · 2026-03-31T09:23:47Z

spec/models/location_report_spec.rb

          it_behaves_like 'a successful report'
        end
+
+        context 'with retention instructions' do


Test for multiple retention instructions if we are supporting it.

wendyyang added 3 commits March 19, 2026 10:20

save changes

a5b5a47

save change

e446636

remove retention instruction param

99653c3

wendyyang linked an issue Mar 23, 2026 that may be closed by this pull request

Y26-031 - Labware Location Report by Retention Instructions #5532

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3 tasks

wendyyang added 4 commits March 25, 2026 14:46

save changes

67bc87f

save changes

fc408a1

refactor

31159ad

merge develop in and resolve conflict

0b1e94f

wendyyang marked this pull request as ready for review March 27, 2026 09:08

add tests

77a9e04

wendyyang requested review from Copilot and dasunpubudumal March 27, 2026 13:22

Copilot started reviewing on behalf of wendyyang March 27, 2026 13:22 View session

Copilot AI reviewed Mar 27, 2026

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wendyyang added 2 commits March 27, 2026 13:30

fix the typo

a2a9912

fix the typo

7e4e26f

wendyyang requested a review from KatyTaylor March 27, 2026 14:00

BenTopping reviewed Mar 31, 2026

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Y26 031 labware location report by retention instructions#5637

Y26 031 labware location report by retention instructions#5637
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Y26-031---labware-location-report-by-retention-instructions

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wendyyang commented Mar 23, 2026 •

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