Y24-382: add example test cases #4641

StephenHulme · 2025-01-27T13:06:36Z

Changes proposed in this pull request

add example test cases from story
- lays the groundwork for Y24-383 - Cherrypicking improvements (minimum volume) [DRAFT] #4413

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StephenHulme · 2025-01-27T13:23:20Z

This is ready for review, I think the failing feature tests are unrelated to the changes (and possibly solved by #4639).

StephenHulme · 2025-01-27T16:29:59Z

spec/models/well_spec.rb

@@ -261,31 +261,46 @@
    end
  end

+  # TODO: Y24-383 - add assertions for final source and destination volumes


I'm half wondering if this should happen as part of this PR to lay a groundwork of completed calculations for a potential meeting with relevant parties next week...

When you say "final source and destination volumes", you mean "current_volume" in well attributes, on the source and target wells - is that right?

Great idea to add these assertions though

I'm not sure... current_volume seems somewhat time invarient to me - I'm not sure at what stage it is current! What I mean is how much volume is left in the original well on the original plate, and how much has been pipetted into the new well in the new plate.
But I think we are talking the same thing...?

Sorry should have submitted all these comments in one go...

Is it possible to check the target well's final volume in this test, because that gets updated after bed verification?

codecov · 2025-01-29T07:12:52Z

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 89.40%. Comparing base (75cf1c5) to head (eee2f17).
Report is 3 commits behind head on develop.

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #4641      +/-   ##
===========================================
+ Coverage    89.34%   89.40%   +0.06%     
===========================================
  Files         1406     1406              
  Lines        30298    30298              
===========================================
+ Hits         27070    27089      +19     
+ Misses        3228     3209      -19

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KatyTaylor · 2025-01-29T14:17:12Z

spec/models/well_spec.rb

+    { target_ng: 10_000, measured_conc: 250, measured_vol: 50, min_vol:10, min_pick_vol: 1, source_pick_vol: 40, buffer_vol: 0, current_vol: nil },
+    { target_ng: 10_000, measured_conc: 250, measured_vol: 30, min_vol:10, min_pick_vol: 1, source_pick_vol: 30, buffer_vol: 0, current_vol: nil },
+    { target_ng: 1000, measured_conc: 70, measured_vol: 50, min_vol:10, min_pick_vol: 5, source_pick_vol: 14.29, buffer_vol: 0, current_vol: nil },# Y24-382: SQPD-10861 v14.29, b0.00
+    { target_ng: 200, measured_conc: 200, measured_vol: 1, min_vol:50, min_pick_vol: 5, source_pick_vol: 1, buffer_vol: 49, current_vol: nil }, # Y24-382: SQPD-10864 v1.00, b49.00


So this one (above) will pass currently, but when Y24-383 is done it should be v5.00, b45.00 - is that right?

If required volume < robot minimum picking volume, round up to the robot minimum picking volume

By the logic quoted, yes I think so.

My plan is to create a number of worked examples/scenarios, and liase with the stakeholders in Y24-383 to confirm which results are expected. Then make the algorithm match those expectations - Test Driven Development for the win 😉

KatyTaylor · 2025-01-29T14:29:40Z

spec/models/well_spec.rb

+    { target_ng: 10_000, measured_conc: 250, measured_vol: 30, min_vol:10, min_pick_vol: 1, source_pick_vol: 30, buffer_vol: 0, current_vol: nil },
+    { target_ng: 1000, measured_conc: 70, measured_vol: 50, min_vol:10, min_pick_vol: 5, source_pick_vol: 14.29, buffer_vol: 0, current_vol: nil },# Y24-382: SQPD-10861 v14.29, b0.00
+    { target_ng: 200, measured_conc: 200, measured_vol: 1, min_vol:50, min_pick_vol: 5, source_pick_vol: 1, buffer_vol: 49, current_vol: nil }, # Y24-382: SQPD-10864 v1.00, b49.00
+    { target_ng: 9800, measured_conc: 98, measured_vol: 100, min_vol:50, min_pick_vol: 5, source_pick_vol: 50, buffer_vol: 0, current_vol: nil }, # Y24-382: SQPD-10866 v50.00, b0.00


The max volume doesn't seem to be specified here (above), but I think is essential to this example - it's why the source pick volume gets set to 50?

It's hardcoded in the test function itself (to 50) but probably should be altogether here... 👀

KatyTaylor · 2025-01-29T14:30:44Z

spec/models/well_spec.rb

+    { target_ng: 1000, measured_conc: 70, measured_vol: 50, min_vol:10, min_pick_vol: 5, source_pick_vol: 14.29, buffer_vol: 0, current_vol: nil },# Y24-382: SQPD-10861 v14.29, b0.00
+    { target_ng: 200, measured_conc: 200, measured_vol: 1, min_vol:50, min_pick_vol: 5, source_pick_vol: 1, buffer_vol: 49, current_vol: nil }, # Y24-382: SQPD-10864 v1.00, b49.00
+    { target_ng: 9800, measured_conc: 98, measured_vol: 100, min_vol:50, min_pick_vol: 5, source_pick_vol: 50, buffer_vol: 0, current_vol: nil }, # Y24-382: SQPD-10866 v50.00, b0.00
+    { target_ng: 9800, measured_conc: 100, measured_vol: 100, min_vol:50, min_pick_vol: 5, source_pick_vol: 50, buffer_vol: 0, current_vol: nil } # Y24-382: SQPD-10868 v50.00, b0.00


Same as above - isn't the max volume needed?

StephenHulme · 2025-01-29T14:34:42Z

spec/models/well_spec.rb

@@ -437,7 +452,8 @@
      [100.0, 5.0, 100.0, 2.0, 5.0, 5.0, 98.0, 'Less DNA than robot minimum pick'],
      [100.0, 50.0, 1.0, 200.0, 5.0, 100.0, 0.0, 'Low concentration, maximum DNA, no buffer'],
      [120.0, 50.0, 0, 60.0, 5.0, 60.0, 60.0, 'Zero concentration, with less volume than required'],
-      [120.0, 50.0, 0, 3.0, 5.0, 5.0, 117.0, 'Zero concentration, with less volume than even the minimum robot pick']
+      [120.0, 50.0, 0, 3.0, 5.0, 5.0, 117.0, 'Zero concentration, with less volume than even the minimum robot pick'],
+      [15.0, 50.0, 70.0, 50, 5.0, 10.7, 5.0, 'Y24-382: SQPD-10859 v10.71 b5.00']


The v10.71, b5.00 example is a concentration example, rather than an amount example.

KatyTaylor · 2025-01-29T14:35:23Z

spec/models/well_spec.rb

@@ -437,7 +452,8 @@
      [100.0, 5.0, 100.0, 2.0, 5.0, 5.0, 98.0, 'Less DNA than robot minimum pick'],
      [100.0, 50.0, 1.0, 200.0, 5.0, 100.0, 0.0, 'Low concentration, maximum DNA, no buffer'],
      [120.0, 50.0, 0, 60.0, 5.0, 60.0, 60.0, 'Zero concentration, with less volume than required'],
-      [120.0, 50.0, 0, 3.0, 5.0, 5.0, 117.0, 'Zero concentration, with less volume than even the minimum robot pick']
+      [120.0, 50.0, 0, 3.0, 5.0, 5.0, 117.0, 'Zero concentration, with less volume than even the minimum robot pick'],
+      [15.0, 50.0, 70.0, 50, 5.0, 10.7, 5.0, 'Y24-382: SQPD-10859 v10.71 b5.00']


So this will need to be updated after Y24-383, to be v10.71, b4.29, I think? (and still 15 final volume)

test: add example test cases

3b50531

StephenHulme self-assigned this Jan 27, 2025

StephenHulme requested a review from KatyTaylor January 27, 2025 13:23

StephenHulme commented Jan 27, 2025

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Merge branch 'develop' into y24-382-add-test-cases

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KatyTaylor reviewed Jan 29, 2025

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Y24-382: add example test cases #4641

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Y24-382: add example test cases #4641

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StephenHulme commented Jan 27, 2025 • edited Loading

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