y24-336 - BGE Request Types and Submissions #4511

dasunpubudumal · 2024-11-21T15:51:29Z

Changes proposed in this pull request

Adding request types and submission templates for BGE (Library type was already there).

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[All PRs] - Confirm PR template filled
[Feature Branches] - Review code
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codecov · 2024-11-21T16:13:38Z

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All modified and coverable lines are covered by tests ✅

Project coverage is 89.21%. Comparing base (168de56) to head (9062dae).
Report is 62 commits behind head on develop.

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@@             Coverage Diff             @@
##           develop    #4511      +/-   ##
===========================================
+ Coverage    86.48%   89.21%   +2.73%     
===========================================
  Files         1392     1392              
  Lines        29830    29931     +101     
===========================================
+ Hits         25797    26703     +906     
+ Misses        4033     3228     -805

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…arify naming

BenTopping

Apologies story was slightly incorrect regarding the ISC part. You may need to add BGE Cherrypicked, BGE Lib XP2 and BGE Lib PCR XP to config/default_records/plate_purposes/* for them to show up as acceptable purposes.

config/default_records/request_types/020_limber_high_throughput_bge.wip.yml

config/default_records/submission_templates/016_bge.wip.yml

BenTopping · 2024-11-26T12:08:19Z

config/default_records/plate_purposes/014_bge.wip.yml

+BGE Lib XP2:
+  type: PlatePurpose::Input
+  target_type: Plate
+  stock_plate: true


I don't think BGE Lib XP2 or BGE Lib PCR XP are stock_plate's. @KatyTaylor might know a bit more about these attributes.

BGE Cherrypick should be an 'input' plate (as you have done) because it's the first one in the pipeline. I'm not sure whether it's necessary for Lib XP2 and Lib PCR XP or not. If it was me I'd start of without and add it back in later if necessary.

I don't think any of them need to be 'stock' plates. A plate needs to be a 'stock' if it's used in a sample manifest - none of these are. And I don't think they would be considered stock plates by the lab as they're not the ones that came directly from the customer.

LB Cherrypick and PF Cherrypicked (that BGE Cherrypick is modelled off) are both set as stock_plate: true.

BenTopping

Nice looks good, just unsure about some of the plate purposes data.

andrewsparkes

Left some questions and things to check

andrewsparkes · 2024-11-26T14:40:58Z

config/default_records/plate_purposes/014_bge.wip.yml

+  size: 96
+BGE Lib XP2:
+  target_type: Plate
+  default_state: passed


don't think default state is passed on these XP plates. maybe for the cherrypick as its an input plate

although I now see there are submissions for each of these plates so not sure

Used here -

sequencescape/app/models/transfer/state.rb

Line 30 in 2f7cdbe

ALL_STATES.detect { |s| unique_states.include?(s) } || default_state || 'unknown'

So when trying to determine a plate's state, it looks first at the state of the transfer requests. If it can't determine the state from the transfer requests (there are 0 or >1 that aren't in the expected list), then it'll use the default state.

So I suppose for plates that are the first in a pipeline, they won't have transfer requests coming into them, so it'll use the default state. That's the cherrypick plate but not the other two.

Got a meeting so can't continue looking into it now, but guess it's also relevant to think about how the submission affects the state (can't remember where that code is).

I think @KatyTaylor is correct. I checked the other purpose configs in SS, and only the BGE Cherrypick should have the passed default state.

andrewsparkes · 2024-11-26T14:41:49Z

config/default_records/plate_purposes/014_bge.wip.yml

+  target_type: Plate
+  default_state: passed
+  stock_plate: false
+  cherrypickable_target: true


and only the cherrypick plate should have the cherrypickable_target true unless something special is happening here

andrewsparkes · 2024-11-26T14:48:11Z

config/default_records/request_types/020_limber_high_throughput_bge.wip.yml

+  acceptable_purposes:
+    - BGE Lib PCR XP
+  library_types:
+    - BGE


Is library type 'BGE' for all 3 of these despite them being different library preps? Seems wrong if they want to analyse the sequencing results differently. Maybe check with users.

BGE Library type is already used across the pipelines (and submissions) that area already in place (that these are modelled off). It is essentially all part of one bigger pipeline where all the samples are recombined and sequenced together.

BenTopping

Looks good, just one comment about whether the BGE Cherrypick needs to be a stock_plate.

BenTopping · 2024-12-02T14:13:58Z

@KatyTaylor @andrewsparkes Any objections to merging? I think this is fine to merge now because its wip'd and unusable until the pipeline is made, in which any additional changes can be made then.

KatyTaylor · 2024-12-03T10:19:01Z

@KatyTaylor @andrewsparkes Any objections to merging? I think this is fine to merge now because its wip'd and unusable until the pipeline is made, in which any additional changes can be made then.

@BenTopping fine by me!

dasunpubudumal added 2 commits November 21, 2024 15:44

Adding new request type and submission

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Adding new request type and submission

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dasunpubudumal self-assigned this Nov 21, 2024

dasunpubudumal linked an issue Nov 21, 2024 that may be closed by this pull request

Y24-366 - As a staff scientist I would like to have a separate submission for the new BGE pipeline. #4402

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dasunpubudumal added 3 commits November 22, 2024 11:07

Adding new request type and submission

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Making prettier happy

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Adding new request type and submission

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dasunpubudumal mentioned this pull request Nov 22, 2024

Y24-366 - As a staff scientist I would like to have a separate submission for the new BGE pipeline. #4402

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dasunpubudumal marked this pull request as draft November 22, 2024 13:25

Update submission templates to remove deprecated request types and cl…

ff622b9

…arify naming

dasunpubudumal requested review from KatyTaylor and BenTopping November 25, 2024 11:55

dasunpubudumal marked this pull request as ready for review November 25, 2024 11:55

BenTopping requested changes Nov 25, 2024

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dasunpubudumal added 4 commits November 25, 2024 15:20

Adding product catalogue

dd2f39e

Adding plate purpose BGE

67a91a7

Making prettier happy

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Adding the missing plate purpose configs

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dasunpubudumal requested a review from BenTopping November 25, 2024 16:04

BenTopping reviewed Nov 26, 2024

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Updating plate purposes config

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dasunpubudumal requested a review from BenTopping November 26, 2024 13:15

Updating plate purposes config

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andrewsparkes reviewed Nov 26, 2024

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dasunpubudumal added 2 commits November 27, 2024 08:08

Updating the cherrypickable_target in plates other than cherrypick.

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Removing default_sate for plates other than input plates

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BenTopping reviewed Nov 29, 2024

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BenTopping merged commit fb6c51f into develop Dec 5, 2024
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BenTopping deleted the 4402-y24-366-as-a-staff-scientist-i-would-like-to-have-a-separate-submission-for-the-new-bge-pipeline branch December 5, 2024 10:54

github-actions bot mentioned this pull request Dec 5, 2024

[release] Merge Develop into Master #4546

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y24-336 - BGE Request Types and Submissions #4511

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y24-336 - BGE Request Types and Submissions #4511

y24-336 - BGE Request Types and Submissions #4511

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