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DPL-947 dna control barcode v12 sequel i ie #1143

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merged 16 commits into from
Nov 16, 2023

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seenanair
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@seenanair seenanair commented Nov 3, 2023

  • DNA control complex box barcode set as a required field in v12 Sequel IIe

    • Feature flag support (dpl947_enable_dna_control_barcode_pacbio_sequel_ii_v12)
    • pacbio_instrument_types yml file versions created which are selected based on feature flag
      • pacbio_instrument_types_v1
      • pacbio_instrument_types_v2 - dna_control_complex_box_barcode set as required_attribute"
    • Added "versions" attribute to "required_attributes" to support fields to be validated as 'required' only for selected smrt_link_versions
  • Samplesheet

    • dna_control_complex_box_barcode field added
    • Sorting of wells changed - Sorted by plates first and then wells
  • SMRT Link Version v11 made inactive in the rake task and database for UAT

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codecov bot commented Nov 3, 2023

Codecov Report

Merging #1143 (40c76ab) into develop (58939c9) will increase coverage by 0.00%.
Report is 10 commits behind head on develop.
The diff coverage is 100.00%.

@@           Coverage Diff            @@
##           develop    #1143   +/-   ##
========================================
  Coverage    97.64%   97.64%           
========================================
  Files          369      369           
  Lines        11002    11003    +1     
========================================
+ Hits         10743    10744    +1     
  Misses         259      259           
Files Coverage Δ
app/models/concerns/sample_sheet.rb 100.00% <100.00%> (ø)
config/application.rb 100.00% <ø> (ø)
lib/tasks/pacbio_data.rake 92.53% <100.00%> (+0.22%) ⬆️
spec/exchanges/run_csv/pacbio_sample_sheet_spec.rb 100.00% <ø> (ø)
spec/lib/tasks/pacbio_data.rake_spec.rb 100.00% <100.00%> (ø)
spec/models/pacbio/run_spec.rb 100.00% <100.00%> (ø)
spec/validators/instrument_type_validator_spec.rb 100.00% <100.00%> (ø)

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@seenanair seenanair changed the title Dpl 947 dna control barcode v12 sequel i ie DPL-947 dna control barcode v12 sequel i ie Nov 3, 2023
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All good. Just worth taking out the version code as it is no longer needed.

return if record.send(required_attribute).present?
# If versions are specified, check that the record's smrt_link_version version
# is included in the list
if versions.present? && versions.exclude?(record.smrt_link_version.name)
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I think we can remove this now.

# TODO: fix this to have separate behaviour for v11 and v12 (see commit 05bfe764a8eafe)
required_attributes:
options:
versions:
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We can definitely remove the versions code but wait to hear back from Craig as to whether this needs to be required. It wasn't previously.

@@ -5,7 +5,7 @@
class MyClass
include ActiveModel::Model

attr_accessor :attr_a, :attr_b, :attr_c, :attr_d
attr_accessor :attr_a, :attr_b, :attr_c, :attr_d, :smrt_link_version
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Again I think we can take this out now.

class RequiredAttributesValidator < ActiveModel::Validator
attr_reader :required_attributes
attr_reader :required_attributes, :versions
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Versions aren't needed anymore?

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Sorry, missed out. Removed now 👍

@stevieing stevieing removed the request for review from BenTopping November 16, 2023 09:00
@seenanair seenanair merged commit cbe9428 into develop Nov 16, 2023
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@seenanair seenanair deleted the dpl-947-dna-control-barcode-v12_sequelIIe branch November 16, 2023 11:42
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2 participants