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Y24-373 - Data migration to update sample_metadata country_of_origin #4406

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neilsycamore opened this issue Oct 9, 2024 · 1 comment · May be fixed by #4601
Open

Y24-373 - Data migration to update sample_metadata country_of_origin #4406

neilsycamore opened this issue Oct 9, 2024 · 1 comment · May be fixed by #4601
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@BenTopping
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Data integrity Data Integrity Size: S Small - low effort & risk Value: 3 Value to the insitute is average

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@neilsycamore
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Two country_of_origin of options ("not applicable: control sample" and "not applicable: sample group") have been identified and Y24-372 created to change these.

The samples in the Sequencescape and MLWH databases requires updating to reflect the changes
not applicable: control sample => missing: control sample
not applicable: sample group => missing: sample group
@neilsycamore neilsycamore added the Data integrity Data Integrity label Oct 9, 2024
@psd-issuer psd-issuer bot changed the title Data migration to update sample_metadata country_of_origin Y24-373 - Data migration to update sample_metadata country_of_origin Oct 9, 2024
@neilsycamore neilsycamore added the Size: S Small - low effort & risk label Oct 9, 2024
@neilsycamore
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neilsycamore commented Oct 10, 2024 •
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this method will update samples table in SS & MLWH

def update_country_of_origin(old_id,new_id)
  ActiveRecord::Base.transaction do
    data = Sample::Metadata.where(country_of_origin: old_id)
    data.each {|sm| sm.update!(country_of_origin: new_id)}
  end
end

@BenTopping BenTopping mentioned this issue Oct 18, 2024
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@stevieing stevieing added Value: 3 Value to the insitute is average and removed Need to Verify labels Jan 9, 2025
@BenTopping BenTopping self-assigned this Jan 15, 2025
@BenTopping BenTopping linked a pull request Jan 15, 2025 that will close this issue
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Data integrity Data Integrity Size: S Small - low effort & risk Value: 3 Value to the insitute is average
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Y24-373 - Sample Metadata migration to update invalid country_or_origin data sanger/sequencescape
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@neilsycamore @stevieing @BenTopping @SujitDey2022