Module: StudyReport::StudyDetails

Included in:
Study
Defined in:
app/models/study_report/study_details.rb

Overview

rubocop:todo Metrics/ModuleLength

Constant Summary collapse

BATCH_SIZE = 
1000

Instance Method Summary collapse

Instance Method Details

#each_stock_well_id_in_study_in_batches ⇒ Object

This will pull out all well ids from stock plates in the study



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# File 'app/models/study_report/study_details.rb', line 7

def each_stock_well_id_in_study_in_batches(&) # rubocop:todo Metrics/MethodLength
  # Stock wells are determined by the requests leading from the stock plate
  handle_wells(
    :requests,
    { requests: { initial_study_id: id } },
    PlatePurpose.where(name: Study::STOCK_PLATE_PURPOSES).pluck(:id),
    &
  )

  # Aliquot 1,2,3,4 & 5 plates are determined by the aliquots in their wells
  handle_wells(
    :aliquots,
    { aliquots: { study_id: id } },
    PlatePurpose.where(
      name: ['Aliquot 1', 'Aliquot 2', 'Aliquot 3', 'Aliquot 4', 'Aliquot 1', 'Pre-Extracted Plate']
    ).pluck(:id),
    &
  )
end

#progress_report_header ⇒ Object 



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# File 'app/models/study_report/study_details.rb', line 40

def progress_report_header
  [
    'Status',
    'Study',
    'Supplier',
    'Sanger Sample Name',
    'Supplier Sample Name',
    'Plate',
    'Well',
    'Supplier Volume',
    'Supplier Gender',
    'Concentration',
    'Initial Volume',
    'Current Volume',
    'Total Micrograms',
    'Sequenome Count',
    'Sequenome Gender',
    'Pico',
    'Gel',
    'Qc Status',
    'QC started date',
    'Pico date',
    'Gel QC date',
    'Seq stamp date',
    'Cohort',
    'Country of Origin',
    'Geographical Region',
    'Ethnicity',
    'DNA Source',
    'Is Resubmitted',
    'Control',
    'Is in Fluidigm'
  ]
end

#progress_report_on_all_assets {|progress_report_header| ... } ⇒ Object

rubocop:todo Metrics/MethodLength

Yields:



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# File 'app/models/study_report/study_details.rb', line 76

def progress_report_on_all_assets # rubocop:todo Metrics/AbcSize
  yield(progress_report_header)

  each_stock_well_id_in_study_in_batches do |asset_ids|
    # eager loading of well_attribute , can only be done on  wells ...
    # We've already split into batches, so find_each here only slows things down.
    Well
      .for_study_report
      .where(id: asset_ids)
      .order(:id)
      .each do |asset|
        asset_progress_data = asset.qc_report
        next if asset_progress_data.nil?

        yield(
          [
            asset_progress_data[:status],
            name,
            asset_progress_data[:supplier],
            asset_progress_data[:sanger_sample_id],
            asset_progress_data[:sample_name],
            asset_progress_data[:plate_barcode],
            asset_progress_data[:well],
            asset_progress_data[:supplier_volume],
            asset_progress_data[:supplier_gender],
            asset_progress_data[:concentration],
            asset_progress_data[:initial_volume],
            asset_progress_data[:current_volume],
            asset_progress_data[:quantity],
            asset_progress_data[:sequenom_count],
            [(asset_progress_data[:sequenom_gender])].flatten.compact.join(''),
            asset_progress_data[:pico],
            asset_progress_data[:gel],
            asset_progress_data[:qc_status],
            asset_progress_data[:qc_started_date],
            asset_progress_data[:pico_date],
            asset_progress_data[:gel_qc_date],
            asset_progress_data[:sequenom_stamp_date],
            asset_progress_data[:cohort],
            asset_progress_data[:country_of_origin],
            asset_progress_data[:geographical_region],
            asset_progress_data[:ethnicity],
            asset_progress_data[:dna_source],
            asset_progress_data[:is_resubmitted],
            asset_progress_data[:control],
            asset_progress_data[:is_in_fluidigm]
          ]
        )
      end
  end
end