Module: Plate::FluidigmBehaviour

Included in:
Plate
Defined in:
app/models/plate/fluidigm_behaviour.rb

Overview

rubocop:todo Style/Documentation

Defined Under Namespace

Classes: FluidigmError

Class Method Summary collapse

Instance Method Summary collapse

Class Method Details

.included(base) ⇒ Object 


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# File 'app/models/plate/fluidigm_behaviour.rb', line 4

def self.included(base)
  base.class_eval do
    scope :requiring_fluidigm_data, -> {
      fluidigm_request_ids = RequestType.where(key: 'pick_to_fluidigm').ids

      joins([
        :well_requests_as_target,
        %(LEFT OUTER JOIN events
          ON eventful_id = #{Plate.table_name}.id
          AND eventful_type = "#{Plate.base_class.name}"
          AND family = "update_fluidigm_plate"
          AND content = "FLUIDIGM_DATA")
      ])
        .includes(:barcodes)
        .where(
          events: { id: nil },
          requests: { request_type_id: fluidigm_request_ids }
        )
        .distinct
    }
  end
end

Instance Method Details

#apply_fluidigm_data(fluidigm_file) ⇒ Object

Raises:


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# File 'app/models/plate/fluidigm_behaviour.rb', line 37

def apply_fluidigm_data(fluidigm_file)
  qc_assay = QcAssay.new
  raise FluidigmError, 'File does not match plate' unless fluidigm_file.for_plate?(fluidigm_barcode)

  wells.located_at(fluidigm_file.well_locations).include_stock_wells.each do |well|
    well.stock_wells.each do |sw|
      gender_markers = fluidigm_file.well_at(well.map_description).gender_markers.join('')
      loci_passed = fluidigm_file.well_at(well.map_description).count
      QcResult.create!([
        { asset: sw, key: 'gender_markers', assay_type: 'FLUIDIGM', assay_version: 'v0.1', value: gender_markers,
          units: 'bases', qc_assay: qc_assay },
        { asset: sw, key: 'loci_passed', assay_type: 'FLUIDIGM', assay_version: 'v0.1', value: loci_passed,
          units: 'bases', qc_assay: qc_assay }
      ])
    end
  end
  events.updated_fluidigm_plate!('FLUIDIGM_DATA')
end

#retrieve_fluidigm_data ⇒ Object 


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# File 'app/models/plate/fluidigm_behaviour.rb', line 27

def retrieve_fluidigm_data
  ActiveRecord::Base.transaction do
    fluidigm_data = FluidigmFile::Finder.find(fluidigm_barcode)
    return false if fluidigm_data.empty? # Return false if we have no data

    apply_fluidigm_data(FluidigmFile.new(fluidigm_data.content))
    return true
  end
end