Class: PlatesController

Inherits:
ApplicationController show all
Defined in:
app/controllers/plates_controller.rb

Overview

rubocop:todo Style/Documentation

Constant Summary

Constants included from FlashTruncation

FlashTruncation::STRING_OVERHEAD

Instance Method Summary collapse

Methods inherited from ApplicationController

#block_api_access, #evil_parameter_hack!, #extract_header_info, #set_cache_disabled!

Methods included from FlashTruncation

#max_flash_size, #truncate_flash, #truncate_flash_array

Instance Method Details

#createObject

rubocop:todo Metrics/MethodLength


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# File 'app/controllers/plates_controller.rb', line 24

def create # rubocop:todo Metrics/AbcSize
  @creator = plate_creator = Plate::Creator.find(params[:plates][:creator_id])
  barcode_printer = BarcodePrinter.find(params[:plates][:barcode_printer])
  source_plate_barcodes = params[:plates][:source_plates]
  create_asset_group = params[:plates][:create_asset_group] == 'Yes'

  scanned_user = User.find_with_barcode_or_swipecard_code(params[:plates][:user_barcode])

  respond_to do |format|
    if scanned_user.nil?
      flash[:error] = 'Please scan your user barcode'
    elsif tube_rack_sources?
      plate_creator.create_plates_from_tube_racks!(tube_racks, barcode_printer, scanned_user, create_asset_group)
    else
      plate_creator.execute(
        source_plate_barcodes,
        barcode_printer,
        scanned_user,
        create_asset_group,
        Plate::CreatorParameters.new(params[:plates])
      )
    end
    flash[:notice] = 'Created plates successfully'
    flash[:warning] = plate_creator.warnings if plate_creator.warnings.present?
    format.html { render(new_plate_path) }
  end
rescue StandardError => e
  respond_to do |format|
    flash[:error] = e.message
    format.html { render(new_plate_path) }
  end
end

#create_sample_tubesObject

rubocop:todo Metrics/AbcSize


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# File 'app/controllers/plates_controller.rb', line 89

def create_sample_tubes # rubocop:todo Metrics/AbcSize
  barcode_printer = BarcodePrinter.find(params[:plates][:barcode_printer])
  barcode_array = params[:plates][:source_plates].scan(/\w+/)
  plates = Plate.with_barcode(barcode_array)
  study = Study.find(params[:plates][:study])

  respond_to do |format|
    asset_group =
      Plate::SampleTubeFactory.create_sample_tubes_asset_group_and_print_barcodes(plates, barcode_printer, study)
    if asset_group
      flash[:notice] = 'Created tubes and printed barcodes'

      # makes request properties partial show
      format.html { redirect_to(new_submission_path(study_id: asset_group.study.id)) }
      format.xml { render xml: asset_group, status: :created }
      format.json { render json: asset_group, status: :created }
    else
      flash[:error] = 'Failed to create sample tubes'
      format.html { redirect_to(to_sample_tubes_plates_path) }
      format.xml { render xml: flash.to_xml, status: :unprocessable_entity }
      format.json { render json: flash.to_json, status: :unprocessable_entity }
    end
  end
end

#fluidigm_fileObject


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# File 'app/controllers/plates_controller.rb', line 114

def fluidigm_file
  if logged_in?
    @plate = Plate.includes(wells: [{ samples: :sample_metadata }, :map]).find(params[:id])
    @parents = @plate.parents
    respond_to { |format| format.csv { render csv: @plate, content_type: 'text/csv' } }
  end
end

#newObject


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# File 'app/controllers/plates_controller.rb', line 11

def new
  respond_to do |format|
    format.html
    format.xml { render xml: @plate }
    format.json { render json: @plate }
  end
end

#set_barcode_printersObject


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# File 'app/controllers/plates_controller.rb', line 63

def set_barcode_printers
  @barcode_printers = BarcodePrinterType96Plate.first.barcode_printers
  @barcode_printers = BarcodePrinter.order('name asc') if @barcode_printers.blank?
end

#set_plate_creatorsObject

rubocop:enable Metrics/MethodLength


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# File 'app/controllers/plates_controller.rb', line 59

def set_plate_creators
  @plate_creators = Plate::Creator.order(:name)
end

#showObject


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# File 'app/controllers/plates_controller.rb', line 19

def show
  @plate = Plate.find(params[:id])
end

#to_sample_tubesObject


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# File 'app/controllers/plates_controller.rb', line 84

def to_sample_tubes
  @barcode_printers = BarcodePrinter.all
  @studies = Study.alphabetical
end

#tube_rack_barcodesObject


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# File 'app/controllers/plates_controller.rb', line 68

def tube_rack_barcodes
  return [] unless params.dig(:plates).dig(:source_plates)

  params[:plates][:source_plates].split(/[\s,]+/)
end

#tube_rack_sources?Boolean

Returns:

  • (Boolean)

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# File 'app/controllers/plates_controller.rb', line 74

def tube_rack_sources?
  return false if tube_rack_barcodes.empty?

  tube_racks.count == tube_rack_barcodes.length
end

#tube_racksObject


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# File 'app/controllers/plates_controller.rb', line 80

def tube_racks
  @tube_racks ||= TubeRack.joins(:barcodes).where(barcodes: { barcode: tube_rack_barcodes })
end