Class: BatchesController

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

Overview

Batches represent collections of requests processed through a Pipeline at the same time. They are created via selecting requests on the pipelines show page

Constant Summary collapse

VERIFICATION_FLAVOUR_TO_MODEL_ACTION =

WARNING! This filter bypasses security mechanisms in rails 4 and mimics rails 2 behaviour. It should be removed wherever possible and the correct Strong Parameter options applied in its place.

{
  tube: :verify_tube_layout,
  amp_plate: :verify_amp_plate_layout
}.freeze

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

#allow_sample_sheet_download? ⇒ Boolean

Checks if the current user is allowed to download the sample sheet for the batch. Ultima sample sheets are allowed to be downloaded without authentication. For all other pipelines, the user must be logged in.

Returns:

  • (Boolean) —

    true if download is allowed, false otherwise



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# File 'app/controllers/batches_controller.rb', line 391

def allow_sample_sheet_download?
  @batch.pipeline.is_a?(UltimaSequencingPipeline) || logged_in?
end

#batch_parameters ⇒ Object

rubocop:enable Metrics/MethodLength



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# File 'app/controllers/batches_controller.rb', line 140

def batch_parameters
  @batch_parameters ||= params.require(:batch).permit(:assignee_id)
end

#completed ⇒ Object 



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# File 'app/controllers/batches_controller.rb', line 180

def completed
  # The params fall-back here reflects an older route where pipeline got passed in as :id. It should be removed
  # in the near future.
  @pipeline = Pipeline.find(params[:pipeline_id] || params[:id])
  @batches = @pipeline.batches.completed.order(id: :desc).includes(%i[user pipeline]).page(params[:page])
end

#create ⇒ Object

rubocop:todo Metrics/MethodLength



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# File 'app/controllers/batches_controller.rb', line 90

def create # rubocop:todo Metrics/AbcSize
  @pipeline = Pipeline.find(params[:id])

  requests = @pipeline.extract_requests_from_input_params(request_parameters)

  # TODO: These should be different endpoints
  case params[:action_on_requests]
  when 'cancel_requests'
    transition_requests(requests, :cancel_before_started!, 'Requests cancelled')
  when 'hide_from_inbox'
    transition_requests(requests, :hold!, 'Requests hidden from inbox')
  else
    # This is the standard create action
    standard_create(requests)
  end
rescue ActiveRecord::RecordInvalid => e
  respond_to do |format|
    format.html do
      flash[:error] = e.record.errors.full_messages
      redirect_to(pipeline_path(@pipeline))
    end
    format.xml { render xml: @batch.errors.to_xml }
  end
end

#download_spreadsheet ⇒ Object

Used in Cherrypicking pipeline to generate the template for CSV driven picks



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# File 'app/controllers/batches_controller.rb', line 361

def download_spreadsheet
  csv_string = Tasks::PlateTemplateHandler.generate_spreadsheet(@batch)
  send_data csv_string, type: 'text/plain', filename: "#{@batch.id}_cherrypick_layout.csv", disposition: 'attachment'
end

#edit ⇒ Object

rubocop:enable Metrics/MethodLength



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# File 'app/controllers/batches_controller.rb', line 82

def edit
  @rits = @batch.pipeline.request_information_types
  @requests = @batch.ordered_requests.includes(:batch_request, :asset, :target_asset, :comments)
  @users = User.all
  @controls = @batch.pipeline.controls
end

#fail ⇒ Object 



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# File 'app/controllers/batches_controller.rb', line 194

def fail
  @fail_reasons = @batch.workflow.source_is_internal? ? FAILURE_REASONS['internal'] : FAILURE_REASONS['external']
end

#fail_items ⇒ Object

rubocop:todo Metrics/AbcSize, Metrics/MethodLength



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# File 'app/controllers/batches_controller.rb', line 198

def fail_items # rubocop:todo Metrics/AbcSize, Metrics/MethodLength
  ActiveRecord::Base.transaction do
    fail_params =
      params.permit(:id, requested_fail: {}, requested_remove: {}, failure: %i[reason comment fail_but_charge])
    fail_and_remover = Batch::RequestFailAndRemover.new(fail_params)
    if fail_and_remover.save
      flash[:notice] = truncate_flash(fail_and_remover.notice)
    else
      flash[:error] = truncate_flash(fail_and_remover.errors.full_messages.join(';'))
    end
    redirect_to action: :fail, id: params[:id]
  end
end

#failed ⇒ Object 



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# File 'app/controllers/batches_controller.rb', line 187

def failed
  # The params fall-back here reflects an older route where pipeline got passed in as :id. It should be removed
  # in the near future.
  @pipeline = Pipeline.find(params[:pipeline_id] || params[:id])
  @batches = @pipeline.batches.failed.order(id: :desc).includes(%i[user pipeline]).page(params[:page])
end

#filtered ⇒ Object 



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# File 'app/controllers/batches_controller.rb', line 337

def filtered
end

#find_batch_by_barcode ⇒ Object 



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# File 'app/controllers/batches_controller.rb', line 374

def find_batch_by_barcode
  batch_id = LabEvent.find_batch_id_by_barcode(params[:id])
  if batch_id.nil?
    @batch_error = 'Batch id not found.'
    render action: 'batch_error', format: :xml
    nil
  else
    @batch = Batch.find(batch_id)
    render action: 'show', format: :xml
  end
end

#find_batch_by_batch_id ⇒ Object 



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# File 'app/controllers/batches_controller.rb', line 370

def find_batch_by_batch_id
  @batch = Batch.find(params[:batch_id])
end

#find_batch_by_id ⇒ Object 



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# File 'app/controllers/batches_controller.rb', line 366

def find_batch_by_id
  @batch = Batch.find(params[:id])
end

#generate_sample_sheet ⇒ void

This method returns an undefined value.

Generates and sends the appropriate sample sheet(s) for the batch.



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# File 'app/controllers/batches_controller.rb', line 397

def generate_sample_sheet
  return redirect_to() unless allow_sample_sheet_download?

  if @batch.pipeline.is_a?(ElementAvitiSequencingPipeline)
    generate_element_aviti_sample_sheet
  elsif @batch.pipeline.is_a?(UltimaSequencingPipeline)
    generate_ultima_sample_sheet
  else
    flash[:error] = 'Sample sheet generation is not supported for this pipeline.'
    redirect_to controller: 'batches', action: 'show', id: @batch.id
  end
end

#index ⇒ Object

rubocop:todo Metrics/AbcSize, Metrics/MethodLength



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# File 'app/controllers/batches_controller.rb', line 40

def index # rubocop:todo Metrics/AbcSize, Metrics/MethodLength
  if logged_in?
    @user = params.fetch(:user, current_user)
    @batches = Batch.for_user(@user).order(id: :desc).includes(:user, :assignee, :pipeline).page(params[:page])
  else
    # Can end up here with XML. And it causes pain.
    @batches = Batch.order(id: :asc).page(params[:page]).limit(10)
  end
  respond_to do |format|
    format.html
    format.xml { render xml: @batches.to_xml }
    format.json { render json: @batches.to_json.gsub('null', '""') }
  end
end

#pending ⇒ Object 



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# File 'app/controllers/batches_controller.rb', line 154

def pending
  # The params fall-back here reflects an older route where pipeline got passed in as :id. It should be removed
  # in the near future.
  @pipeline = Pipeline.find(params[:pipeline_id] || params[:id])
  @batches = @pipeline.batches.pending.order(id: :desc).includes(%i[user pipeline]).page(params[:page])
end

#pipeline ⇒ Object 



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# File 'app/controllers/batches_controller.rb', line 144

def pipeline
  # All pipeline batches routes should just direct to batches#index with pipeline and state as filter parameters
  @batches =
    Batch
      .where(pipeline_id: params[:pipeline_id] || params[:id])
      .order(id: :desc)
      .includes(:user, :pipeline)
      .page(params[:page])
end

#previous_qc_state ⇒ Object 



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# File 'app/controllers/batches_controller.rb', line 330

def previous_qc_state
  @batch.qc_previous_state!(current_user)
  @batch.save
  flash[:notice] = "Batch #{@batch.id} reset to state #{@batch.qc_state}"
  redirect_to batch_url(@batch)
end

#print ⇒ Object

Handles printing of the worksheet



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# File 'app/controllers/batches_controller.rb', line 273

def print # rubocop:todo Metrics/AbcSize, Metrics/MethodLength
  @task = Task.find_by(id: params[:task_id])
  @pipeline = @batch.pipeline
  @comments = @batch.comments
  template = @pipeline.batch_worksheet

  if template == 'cherrypick_worksheet'
    robot_id = params.fetch(:robot_id, @batch.robot_id)
    @robot = robot_id ? Robot.find(robot_id) : Robot.default_for_verification
    @plates = params[:barcode] ? Plate.with_barcode(params[:barcode]) : @batch.output_plates
  end

  if template
    render action: template, layout: false
  else
    redirect_back_or_to(batch_path(@batch), alert: "No worksheet for #{@pipeline.name}")
  end
end

#print_amp_plate_barcodes ⇒ Object 



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# File 'app/controllers/batches_controller.rb', line 263

def print_amp_plate_barcodes
  if @batch.requests.empty?
    flash[:notice] = 'Your batch contains no requests.'
    redirect_to controller: 'batches', action: 'show', id: @batch.id
  else
    print_handler(LabelPrinter::Label::BatchPlateAmp)
  end
end

#print_amp_plate_labels ⇒ Object 



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# File 'app/controllers/batches_controller.rb', line 227

def print_amp_plate_labels
end

#print_barcodes ⇒ Object 



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# File 'app/controllers/batches_controller.rb', line 254

def print_barcodes
  if @batch.requests.empty?
    flash[:notice] = 'Your batch contains no requests.'
    redirect_to controller: 'batches', action: 'show', id: @batch.id
  else
    print_handler(LabelPrinter::Label::BatchTube)
  end
end

#print_labels ⇒ Object 



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# File 'app/controllers/batches_controller.rb', line 224

def print_labels
end

#print_plate_barcodes ⇒ Object 



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# File 'app/controllers/batches_controller.rb', line 250

def print_plate_barcodes
  print_handler(LabelPrinter::Label::BatchRedirect)
end

#print_plate_labels ⇒ Object

rubocop:todo Metrics/MethodLength



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# File 'app/controllers/batches_controller.rb', line 230

def print_plate_labels # rubocop:todo Metrics/MethodLength
  @pipeline = @batch.pipeline
  @output_barcodes = []

  @output_labware = @batch.plate_group_barcodes || []

  @output_labware.each_key do |parent|
    next if parent.nil?

    plate_barcode = parent.human_barcode
    @output_barcodes << plate_barcode if plate_barcode.present?
  end

  return if @output_barcodes.present?

  # We have no output barcodes, which means a problem
  flash[:error] = 'Output plates do not have barcodes to print'
  redirect_to controller: 'batches', action: 'show', id: @batch.id
end

#released ⇒ Object 



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# File 'app/controllers/batches_controller.rb', line 168

def released
  # The params fall-back here reflects an older route where pipeline got passed in as :id. It should be removed
  # in the near future.
  @pipeline = Pipeline.find(params[:pipeline_id] || params[:id])

  @batches = @pipeline.batches.released.order(id: :desc).includes(%i[user pipeline]).page(params[:page])
  respond_to do |format|
    format.html
    format.xml { render layout: false }
  end
end

#reset_batch ⇒ Object 



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# File 'app/controllers/batches_controller.rb', line 323

def reset_batch
  pipeline = @batch.pipeline
  @batch.reset!(current_user)
  flash[:notice] = "Batch #{@batch.id} has been reset"
  redirect_to controller: 'pipelines', action: :show, id: pipeline.id
end

#save ⇒ Object 



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# File 'app/controllers/batches_controller.rb', line 220

def save
  redirect_to action: :show, id: @batch.id
end

#show ⇒ Object

rubocop:todo Metrics/MethodLength



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# File 'app/controllers/batches_controller.rb', line 56

def show # rubocop:todo Metrics/AbcSize
  respond_to do |format|
    format.html do
      @submenu_presenter = Presenters::BatchSubmenuPresenter.new(current_user, @batch)

      @pipeline = @batch.pipeline
      @tasks = @batch.tasks.sort_by(&:sorted)
      @rits = @pipeline.request_information_types
      @input_labware = @batch.input_labware_report
      @output_labware = @batch.output_labware_report

      if @pipeline.pick_data
        @robot = @batch.robot_id ? Robot.find(@batch.robot_id) : Robot.with_verification_behaviour.first

        # In the event we have no robots with the correct behaviour, and none are specialised on the batch, fall-back
        # to the first robot.
        @robot ||= Robot.first
        @robots = Robot.with_verification_behaviour
      end
    end
    format.xml { render layout: false }
  end
end

#sort ⇒ Object 



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# File 'app/controllers/batches_controller.rb', line 212

def sort
  @batch.assign_positions_to_requests!(params['requests_list'].map(&:to_i))

  # Touch the batch to update its timestamp and trigger re-broadcast
  @batch.touch # rubocop:disable Rails/SkipsModelValidations
  head :ok
end

#started ⇒ Object 



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# File 'app/controllers/batches_controller.rb', line 161

def started
  # The params fall-back here reflects an older route where pipeline got passed in as :id. It should be removed
  # in the near future.
  @pipeline = Pipeline.find(params[:pipeline_id] || params[:id])
  @batches = @pipeline.batches.started.order(id: :desc).includes(%i[user pipeline]).page(params[:page])
end

#swap ⇒ Object

rubocop:todo Metrics/AbcSize



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# File 'app/controllers/batches_controller.rb', line 340

def swap # rubocop:todo Metrics/AbcSize
  if @batch.swap(
    current_user,
    'batch_1' => {
      'id' => params['batch']['1'],
      'lane' => params['batch']['position']['1']
    },
    'batch_2' => {
      'id' => params['batch']['2'],
      'lane' => params['batch']['position']['2']
    }
  )
    flash[:notice] = 'Successfully swapped lane positions'
    redirect_to batch_path(@batch)
  else
    flash[:error] = @batch.errors.full_messages.join('<br />')
    redirect_to action: :filtered, id: @batch.id
  end
end

#update ⇒ Object

rubocop:todo Metrics/MethodLength



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# File 'app/controllers/batches_controller.rb', line 118

def update # rubocop:todo Metrics/AbcSize
  if batch_parameters[:assignee_id]
    user = User.find(batch_parameters[:assignee_id])
    assigned_message = "Assigned to #{user.name} (#{user.})."
  else
    assigned_message = ''
  end

  respond_to do |format|
    if @batch.update(batch_parameters)
      flash[:notice] = "Batch was successfully updated. #{assigned_message}"
      format.html { redirect_to batch_url(@batch) }
      format.xml { head :ok }
    else
      format.html { render action: 'edit' }
      format.xml { render xml: @batch.errors.to_xml }
    end
  end
end

#verify ⇒ Object 



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# File 'app/controllers/batches_controller.rb', line 292

def verify
  @requests = @batch.ordered_requests
  @pipeline = @batch.pipeline
  @count = @requests.length
  @verification_flavour = params[:verification_flavour]
end

#verify_layout ⇒ Object 



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# File 'app/controllers/batches_controller.rb', line 299

def verify_layout
  # scanned tube barcode params from page are called barcode_0, barcode_1, ... barcode_n
  scanned_barcodes = Array.new(@batch.requests.count) { |i| params["barcode_#{i}"] }
  verification_flavour = params[:verification_flavour].to_sym
  model_method = VERIFICATION_FLAVOUR_TO_MODEL_ACTION[verification_flavour]

  if @batch.send(model_method, scanned_barcodes, current_user)
    verify_layout_success(verification_flavour)
  else
    verify_layout_failure(verification_flavour)
  end
end

#verify_layout_failure(verification_flavour) ⇒ Object 



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# File 'app/controllers/batches_controller.rb', line 318

def verify_layout_failure(verification_flavour)
  flash[:error] = @batch.errors.full_messages.sort
  redirect_to action: :verify, id: @batch.id, verification_flavour: verification_flavour
end

#verify_layout_success(verification_flavour) ⇒ Object 



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# File 'app/controllers/batches_controller.rb', line 312

def verify_layout_success(verification_flavour)
  flash[:notice] =
    "All of the #{verification_flavour.to_s.humanize.downcase.pluralize} are in their correct positions."
  redirect_to batch_path(@batch)
end