sanger/limber

<%# This is a report of the contents of the tubes in the PBMC Bank plate %>
<%# Based on app/views/exports/hamilton_lrc_pbmc_bank_to_lrc_bank_seq_and_spare.csv.erb %>
<%= CSV.generate_line ['Workflow', @workflow], row_sep: '' %>

<%=
  CSV.generate_line [
                      'Well name',
                      'Donor ID',
                      'Stock barcode',
                      'FluidX barcode',
                      'Extraction and freeze date',
                      'Sequencing or contingency',
                      'Cell count (cells/ml)',
                      'Viability (%)',
                      'Volume (µl)',
                      'Study name',
                      'Collection site'
                    ],
                    row_sep: ''
%>
<%
  rows_array = []
  @plate.wells_in_columns.each do |source_well|
    # skip if well empty (not all wells have samples in them)
    next if source_well.empty?

    # skip if well not in passed state
    next unless source_well.passed?

    # skip if no downstream tubes for this well (not set up children in Limber yet)
    next if source_well.downstream_tubes.empty?

    child_tube_v1 = source_well.downstream_tubes.last
    child_tube_v2 =
      Sequencescape::Api::V2.tube_with_custom_includes(
        'custom_metadatum_collection',
        nil,
        barcode: child_tube_v1.labware_barcode.machine
      )

    next unless child_tube_v2 && child_tube_v2.custom_metadatum_collection

    # get tube metadata from child_tube
    metadata = child_tube_v2.custom_metadatum_collection.metadata

    next unless metadata

    tube_rack_barcode = metadata['tube_rack_barcode']
    tube_rack_position = metadata['tube_rack_position']

    next unless tube_rack_barcode && tube_rack_position

    sample_uuid = source_well.aliquots.first.sample.uuid
    source_well_posn = source_well.position['name']

    sample_metadata = source_well.aliquots.first.sample.sample_metadata

    # donor_id is sourced from the sample metadata provided by Sequencescape
    donor_id = sample_metadata.respond_to?(:donor_id) ? sample_metadata.donor_id : nil
    child_tube_purpose = child_tube_v2.purpose.name
    destination = ((child_tube_purpose == 'LRC Bank Seq') ? 'Sequencing' : 'Contingency')
    volume = 125

    rows_array << [
      source_well.name, # Well name
      donor_id, # Donor ID
      @ancestor_tubes[sample_uuid].labware_barcode.human, # LRC Blood Vac purpose barcode
      child_tube_v2.barcode, # FluidX barcode
      child_tube_v2.created_at, # Extraction and freeze date
      destination, # Sequencing or contingency
      source_well.latest_live_cell_count&.value, # Cell count
      source_well.latest_cell_viability&.value, # Viability
      volume, # Volume
      source_well.aliquots.first.study.name, # Study name
      source_well.aliquots.first.sample.sample_metadata&.collected_by # Collection site
    ]
  end
%>
<% rows_array.sort_by{ |a| WellHelpers.well_coordinate(a[0]) }.each do |row| %>
<%= CSV.generate_line(row.map(&:to_s), row_sep: '').html_safe %>
<% end %>