Y26-112 - Generate Summary of Final Pooling Strategy for scRNA Pipeline

app/models/exports/filename_handler/ultima_balancing.rb

@@ -6,6 +6,7 @@ module FilenameHandler
     class UltimaBalancing
       def self.build_filename(labware, _page, _export)
         batch_ids = labware.aliquots.collect do |aliquot|
+          # TODO: change (and other uses) to 'detect' - 'find' just brings back .all
           aliquot.poly_metadata.find { |pm| pm.key == 'batch_id' }&.value
         end
 

app/views/exports/scrna_core_final_pooling_strategy.csv.erb

@@ -0,0 +1,71 @@
+<%
+  csv_rows = [
+    [
+      'DONOR ID',
+      'SAMPLE DESCRIPTION',
+      'SANGER TUBE ID',
+      'SANGER SAMPLE ID',
+      'LRC PBMC Defrost 1ml or Aliquot ID',
+      'Source Well',
+      'LRC PBMC Defrost 1ml/ Aliquot plate Total Cells/mL',
+      'LRC PBMC Defrost 1ml/ Aliquot plate Viability',
+      'LRC PBMC Defrost 1ml/Aliquot plate Status',
+      'LRC PBMC Pools plate ID',
+      'Destination Well',
+      'LRC PBMC Pools plate Total Cells/mL',
+      'LRC PBMC Pools plate Viability',
+      'Requested scRNA Core Cells per Chip Well',
+      'Actual scRNA Core Cells per Chip Well']
+  ]
+
+  # Get parent plates using parents association, which brings back Sequencescape::Api::V2::Asset objects.
+  parent_plate_barcodes = @plate.parents.map { |parent_plate| parent_plate.barcode&.human }
+  # Requery parent plates as Sequencescape::Api::V2::Plate to get access to wells and samples
+  parent_plates = Sequencescape::Api::V2::Plate.where(barcode: parent_plate_barcodes)
+
+  parent_plates.each do |parent_plate|
+    parent_plate.wells_in_columns.each do |parent_well|
+      sample = parent_well.aliquots.first&.sample
+      next unless sample
+
+      # binding.pry
+
+      pools_plate_well = parent_well.downstream_wells.first
+
+      donor_id = sample.sample_metadata.donor_id
+      sample_description = sample.sample_metadata.sample_description
+      sanger_tube_id = parent_well.upstream_tubes.first.human_barcode if parent_well.upstream_tubes.any? # sample.sample_metadata.supplier_name
+      sanger_sample_id = sample.sanger_sample_id
+      lrc_pbmc_defrost_1ml_or_aliquot_id = parent_plate.barcode.human
+      source_well = parent_well.position['name']
+      lrc_pbmc_defrost_1ml_or_aliquot_plate_total_cells_per_ml = parent_well.latest_total_cell_count&.value
+      lrc_pbmc_defrost_1ml_or_aliquot_plate_viability = parent_well.latest_cell_viability&.value
+      lrc_pbmc_defrost_1ml_or_aliquot_plate_status = nil # TODO - what did we decide for this?
+      lrc_pbmc_pools_plate_id = @plate.barcode.human
+      destination_well = pools_plate_well.position['name']
+      lrc_pbmc_pools_plate_total_cells_per_ml = pools_plate_well.latest_total_cell_count&.value
+      lrc_pbmc_pools_plate_viability = pools_plate_well.latest_cell_viability&.value
+      requested_scrna_core_cells_per_chip_well = pools_plate_well.aliquots.first.request.first.request_metadata.cells_per_chip_well
+      actual_scrna_core_cells_per_chip_well = pools_plate_well.poly_metadata.detect { |pm| pm.key == 'scrna_core_pbmc_donor_pooling_number_of_cells_per_chip_well' }&.value
+
+      csv_rows << [
+        donor_id,
+        sample_description,
+        sanger_tube_id,
+        sanger_sample_id,
+        lrc_pbmc_defrost_1ml_or_aliquot_id,
+        source_well,
+        lrc_pbmc_defrost_1ml_or_aliquot_plate_total_cells_per_ml,
+        lrc_pbmc_defrost_1ml_or_aliquot_plate_viability,
+        lrc_pbmc_defrost_1ml_or_aliquot_plate_status,
+        lrc_pbmc_pools_plate_id,
+        destination_well,
+        lrc_pbmc_pools_plate_total_cells_per_ml,
+        lrc_pbmc_pools_plate_viability,
+        requested_scrna_core_cells_per_chip_well,
+        actual_scrna_core_cells_per_chip_well
+      ]
+    end
+  end
+%>
+<%= csv_rows.map(&:to_csv).join %>

config/exports/exports.yml

@@ -153,6 +153,10 @@ scrna_core_cell_extraction_sample_arraying_tube_layout:
   csv: scrna_core_cell_extraction_sample_arraying_tube_layout
   plate_includes:
     - wells.upstream_tubes
+scrna_core_final_pooling_strategy:
+  csv: scrna_core_final_pooling_strategy
+  plate_includes:
+    - wells.upstream_tubes
 hamilton_lrc_pbmc_bank_to_lrc_bank_seq_and_spare:
   csv: hamilton_lrc_pbmc_bank_to_lrc_bank_seq_and_spare
   workflow: scRNA Core PBMC Bank

config/purposes/scrna_core_cdna_prep.yml

@@ -112,6 +112,8 @@ LRC PBMC Pools:
       parent: 'LRC PBMC Aliquot'
     - name: 'Download Cellaca Count CSV'
       id: 'hamilton_lrc_pbmc_pools_to_cellaca_count'
+    - name: 'Download final pooling strategy CSV'
+      id: 'scrna_core_final_pooling_strategy'
 # Plate containing pooled PBMCs from different donors.
 # This plate has come from faculty and is entering the SeqOps pipeline for the first time here.
 LRC GEM-X 5p GEMs Input:

spec/views/exports/scrna_core_final_pooling_strategy.csv.erb_spec.rb

@@ -0,0 +1,53 @@
+# frozen_string_literal: true
+
+require 'spec_helper'
+
+RSpec.describe 'exports/scrna_core_final_pooling_strategy.csv.erb' do
+#   let(:tube_a1) { create(:stock_tube, state: 'passed', purpose_name: 'Example Purpose', barcode_number: 2) }
+#   let(:tube_b1) { create(:stock_tube, state: 'passed', purpose_name: 'Example Purpose', barcode_number: 3) }
+#   let(:tube_c1) { create(:stock_tube, state: 'passed', purpose_name: 'Example Purpose', barcode_number: 4) }
+#   let(:tube_e7) { create(:stock_tube, state: 'passed', purpose_name: 'Example Purpose', barcode_number: 5) }
+#   let(:tube_g12) { create(:stock_tube, state: 'passed', purpose_name: 'Example Purpose', barcode_number: 6) }
+
+#   let(:well_a1) { create(:stock_well, location: 'A1', state: 'passed', upstream_tubes: [tube_a1]) }
+#   let(:well_b1) { create(:stock_well, location: 'B1', state: 'passed', upstream_tubes: [tube_b1]) }
+#   let(:well_c1) { create(:stock_well, location: 'C1', state: 'passed', upstream_tubes: [tube_c1]) }
+#   let(:well_e7) { create(:stock_well, location: 'E7', state: 'passed', upstream_tubes: [tube_e7]) }
+#   let(:well_g12) { create(:stock_well, location: 'G12', state: 'passed', upstream_tubes: [tube_g12]) }
+
+  let(:parent_plate_1) { create(:plate) }
+  let(:parent_plate_2) { create(:plate) }
+  let(:pools_plate) { create(:plate, parents: [parent_plate_1, parent_plate_2]) }
+
+  before { assign(:plate, pools_plate) }
+
+  def get_column(csv, index)
+    csv[1..].pluck(index)
+  end
+
+  it 'renders the expected content' do
+    parsed_csv = CSV.parse(render)
+    # expect(parsed_csv.size).to eq 11
+    # barcode = labware.labware_barcode.human
+
+    expected_column_names = ['DONOR ID', 'SAMPLE DESCRIPTION', 'SANGER TUBE ID', 'SANGER SAMPLE ID', 'LRC PBMC Defrost 1ml or Aliquot ID', 'Source Well', 'LRC PBMC Defrost 1ml/ Aliquot plate Total Cells/mL', 'LRC PBMC Defrost 1ml/ Aliquot plate Viability', 'LRC PBMC Defrost 1ml/Aliquot plate Status', 'LRC PBMC Pools plate ID', 'Proposed Destination Well', 'Destination Well', 'LRC PBMC Pools plate Total Cells/mL', 'LRC PBMC Pools plate Viability', 'Requested scRNA Core Cells per Chip Well', 'Actual scRNA Core Cells per Chip Well']
+    expect(parsed_csv[0]).to eq expected_column_names
+
+    expected_sample_1 = ['DONOR-1', nil, nil, nil, nil, nil, nil, nil, nil, nil, nil, nil, nil, nil, nil, nil]
+    expect(parsed_csv[1]).to eq expected_sample_1
+
+    # Donor ID column
+    # expect(get_column(parsed_csv, 0)).to eq(['DONOR-1', 'DONOR-2', nil])
+
+    # # chek for tube barcode content in wells
+    # expect(get_column(parsed_csv, 1)).to eq(
+    #   [nil, '1', 'NT2P', 'NT3Q', 'NT4R', 'empty', 'empty', 'empty', 'empty', 'empty']
+    # )
+    # expect(get_column(parsed_csv, 7)).to eq(
+    #   [nil, '7', 'empty', 'empty', 'empty', 'empty', 'NT5S', 'empty', 'empty', 'empty']
+    # )
+    # expect(get_column(parsed_csv, 12)).to eq(
+    #   [nil, '12', 'empty', 'empty', 'empty', 'empty', 'empty', 'empty', 'NT6T', 'empty']
+    # )
+  end
+end