Merge pull request #1433 from sanger/dpl-812-fluidx-tube-rack-data-re…

…port

DPL-812: FluidX tube rack data report

app/sequencescape/sequencescape/api/v2/well.rb

@@ -35,6 +35,10 @@ def latest_live_cell_count
     latest_qc(key: 'live_cell_count', units: 'cells/ml')
   end
 
+  def latest_cell_viability
+    latest_qc(key: 'viability', units: '%')
+  end
+
   def latest_qc(key:, units:)
     qc_results.to_a # Convert to array to resolve any api queries. Otherwise select fails to work.
       .select { |qc| qc.key.casecmp(key).zero? }

app/views/exports/pbmc_bank_tubes_content_report.csv.erb

@@ -0,0 +1,81 @@
+<%# 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 : nils
+    child_tube_purpose = child_tube_v2.purpose.name
+    destination = ((child_tube_purpose == 'LRC Blood Seq') ? 'Sequencing' : 'Contingency')
+    volume = 135
+
+    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, row_sep: '' %>
+<% end %>

config/exports/exports.yml

@@ -164,3 +164,12 @@ hamilton_lrc_blood_bank_to_lrc_pbmc_bank:
     - wells.transfer_requests_as_target.source_asset
   ancestor_tube_purpose: LRC Blood Vac
   ancestor_purpose: LRC Blood Bank
+pbmc_bank_tubes_content_report:
+  csv: pbmc_bank_tubes_content_report
+  workflow: scRNA Core PBMC Bank
+  plate_includes:
+    - wells.downstream_tubes
+    - wells.aliquots
+    - wells.aliquots.sample
+    - wells.aliquots.sample.sample_metadata
+  ancestor_tube_purpose: LRC Blood Vac

config/purposes/scrna_core_cell_extraction.wip.yml

@@ -81,6 +81,8 @@ LRC PBMC Bank:
       id: hamilton_lrc_blood_bank_to_lrc_pbmc_bank
     - name: 'Download Hamilton LRC PBMC Bank plate to LRC Bank Seq and Spare tubes CSV'
       id: hamilton_lrc_pbmc_bank_to_lrc_bank_seq_and_spare
+    - name: 'Download PBMC Bank Tubes Content Report'
+      id: pbmc_bank_tubes_content_report
   :qc_thresholds:
     viability:
       units: '%'

spec/factories/plate_factories.rb

@@ -60,6 +60,9 @@
       # associated request. This allows us to over-ride that
       aliquots_without_requests { 0 }
 
+      study { create :v2_study, name: 'Plate Study' }
+      project { create :v2_project, name: 'Plate Project' }
+
       # Constructs the wells for the plate. Constructs
       # well_count wells using the factory specified in well_factory
       # Sets requests on wells by pulling them off the outer_request array
@@ -73,7 +76,9 @@
                  outer_request: outer_requests[i],
                  downstream_tubes: transfer_targets[location],
                  uuid: well_uuid_result % location,
-                 aliquot_count: outer_requests[i] ? 1 : aliquots_without_requests
+                 aliquot_count: outer_requests[i] ? 1 : aliquots_without_requests,
+                 study: study,
+                 project: project
         end
       end
 

spec/factories/project_factories.rb

@@ -5,6 +5,8 @@
   factory :v2_project, class: Sequencescape::Api::V2::Project do
     skip_create
 
+    id
+
     name { 'Test Project' }
 
     uuid { SecureRandom.uuid }

spec/factories/sample_factories.rb

@@ -38,6 +38,7 @@
     collected_by { 'Sanger' }
     cohort { 'Cohort' }
     sample_description { 'Description' }
+    sequence(:donor_id) { |i| "donor#{i}" }
   end
 
   factory :v2_sample_metadata_for_mbrave, class: Sequencescape::Api::V2::SampleMetadata do

spec/factories/study_factories.rb

@@ -5,6 +5,8 @@
   factory :v2_study, class: Sequencescape::Api::V2::Study do
     skip_create
 
+    id
+
     name { 'Test Study' }
 
     uuid { SecureRandom.uuid }

spec/factories/well_factories.rb

@@ -53,12 +53,15 @@
       # Use the stock well factory if you want the request comming out of the well
       outer_request { create request_factory, state: library_state }
 
+      study { create :v2_study, name: 'Well Study' }
+      project { create :v2_project, name: 'Well Project' }
+
       # The factory to use for aliquots
       aliquot_factory { :v2_aliquot }
       aliquots do
         # Conditional to avoid generating requests when not required
         if aliquot_count > 0
-          create_list aliquot_factory, aliquot_count, outer_request: outer_request
+          create_list aliquot_factory, aliquot_count, outer_request: outer_request, study: study, project: project
         else
           []
         end
@@ -256,8 +259,8 @@
       # Alias for request: The request set on the aliquot itself
       outer_request { create :library_request, state: library_state }
       well_location { 'A1' }
-      study_id { 1 }
-      project_id { 1 }
+      study { create :v2_study, name: 'Test Aliquot Study' }
+      project { create :v2_project, name: 'Test Aliquot Project' }
       sample_attributes { {} }
     end
 
@@ -271,16 +274,19 @@
     request { outer_request }
 
     after(:build) do |aliquot, evaluator|
-      aliquot._cached_relationship(:request) { evaluator.request }
-      aliquot._cached_relationship(:sample) { evaluator.sample }
+      # Set up relationships downstream
+      Sequencescape::Api::V2::Aliquot.associations.each do |association|
+        aliquot._cached_relationship(association.attr_name) { evaluator.send(association.attr_name) }
+      end
+
       aliquot.relationships.study = {
         'links' => {
           'self' => "http://localhost:3000/api/v2/aliquots/#{aliquot.id}/relationships/study",
           'related' => "http://localhost:3000/api/v2/aliquots/#{aliquot.id}/study"
         },
         'data' => {
           'type' => 'studies',
-          'id' => evaluator.study_id.to_s
+          'id' => evaluator.study.id.to_s
         }
       }
       aliquot.relationships.project = {
@@ -290,7 +296,7 @@
         },
         'data' => {
           'type' => 'projects',
-          'id' => evaluator.project_id.to_s
+          'id' => evaluator.project.id.to_s
         }
       }
     end

spec/factory_outputs/plate_factory_spec.rb

@@ -177,3 +177,87 @@
     expect(JSON.parse(subject)).to include_json(JSON.parse(json_content))
   end
 end
+
+RSpec.describe 'v2_plate' do
+  context 'with specified study and project at plate level' do
+    subject { create(:v2_plate, aliquots_without_requests: 1, study: study, project: project) }
+
+    # study
+    let(:study_uuid) { SecureRandom.uuid }
+    let(:study) { create(:v2_study, name: 'Provided Study', uuid: study_uuid) }
+
+    # project
+    let(:project_uuid) { SecureRandom.uuid }
+    let(:project) { create(:v2_project, name: 'Provided Project', uuid: project_uuid) }
+
+    describe 'first aliquot' do
+      let(:first_aliquot) { subject.wells.first.aliquots.first }
+
+      it 'should be a version 2 aliquot' do
+        expect(first_aliquot.class).to eq(Sequencescape::Api::V2::Aliquot)
+      end
+
+      it 'should have a valid study' do
+        expect(first_aliquot.study).to be_kind_of(Sequencescape::Api::V2::Study)
+      end
+      it 'should have a valid study uuid' do
+        expect(first_aliquot.study.uuid).to eq(study_uuid)
+      end
+      it 'should have a valid study name' do
+        expect(first_aliquot.study.name).to eq('Provided Study')
+      end
+
+      it 'should have a valid project' do
+        expect(first_aliquot.project).to be_kind_of(Sequencescape::Api::V2::Project)
+      end
+      it 'should have a valid project uuid' do
+        expect(first_aliquot.project.uuid).to eq(project_uuid)
+      end
+      it 'should have a valid project name' do
+        expect(first_aliquot.project.name).to eq('Provided Project')
+      end
+    end
+  end
+end
+
+RSpec.describe 'v2_plate_for_submission' do
+  context 'with specified study and project at plate level' do
+    subject { create(:v2_plate_for_submission, aliquots_without_requests: 1, study: study, project: project) }
+
+    # study
+    let(:study_uuid) { SecureRandom.uuid }
+    let(:study) { create(:v2_study, name: 'Provided Study', uuid: study_uuid) }
+
+    # project
+    let(:project_uuid) { SecureRandom.uuid }
+    let(:project) { create(:v2_project, name: 'Provided Project', uuid: project_uuid) }
+
+    describe 'first aliquot' do
+      let(:first_aliquot) { subject.wells.first.aliquots.first }
+
+      it 'should be a version 2 aliquot' do
+        expect(first_aliquot.class).to eq(Sequencescape::Api::V2::Aliquot)
+      end
+
+      it 'should have a valid study' do
+        expect(first_aliquot.study).to be_kind_of(Sequencescape::Api::V2::Study)
+      end
+      it 'should have a valid study uuid' do
+        expect(first_aliquot.study.uuid).to eq(study_uuid)
+      end
+      it 'should have a valid study name' do
+        expect(first_aliquot.study.name).to eq('Provided Study')
+      end
+
+      it 'should have a valid project' do
+        expect(first_aliquot.project).to be_kind_of(Sequencescape::Api::V2::Project)
+      end
+      it 'should have a valid project uuid' do
+        expect(first_aliquot.project.uuid).to eq(project_uuid)
+      end
+      it 'should have a valid project name' do
+        expect(first_aliquot.project.name).to eq('Provided Project')
+      end
+    end
+  end
+end