Merge pull request #71 from emrojo/add_runner_move_barcodes_from_tube_rack_into_plate

Add runner move barcodes from tube rack into plate

Author: emrojo

script/runners/move_barcodes_from_tube_rack_to_plate.rb

@@ -0,0 +1,92 @@
+# # This rule applies the barcodes from a rack into a plate
+# {
+#   ?plate se:a """Plate""" .
+#   ?rack se:a """TubeRack""" .
+#   ?rack se:mergeInto ?plate .
+#   ?rack se:contains ?tube .
+#   ?plate se:contains ?well .
+#   ?tube se:location ?location .
+#   ?tube se:barcode ?barcode .
+#   ?well se:location ?location .
+#   } => {
+#     :step :addFacts { ?well se:barcode ?barcode . } .
+#     :step :removeFacts { ?tube se:barcode ?barcode . } .
+#     :step :addFacts { ?tube se:barcode """""" . } .
+#     :step :addFacts { ?tube se:previousBarcode ?barcode . } .
+#     :step :addFacts { ?tube se:appliedBarcodeTo ?well . } .
+#     :step :addFacts { ?rack se:mergedInto ?plate .}.
+#     :step :addFacts { ?plate se:mergedFrom ?rack .}.
+#   }.
+
+class MoveBarcodesFromTubeRackToPlate
+  attr_reader :asset_group
+
+
+  def initialize(params)
+    @asset_group = params[:asset_group]
+  end
+
+  def assets_compatible_with_step_type
+    [plate, tube_rack].flatten.compact.count > 0
+  end
+
+
+  def plate
+    asset_group.assets.select{|a| a.facts.where(predicate: 'a', object: 'Plate').count > 0 }.first
+  end
+
+  def tube_rack
+    asset_group.assets.select{|a| a.facts.where(predicate: 'a', object: 'TubeRack').count > 0}.first
+  end
+
+  def wells_for(asset)
+    asset.facts.where(predicate: 'contains').map(&:object_asset)
+  end
+
+  def well_at_location(asset, location)
+    wells_for(asset).select{|w| w.facts.where(predicate: 'location', object: location).count > 0}.first
+  end
+
+  def traverse_wells(asset, &block)
+    wells_for(asset).each do |w|
+      location = w.facts.where(predicate: 'location').first.object
+      yield w, location
+    end
+  end
+
+  def process
+    FactChanges.new.tap do |updates|
+      if assets_compatible_with_step_type
+        traverse_wells(tube_rack) do |well_from_tube_rack, location|
+          well_from_plate = well_at_location(plate, location)
+          updates.remove_where(well_from_tube_rack, 'barcode', well_from_tube_rack.barcode)
+          updates.add(well_from_tube_rack, 'previousBarcode', well_from_tube_rack.barcode)
+          updates.add(well_from_tube_rack, 'appliedBarcodeTo', well_from_plate)
+          updates.add(well_from_plate, 'barcode', well_from_tube_rack.barcode)
+        end
+
+        updates.add(tube_rack, 'mergedInto', plate)
+        updates.add(plate, 'mergedFrom', tube_rack)
+      end
+    end
+  end
+end
+
+return unless ARGV.any?{|s| s.match(".json")}
+
+args = ARGV[0]
+asset_group_id = args.match(/(\d*)\.json/)[1]
+asset_group = AssetGroup.find(asset_group_id)
+
+begin
+  updates = MoveBarcodesFromTubeRackToPlate.new(asset_group: asset_group).process
+  json = updates.to_json
+  JSON.parse(json)
+  puts json
+rescue InvalidDataParams => e
+  puts ({ set_errors: e.errors }.to_json)
+rescue StandardError => e
+  puts ({ set_errors: ['Unknown error while parsing file'+e.backtrace.to_s]}.to_json)
+end
+
+

spec/script/runners/move_barcodes_from_tube_rack_to_plate_spec.rb

@@ -0,0 +1,68 @@
+require 'rails_helper'
+
+require Rails.root.to_s+'/script/runners/move_barcodes_from_tube_rack_to_plate'
+
+RSpec.describe 'MoveBarcodesFromTubeRackToPlate' do
+  NUM_WELLS = 3
+
+  let(:barcodes) {
+    NUM_WELLS.times.map{|i| "FR00#{i}"}
+  }
+  let(:locations) {
+    NUM_WELLS.times.map{|i| "A#{i}"}
+  }
+  let(:wells_for_rack) {
+    NUM_WELLS.times.map do |i|
+      asset = create(:asset, barcode: barcodes[i])
+      asset.facts << create(:fact, predicate: 'a', object: 'Tube')
+      asset.facts << create(:fact, predicate: 'location', object: locations[i])
+      asset
+    end
+  }
+  let(:wells_for_plate) {
+    NUM_WELLS.times.map do |i|
+      asset = create(:asset)
+      asset.facts << create(:fact, predicate: 'a', object: 'Well')
+      asset.facts << create(:fact, predicate: 'location', object: locations[i])
+      asset
+    end
+  }
+  let(:tube_rack) {
+    asset = create :asset
+    asset.facts << create(:fact, predicate: 'a', object: 'TubeRack')
+    asset.facts << wells_for_rack.map{|a| create(:fact, predicate: 'contains', object_asset: a)}
+    asset
+  }
+  let(:plate) {
+    asset = create :asset
+    asset.facts << create(:fact, predicate: 'a', object: 'Plate')
+    asset.facts << wells_for_plate.map{|a| create(:fact, predicate: 'contains', object_asset: a)}
+    asset
+  }
+
+  context 'when run with a tube rack and a plate' do
+    it 'adds the barcodes of the tube rack into the wells of the plate' do
+      group = create(:asset_group, assets: [plate, tube_rack])
+      changes = MoveBarcodesFromTubeRackToPlate.new(asset_group: group).process.to_h
+
+      expect(changes[:add_facts].select{|t| t[1] == 'barcode'}.count).to eq(NUM_WELLS)
+
+      wells_for_plate.each_with_index do |w, pos|
+        expect(changes[:add_facts]).to include(
+          [w.uuid, 'barcode', barcodes[pos]])
+      end
+    end
+    it 'removes the barcodes from the tubes of the tube rack' do
+      group = create(:asset_group, assets: [plate, tube_rack])
+      changes = MoveBarcodesFromTubeRackToPlate.new(asset_group: group).process.to_h
+
+      expect(changes[:remove_facts].select{|t| t[1] == 'barcode'}.count).to eq(NUM_WELLS)
+
+      wells_for_rack.each_with_index do |w, pos|
+        expect(changes[:remove_facts]).to include(
+          [w.uuid, 'barcode', barcodes[pos]])
+      end
+    end
+
+  end
+end