sequencescape-client-api 0.3.7 → 0.4.0.pre.rc2

data/lib/sequencescape-api/resource_model_proxy.rb

@@ -8,21 +8,23 @@ require 'ostruct'
 # Any interaction with the API isn't done directly through a model but through an instance of this
 # class, that proxies the model and ensures that it uses the correct instance of Sequencescape::Api.
 class Sequencescape::Api::ResourceModelProxy
-  self.instance_methods.each { |m| undef_method(m) unless m.to_s =~ /^(__.+__|respond_to\?|object_id)$/ }
+  instance_methods.each { |m| undef_method(m) unless m.to_s =~ /^(__.+__|respond_to\?|object_id)$/ }
 
   include ::Sequencescape::Api::FinderMethods
   extend ::Sequencescape::Api::Actions
 
   def initialize(api, model, actions)
-    @api, @model, @actions = api, model, OpenStruct.new(actions)
+    @api = api
+    @model = model
+    @actions = OpenStruct.new(actions)
     @model.send(:initialize_class_actions, self)
   end
 
   attr_reader :api, :actions, :model
   private :api, :actions, :model
 
-  delegate :nil?, :inspect, :to => :model
-  delegate :read_timeout, :to => :api
+  delegate :nil?, :inspect, to: :model
+  delegate :read_timeout, to: :api
 
   has_create_action
 
@@ -40,5 +42,5 @@ class Sequencescape::Api::ResourceModelProxy
   end
 
   # Here are some methods that need to be delegated directly.
-  delegate :ai, :to => :model
+  delegate :ai, to: :model
 end

data/lib/sequencescape-api/version.rb

@@ -1,5 +1,5 @@
 module Sequencescape
   class Api
-    VERSION = "0.3.7"
+    VERSION = '0.4.0-rc2'.freeze
   end
 end

data/lib/sequencescape.rb

@@ -1,7 +1,6 @@
 require 'sequencescape-api'
 
 module Sequencescape
-
 end
 
 require 'sequencescape/user'
@@ -74,8 +73,11 @@ require 'sequencescape/qcable_creator'
 require 'sequencescape/qc_decision'
 require 'sequencescape/plate_conversion'
 
+# Support Extraction
+require 'sequencescape/extraction_attribute'
+
 # Events
 require 'sequencescape/library_event'
 
 # Ensure that the I18n stuff has been properly configured
-I18n.config.load_path << File.expand_path(File.join(File.dirname(__FILE__), %w{sequencescape locale en.yml}))
+I18n.config.load_path << File.expand_path(File.join(File.dirname(__FILE__), %w[sequencescape locale en.yml]))

data/lib/sequencescape/bait_library.rb

@@ -2,7 +2,7 @@ class BaitLibrary
   include Sequencescape::Api::Composition::Target
 
   attribute_accessor :name
-  attribute_accessor :created_at, :updated_at, :conversion => :to_time
+  attribute_accessor :created_at, :updated_at, conversion: :to_time
 
   attribute_group :supplier do
     attribute_accessor :name, :identifier

data/lib/sequencescape/bait_library_layout.rb

@@ -2,8 +2,8 @@ require 'sequencescape-api/resource'
 
 class Sequencescape::BaitLibraryLayout < ::Sequencescape::Api::Resource
   belongs_to :user
-  belongs_to :plate, :class_name => 'Plate'
+  belongs_to :plate, class_name: 'Plate'
   attribute_reader :layout
 
-  has_class_create_action(:preview!, :action => :preview)
+  has_class_create_action(:preview!, action: :preview)
 end

data/lib/sequencescape/barcoded_asset.rb

@@ -8,5 +8,5 @@ class Sequencescape::BarcodedAsset < ::Sequencescape::Asset
   include Sequencescape::Behaviour::Barcoded
   include Sequencescape::Behaviour::Qced
 
-  belongs_to :stock_plate, :class_name => 'Plate'
+  belongs_to :stock_plate, class_name: 'Plate'
 end

data/lib/sequencescape/batch.rb

@@ -2,17 +2,17 @@ require 'sequencescape-api/resource'
 
 class Sequencescape::Batch < ::Sequencescape::Api::Resource
   belongs_to  :pipeline
-  has_many    :requests, :disposition => :inline
+  has_many    :requests, disposition: :inline
   composed_of :user
 
-  has_update_action :start!,    :action => 'start'
-  has_update_action :complete!, :action => 'complete'
-  has_update_action :release!,  :action => 'release'
+  has_update_action :start!,    action: 'start'
+  has_update_action :complete!, action: 'complete'
+  has_update_action :release!,  action: 'release'
 
   attribute_accessor :state, :production_state, :qc_state, :barcode
 
   def self.state_method(name)
-    class_eval(%Q{def #{name}? ; state == #{name.to_s.inspect} ; end})
+    class_eval("def #{name}? ; state == #{name.to_s.inspect} ; end")
   end
 
   state_method(:pending)
@@ -20,5 +20,5 @@ class Sequencescape::Batch < ::Sequencescape::Api::Resource
   state_method(:completed)
   state_method(:released)
 
-  validates_presence_of :requests, :allow_blank => false
+  validates_presence_of :requests, allow_blank: false
 end

data/lib/sequencescape/behaviour/qced.rb

@@ -1,6 +1,5 @@
 module Sequencescape::Behaviour
   module Qced
-
     module QcFile
       def create!(attributes = nil)
         attributes ||= {}
@@ -14,7 +13,8 @@ module Sequencescape::Behaviour
         attributes ||= {}
 
         new({}, false).tap do |qc_file|
-          api.create_from_file(actions.create, file, filename, 'sequencescape/qc_file', Sequencescape::Api::ModifyingHandler.new(qc_file))
+          api.create_from_file(actions.create, file, filename, 'sequencescape/qc_file',
+                               Sequencescape::Api::ModifyingHandler.new(qc_file))
         end
       end
     end
@@ -22,10 +22,9 @@ module Sequencescape::Behaviour
     def self.included(base)
       base.class_eval do
         has_many :qc_files do
-         include Sequencescape::Behaviour::Qced::QcFile
+          include Sequencescape::Behaviour::Qced::QcFile
         end
       end
     end
-
   end
 end

data/lib/sequencescape/behaviour/receptacle.rb

@@ -4,9 +4,9 @@ require 'sequencescape/bait_library'
 module Sequencescape::Behaviour
   module Receptacle
     class Aliquot < Sequencescape::Api::Resource
-      belongs_to :sample, :disposition => :inline
+      belongs_to :sample, disposition: :inline
       composed_of :tag
-      composed_of :tag2, :class_name => 'Tag'
+      composed_of :tag2, class_name: 'Tag'
       composed_of :bait_library
 
       attribute_accessor :suboptimal
@@ -14,7 +14,7 @@ module Sequencescape::Behaviour
 
     def self.included(base)
       base.class_eval do
-        has_many :aliquots, :disposition => :inline, :class_name => 'Behaviours::Receptacle::Aliquot'
+        has_many :aliquots, disposition: :inline, class_name: 'Behaviours::Receptacle::Aliquot'
       end
     end
   end

data/lib/sequencescape/behaviour/state_driven.rb

@@ -1,17 +1,17 @@
 module Sequencescape::Behaviour
   module StateDriven
-    def self.included(base)
+    def self.included(base) # rubocop:todo Metrics/MethodLength
       base.class_eval do
         attribute_reader :state
 
         # Define a few default states
-        [ :pending, :started, :passed, :failed, :cancelled, :unknown, :qc_complete ].each do |state|
+        %i[pending started passed failed cancelled unknown qc_complete].each do |state|
           line = __LINE__ + 1
-          class_eval(%Q{
+          class_eval("
             def #{state}?
               state == #{state.to_s.inspect}
             end
-          }, __FILE__, line)
+          ", __FILE__, line)
         end
       end
     end

data/lib/sequencescape/bulk_transfer.rb

@@ -2,7 +2,7 @@ require 'sequencescape-api/resource'
 
 class Sequencescape::BulkTransfer < ::Sequencescape::Api::Resource
   belongs_to :user
-  has_many :transfers, :class_name => 'Transfer'
+  has_many :transfers, class_name: 'Transfer'
 
   attribute_accessor :well_transfers
 end

data/lib/sequencescape/comment.rb

@@ -1,7 +1,5 @@
 require 'sequencescape-api/resource'
 
 class Sequencescape::Comment < ::Sequencescape::Api::Resource
-
   attribute_accessor :description, :title
-
 end

data/lib/sequencescape/extraction_attribute.rb

@@ -0,0 +1,6 @@
+require 'sequencescape-api/resource'
+
+class Sequencescape::ExtractionAttribute < ::Sequencescape::Api::Resource
+  belongs_to :plate, class_name: 'Asset', disposition: :inline
+  attribute_accessor :attributes_update, :created_by
+end

data/lib/sequencescape/library_event.rb

@@ -1,5 +1,5 @@
 class Sequencescape::LibraryEvent < ::Sequencescape::Api::Resource
   belongs_to :user
-  belongs_to :seed, :class_name => 'Plate'
+  belongs_to :seed, class_name: 'Plate'
   attribute_accessor :event_type
 end

data/lib/sequencescape/library_tube.rb

@@ -2,6 +2,6 @@ require 'sequencescape/tube'
 
 class Sequencescape::LibraryTube < ::Sequencescape::Tube
   has_many   :requests
-  belongs_to :source_request, :class_name => 'Sequencescape::Request'
+  belongs_to :source_request, class_name: 'Sequencescape::Request'
   belongs_to :custom_metadatum_collection
 end

data/lib/sequencescape/lot.rb

@@ -1,7 +1,6 @@
 require 'sequencescape-api/resource'
 
 class Sequencescape::Lot < ::Sequencescape::Api::Resource
-
   belongs_to :user
   belongs_to :lot_type
   belongs_to :template

data/lib/sequencescape/lot_type.rb

@@ -1,9 +1,8 @@
 require 'sequencescape-api/resource'
 
 class Sequencescape::LotType < ::Sequencescape::Api::Resource
-
   module LotCreator
-    def create!(attributes=nil)
+    def create!(attributes = nil)
       attributes ||= {}
       new({}, false).tap do |lot|
         api.create(actions.create, { 'lot' => attributes }, Sequencescape::Api::ModifyingHandler.new(lot))

data/lib/sequencescape/order_template.rb

@@ -1,9 +1,8 @@
 require 'sequencescape-api/resource'
 
 class Sequencescape::OrderTemplate < ::Sequencescape::Api::Resource
-
   module OrderCreator
-    def create!(attributes=nil)
+    def create!(attributes = nil)
       attributes ||= {}
       new({}, false).tap do |order|
         api.create(actions.create, { 'order' => attributes }, Sequencescape::Api::ModifyingHandler.new(order))

data/lib/sequencescape/pipeline.rb

@@ -2,7 +2,7 @@ require 'sequencescape-api/resource'
 
 class Sequencescape::Pipeline < ::Sequencescape::Api::Resource
   attribute_accessor :name
-  
+
   has_many :requests
   has_many :batches do
     has_create_action

data/lib/sequencescape/plate.rb

@@ -21,17 +21,18 @@ class Sequencescape::Plate < ::Sequencescape::Asset
 
   belongs_to :plate_purpose
   belongs_to :custom_metadatum_collection
-  composed_of :stock_plate, :class_name => 'Plate'
+  composed_of :stock_plate, class_name: 'Plate'
 
   module CommentsCreation
     def create!(attributes = nil)
       attributes ||= {}
 
       new({}, false).tap do |comment|
-        api.create(actions.create, { 'comment' => attributes }, Sequencescape::Api::ModifyingHandler.new(comment))
+        api.create(actions.create,
+                   { 'comment' => attributes },
+                   Sequencescape::Api::ModifyingHandler.new(comment))
       end
     end
-
   end
 
   module CurrentVolumeSubstraction
@@ -39,12 +40,14 @@ class Sequencescape::Plate < ::Sequencescape::Asset
       attributes ||= {}
 
       new({}, false).tap do |volume_update|
-        api.create(actions.create, { 'volume_update' => attributes }, Sequencescape::Api::ModifyingHandler.new(volume_update))
+        api.create(actions.create,
+                   { 'volume_update' => attributes },
+                   Sequencescape::Api::ModifyingHandler.new(volume_update))
       end
     end
 
     def substract_volume!(volume_change)
-      create!({ :volume_change => volume_change})
+      create!({ volume_change: volume_change })
     end
   end
   has_many :volume_updates do
@@ -55,17 +58,32 @@ class Sequencescape::Plate < ::Sequencescape::Asset
     include Sequencescape::Plate::CommentsCreation
   end
 
-  has_many :source_transfers, :class_name => 'Transfer'
-  has_many :transfers_to_tubes, :class_name => 'Transfer'
-  has_many :creation_transfers, :class_name => 'Transfer'
+  has_many :source_transfers, class_name: 'Transfer'
+  has_many :transfers_to_tubes, class_name: 'Transfer'
+  has_many :creation_transfers, class_name: 'Transfer'
 
   attribute_accessor :size, :iteration, :pools, :pre_cap_groups, :location, :priority
 
   # Provides backwards compatability
   def creation_transfer
-    Rails.logger.warn "Creation transfer is deprecated, use creation_transfers instead"
-    return creation_transfers.first if creation_transfers.count == 1
-    raise Sequencescape::Api::Error, "Unexpected number of transfers found: #{creation_transfers.count} found, 1 expected."
+    Rails.logger.warn 'Creation transfer is deprecated, use creation_transfers instead'
+    transfers_found = creation_transfers.count
+    return creation_transfers.first if transfers_found == 1
+
+    raise Sequencescape::Api::Error, "Unexpected number of transfers found: #{transfers_found} found, 1 expected."
   end
 
+  module UpdateExtractionAttributes
+    def create!(attributes = nil)
+      attributes ||= {}
+      new({}, false).tap do |attrs|
+        api.create(actions.create, { extraction_attribute: attributes },
+                   Sequencescape::Api::ModifyingHandler.new(attrs))
+      end
+    end
+  end
+
+  has_many :extraction_attributes, class_name: 'ExtractionAttribute' do
+    include Sequencescape::Plate::UpdateExtractionAttributes
+  end
 end

data/lib/sequencescape/plate/pooling.rb

@@ -3,21 +3,27 @@ module Sequencescape::Plate::Pooling
     wells.each do |well|
       pool_id, pool = pools.detect { |_, pool| pool['wells'].include?(well.location) }
       next if pool.nil?
+
       well.pool = pool
     end
   end
 
   def populate_wells_with_pre_cap_group
     wells.each do |well|
-      pre_cap_group_id, pre_cap_group = pre_cap_groups.detect { |_, pre_cap_group| pre_cap_group['wells'].include?(well.location) }
+      pre_cap_group_id, pre_cap_group = pre_cap_groups.detect do |_, pre_cap_group|
+        pre_cap_group['wells'].include?(well.location)
+      end
       next if pre_cap_group.nil?
+
       well.pre_cap_group = pre_cap_group
     end
   end
 
   def after_load
-    pools.each { |pool_id, pool| pool['id'] = pool_id } unless pools.nil?
-    pre_cap_groups.each { |pre_cap_group_id, pre_cap_group| pre_cap_group['id'] = pre_cap_group_id } unless pre_cap_groups.nil?
+    pools&.each { |pool_id, pool| pool['id'] = pool_id }
+    return if pre_cap_groups.nil?
+
+    pre_cap_groups.each { |pre_cap_group_id, pre_cap_group| pre_cap_group['id'] = pre_cap_group_id }
   end
   private :after_load
 end

data/lib/sequencescape/plate/well_structure.rb

@@ -1,24 +1,24 @@
 module Sequencescape::Plate::WellStructure
   def rows
-    case self.size
+    case size
     when 96  then ('A'..'H')
     when 384 then ('A'..'P')
-    else          raise RuntimeError, "Unknown plate size #{self.size}"
+    else          raise "Unknown plate size #{size}"
     end
   end
 
   def columns
-    case self.size
+    case size
     when 96  then (1..12)
     when 384 then (1..24)
-    else          raise RuntimeError, "Unknown plate size #{self.size}"
+    else          raise "Unknown plate size #{size}"
     end
   end
 
   def locations_in_rows
     [].tap do |locations|
-      self.rows.each do |row|
-        self.columns.each do |column|
+      rows.each do |row|
+        columns.each do |column|
           locations << "#{row}#{column}"
         end
       end

data/lib/sequencescape/plate_conversion.rb

@@ -2,7 +2,7 @@ require 'sequencescape-api/resource'
 
 class Sequencescape::PlateConversion < ::Sequencescape::Api::Resource
   belongs_to :user
-  belongs_to :target, :class_name => 'Plate'
-  belongs_to :parent, :class_name => 'Plate'
-  belongs_to :purpose, :class_name => 'PlatePurpose'
+  belongs_to :target, class_name: 'Plate'
+  belongs_to :parent, class_name: 'Plate'
+  belongs_to :purpose, class_name: 'PlatePurpose'
 end

data/lib/sequencescape/plate_creation.rb

@@ -2,7 +2,7 @@ require 'sequencescape-api/resource'
 
 class Sequencescape::PlateCreation < ::Sequencescape::Api::Resource
   belongs_to :user
-  belongs_to :parent, :class_name => 'Plate'
-  belongs_to :child_purpose, :class_name => 'PlatePurpose'
-  belongs_to :child, :class_name => 'Plate'
+  belongs_to :parent, class_name: 'Plate'
+  belongs_to :child_purpose, class_name: 'PlatePurpose'
+  belongs_to :child, class_name: 'Plate'
 end