sequencescape-client-api 0.3.5

data/lib/sequencescape/lot.rb

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+require 'sequencescape-api/resource'
+
+class Sequencescape::Lot < ::Sequencescape::Api::Resource
+
+  belongs_to :user
+  belongs_to :lot_type
+  belongs_to :template
+  has_many :qcables
+
+  attribute_accessor :lot_number, :received_at, :template_name, :lot_type_name
+end

data/lib/sequencescape/lot_type.rb

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+require 'sequencescape-api/resource'
+
+class Sequencescape::LotType < ::Sequencescape::Api::Resource
+
+  module LotCreator
+    def create!(attributes=nil)
+      attributes ||= {}
+      new({}, false).tap do |lot|
+        api.create(actions.create, { 'lot' => attributes }, Sequencescape::Api::ModifyingHandler.new(lot))
+      end
+    end
+  end
+
+  has_many :lots do
+    # has_create_action
+    include Sequencescape::LotType::LotCreator
+  end
+
+  attribute_accessor :name, :template_class, :printer_type, :qcable_name
+end

data/lib/sequencescape/multiplexed_library_tube.rb

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+require 'sequencescape/library_tube'
+
+class Sequencescape::MultiplexedLibraryTube < Sequencescape::LibraryTube
+  attribute_reader :state
+  belongs_to :custom_metadatum_collection
+end

data/lib/sequencescape/order.rb

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+require 'sequencescape-api/resource'
+
+class Sequencescape::Order < ::Sequencescape::Api::Resource
+  has_many :assets
+  belongs_to :user
+  belongs_to :study
+  belongs_to :project
+
+  # It does, but we don't care for now.
+  # has_many :request_types
+
+  attr_accessor :request_options
+end

data/lib/sequencescape/order_template.rb

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+require 'sequencescape-api/resource'
+
+class Sequencescape::OrderTemplate < ::Sequencescape::Api::Resource
+
+  module OrderCreator
+    def create!(attributes=nil)
+      attributes ||= {}
+      new({}, false).tap do |order|
+        api.create(actions.create, { 'order' => attributes }, Sequencescape::Api::ModifyingHandler.new(order))
+      end
+    end
+  end
+
+  has_many :orders do
+    include Sequencescape::OrderTemplate::OrderCreator
+  end
+
+  attribute_accessor :name
+end

data/lib/sequencescape/pipeline.rb

@@ -0,0 +1,10 @@
+require 'sequencescape-api/resource'
+
+class Sequencescape::Pipeline < ::Sequencescape::Api::Resource
+  attribute_accessor :name
+  
+  has_many :requests
+  has_many :batches do
+    has_create_action
+  end
+end

data/lib/sequencescape/plate/pooling.rb

@@ -0,0 +1,23 @@
+module Sequencescape::Plate::Pooling
+  def populate_wells_with_pool
+    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) }
+      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?
+  end
+  private :after_load
+end

data/lib/sequencescape/plate/well_structure.rb

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

data/lib/sequencescape/plate.rb

@@ -0,0 +1,71 @@
+require 'sequencescape/asset'
+
+class Sequencescape::Plate < ::Sequencescape::Asset
+  require 'sequencescape/behaviour/barcoded'
+  require 'sequencescape/behaviour/state_driven'
+  require 'sequencescape/plate/well_structure'
+  require 'sequencescape/plate/pooling'
+  require 'sequencescape/behaviour/labeled'
+  require 'sequencescape/behaviour/qced'
+
+  include Sequencescape::Behaviour::Barcoded
+  include Sequencescape::Behaviour::StateDriven
+  include Sequencescape::Plate::WellStructure
+  include Sequencescape::Plate::Pooling
+  include Sequencescape::Behaviour::Labeled
+  include Sequencescape::Behaviour::Qced
+
+  has_many :wells
+  has_many :submission_pools
+  has_many :transfer_request_collections
+
+  belongs_to :plate_purpose
+  belongs_to :custom_metadatum_collection
+  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))
+      end
+    end
+
+  end
+
+  module CurrentVolumeSubstraction
+    def create!(attributes = nil)
+      attributes ||= {}
+
+      new({}, false).tap do |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})
+    end
+  end
+  has_many :volume_updates do
+    include Sequencescape::Plate::CurrentVolumeSubstraction
+  end
+
+  has_many :comments do
+    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'
+
+  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."
+  end
+
+end

data/lib/sequencescape/plate_conversion.rb

@@ -0,0 +1,8 @@
+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'
+end

data/lib/sequencescape/plate_creation.rb

@@ -0,0 +1,8 @@
+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'
+end

data/lib/sequencescape/plate_purpose.rb

@@ -0,0 +1,24 @@
+require 'sequencescape-api/resource'
+
+class Sequencescape::PlatePurpose < ::Sequencescape::Api::Resource
+  module PlateCreation
+    def create!(attributes = nil)
+      attributes ||= {}
+      attributes[:wells].delete_if { |_,v| v.blank? } if attributes.key?(:wells)
+
+      new({}, false).tap do |plate|
+        api.create(actions.create, { 'plate' => attributes }, Sequencescape::Api::ModifyingHandler.new(plate))
+      end
+    end
+  end
+
+  has_many :children, :class_name => 'PlatePurpose'
+  has_many :parents, :class_name => 'PlatePurpose'
+
+  has_many :plates do
+    include Sequencescape::PlatePurpose::PlateCreation
+  end
+
+  attribute_accessor :name, :lifespan, :cherrypickable_target, :stock_plate, :size
+  attribute_writer :input_plate
+end

data/lib/sequencescape/plate_template.rb

@@ -0,0 +1,13 @@
+require 'sequencescape/asset'
+
+class Sequencescape::PlateTemplate < ::Sequencescape::Asset
+
+  require 'sequencescape/plate/well_structure'
+
+  include Sequencescape::Plate::WellStructure
+
+  has_many :wells
+
+  attribute_accessor :size, :name
+
+end

data/lib/sequencescape/pooled_plate_creation.rb

@@ -0,0 +1,8 @@
+require 'sequencescape-api/resource'
+
+class Sequencescape::PooledPlateCreation < ::Sequencescape::Api::Resource
+  belongs_to :user
+  has_many   :parents, :class_name => 'Plate', :disposition => :inline
+  belongs_to :child_purpose, :class_name => 'PlatePurpose'
+  belongs_to :child, :class_name => 'Plate'
+end

data/lib/sequencescape/project.rb

@@ -0,0 +1,11 @@
+require 'sequencescape-api/resource'
+
+class Sequencescape::Project < ::Sequencescape::Api::Resource
+  has_many :submissions
+
+  attribute_accessor :name
+  attribute_accessor :approved, :state
+  attribute_accessor :project_manager, :cost_code, :funding_comments, :external_funding_source, :budget_division, :budget_cost_centre, :funding_model
+  attribute_accessor :collaborators
+  attribute_accessor :roles
+end

data/lib/sequencescape/qc_decision.rb

@@ -0,0 +1,9 @@
+require 'sequencescape-api/resource'
+
+class Sequencescape::QcDecision < ::Sequencescape::Api::Resource
+
+  belongs_to :user
+  belongs_to :lot
+
+  attribute_accessor :decisions
+end

data/lib/sequencescape/qc_file.rb

@@ -0,0 +1,14 @@
+
+require 'sequencescape-api/resource'
+
+class Sequencescape::QcFile < ::Sequencescape::Api::Resource
+
+  belongs_to :asset
+
+  attribute_accessor :filename, :size
+
+  def retrieve
+    api.retrieve(actions.read, Sequencescape::Api::ModifyingHandler.new(self), 'sequencescape/qc_file')
+  end
+
+end

data/lib/sequencescape/qcable.rb

@@ -0,0 +1,17 @@
+
+require 'sequencescape-api/resource'
+
+class Sequencescape::Qcable < ::Sequencescape::Api::Resource
+
+  belongs_to :lot
+  belongs_to :qcable_creator
+  belongs_to :asset
+
+  attribute_accessor :state, :stamp_bed, :stamp_index
+
+  attribute_group :barcode do
+    attribute_accessor :prefix, :number     # The pieces that make up a barcode
+    attribute_accessor :ean13               # The EAN13 barcode number
+  end
+
+end

data/lib/sequencescape/qcable_creator.rb

@@ -0,0 +1,13 @@
+
+require 'sequencescape-api/resource'
+
+class Sequencescape::QcableCreator < ::Sequencescape::Api::Resource
+
+  belongs_to :user
+  belongs_to :lot
+
+  has_many :qcables
+
+  attribute_accessor :count
+
+end

data/lib/sequencescape/request.rb

@@ -0,0 +1,16 @@
+require 'sequencescape-api/resource'
+
+class Sequencescape::Request < ::Sequencescape::Api::Resource
+  belongs_to :project
+  belongs_to :study
+  belongs_to :sample
+  belongs_to :submission
+
+  belongs_to :source_asset, :class_name => 'Asset'
+  belongs_to :target_asset, :class_name => 'Asset'
+
+  attribute_accessor :type, :state
+  validates_inclusion_of :state, :in => %w{pending started failed passed cancelled blocked hold}
+
+  attribute_accessor :read_length, :library_type, :fragment_size
+end

data/lib/sequencescape/robot.rb

@@ -0,0 +1,5 @@
+require 'sequencescape-api/resource'
+
+class Sequencescape::Robot < ::Sequencescape::Api::Resource
+  attribute_accessor :name, :robot_properties
+end

data/lib/sequencescape/sample.rb

@@ -0,0 +1,51 @@
+require 'sequencescape-api/resource'
+
+class Sequencescape::Sample < ::Sequencescape::Api::Resource
+  has_many :sample_tubes
+
+  attribute_group :sanger do
+    attribute_accessor :name, :sample_id, :resubmitted, :description
+  end
+  attribute_group :supplier do
+    attribute_accessor :sample_name, :storage_conditions
+
+    attribute_group :collection do
+      attribute_accessor :date
+    end
+    attribute_group :extraction do
+      attribute_accessor :date, :method
+    end
+    attribute_group :purification do
+      attribute_accessor :purified, :method
+    end
+    attribute_group :measurements do
+      attribute_accessor :volume, :concentration, :concentration_determined_by
+      attribute_accessor :gc_content, :gender
+    end
+  end
+  attribute_group :source do
+    attribute_accessor :dna_source, :cohort, :country, :region, :ethnicity, :control
+  end
+  attribute_group :family do
+    attribute_accessor :mother, :father, :replicate, :sibling
+  end
+  attribute_group :taxonomy do
+    attribute_accessor :id, :strain, :common_name, :organism
+  end
+  attribute_group :reference do
+    attribute_accessor :genome
+  end
+  attribute_group :data_release do
+    attribute_accessor :sample_type, :accession_number, :visibility, :public_name, :description
+
+    attribute_group :metagenomics do
+      attribute_accessor :genotype, :phenotype
+      attribute_accessor :age, :developmental_stage, :cell_type, :disease_state
+      attribute_accessor :compound, :dose, :immunoprecipitate, :growth_condition
+      attribute_accessor :rnai, :organism_part, :time_point, :treatment, :subject, :disease
+    end
+    attribute_group :managed do
+      attribute_accessor :treatment, :subject, :disease
+    end
+  end
+end

data/lib/sequencescape/sample_tube.rb

@@ -0,0 +1,7 @@
+require 'sequencescape/tube'
+
+class Sequencescape::SampleTube < ::Sequencescape::Tube
+  has_many   :requests
+  has_many   :library_tubes
+  belongs_to :custom_metadatum_collection
+end