sequencescape-client-api 0.3.10 → 0.4.0.pre.rc1

data/lib/sequencescape/plate_template.rb

@@ -1,7 +1,6 @@
 require 'sequencescape/asset'
 
 class Sequencescape::PlateTemplate < ::Sequencescape::Asset
-
   require 'sequencescape/plate/well_structure'
 
   include Sequencescape::Plate::WellStructure
@@ -9,5 +8,4 @@ class Sequencescape::PlateTemplate < ::Sequencescape::Asset
   has_many :wells
 
   attribute_accessor :size, :name
-
 end

data/lib/sequencescape/pooled_plate_creation.rb

@@ -2,7 +2,7 @@ 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'
+  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

@@ -5,7 +5,8 @@ class Sequencescape::Project < ::Sequencescape::Api::Resource
 
   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 :project_manager, :cost_code, :funding_comments, :external_funding_source, :budget_division
+  attribute_accessor :budget_cost_centre, :funding_model
   attribute_accessor :collaborators
   attribute_accessor :roles
 end

data/lib/sequencescape/qc_decision.rb

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

data/lib/sequencescape/qc_file.rb

@@ -1,8 +1,6 @@
-
 require 'sequencescape-api/resource'
 
 class Sequencescape::QcFile < ::Sequencescape::Api::Resource
-
   belongs_to :asset
 
   attribute_accessor :filename, :size
@@ -10,5 +8,4 @@ class Sequencescape::QcFile < ::Sequencescape::Api::Resource
   def retrieve
     api.retrieve(actions.read, Sequencescape::Api::ModifyingHandler.new(self), 'sequencescape/qc_file')
   end
-
 end

data/lib/sequencescape/qcable.rb

@@ -1,8 +1,6 @@
-
 require 'sequencescape-api/resource'
 
 class Sequencescape::Qcable < ::Sequencescape::Api::Resource
-
   belongs_to :lot
   belongs_to :qcable_creator
   belongs_to :asset
@@ -14,5 +12,4 @@ class Sequencescape::Qcable < ::Sequencescape::Api::Resource
     attribute_accessor :ean13               # The EAN13 barcode number
     attribute_accessor :machine             # The barcode printed on the label
   end
-
 end

data/lib/sequencescape/qcable_creator.rb

@@ -1,13 +1,10 @@
-
 require 'sequencescape-api/resource'
 
 class Sequencescape::QcableCreator < ::Sequencescape::Api::Resource
-
   belongs_to :user
   belongs_to :lot
 
   has_many :qcables
 
   attribute_accessor :count, :barcodes
-
 end

data/lib/sequencescape/request.rb

@@ -6,11 +6,11 @@ class Sequencescape::Request < ::Sequencescape::Api::Resource
   belongs_to :sample
   belongs_to :submission
 
-  belongs_to :source_asset, :class_name => 'Asset'
-  belongs_to :target_asset, :class_name => 'Asset'
+  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}
+  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/search.rb

@@ -4,7 +4,7 @@ class Sequencescape::Search < ::Sequencescape::Api::Resource
   class BaseHandler
     include Sequencescape::Api::BasicErrorHandling
 
-    def success(attributes)
+    def success(_attributes)
       raise Sequencescape::Api::Error, 'A success response from a search is unexpected'
     end
   end
@@ -17,7 +17,7 @@ class Sequencescape::Search < ::Sequencescape::Api::Resource
       @api = api
     end
 
-    def redirection(json, &block)
+    def redirection(json)
       json.delete('uuids_to_ids')
       Sequencescape::Api::FinderMethods::FindByUuidHandler.new(@api.send(json.keys.first)).success(json)
     end
@@ -28,6 +28,7 @@ class Sequencescape::Search < ::Sequencescape::Api::Resource
   class MultipleResultPaged
     include Enumerable
     attr_reader :objects, :size
+
     def initialize(objects, size)
       @objects = objects
       @size = size
@@ -39,18 +40,19 @@ class Sequencescape::Search < ::Sequencescape::Api::Resource
   # The response from the server contains the JSON for each of the resources found.  We simply
   # need to be able to create the resources from each of these.
   class MultipleResultHandler
-    def initialize(api,model)
-      @api, @model = api, model
+    def initialize(api, model)
+      @api = api
+      @model = model
     end
 
-    def redirection(json, &block)
+    def redirection(json)
       items = json['searches'].map(&method(:new))
       size = json['size']
       MultipleResultPaged.new(items, size)
     end
 
     def new(json)
-      args = [ json, false ]
+      args = [json, false]
       args.unshift(@api) unless @model.is_a_proxied_model?
       @model.new(*args)
     end
@@ -59,11 +61,11 @@ class Sequencescape::Search < ::Sequencescape::Api::Resource
 
   def self.search_action(name)
     line = __LINE__ + 1
-    class_eval(%Q{
+    class_eval("
       def #{name}(criteria = {})
         api.create(actions.#{name}, { 'search' => criteria }, SingleResultHandler.new(api))
       end
-    }, __FILE__, line)
+    ", __FILE__, line)
   end
 
   attribute_reader :name

data/lib/sequencescape/specific_tube_creation.rb

@@ -2,7 +2,7 @@ require 'sequencescape-api/resource'
 
 class Sequencescape::SpecificTubeCreation < ::Sequencescape::Api::Resource
   belongs_to :user
-  belongs_to :parent, :class_name => 'Plate'
+  belongs_to :parent, class_name: 'Plate'
   attribute_writer :child_purposes, :tube_attributes
-  has_many :children, :class_name => 'Tube'
+  has_many :children, class_name: 'Tube'
 end

data/lib/sequencescape/stamp.rb

@@ -1,7 +1,6 @@
 require 'sequencescape-api/resource'
 
 class Sequencescape::Stamp < ::Sequencescape::Api::Resource
-
   belongs_to :user
   belongs_to :lot
   belongs_to :robot

data/lib/sequencescape/state_change.rb

@@ -2,8 +2,8 @@ require 'sequencescape-api/resource'
 
 class Sequencescape::StateChange < ::Sequencescape::Api::Resource
   belongs_to :user
-  belongs_to :target, :class_name => 'Asset', :disposition => :inline
-  attribute_accessor :contents          # Array of "contents" to fail, deciphered by the target, can be nil
+  belongs_to :target, class_name: 'Asset', disposition: :inline
+  attribute_accessor :contents # Array of "contents" to fail, deciphered by the target, can be nil
   attribute_accessor :target_state
   attribute_accessor :previous_state
   attribute_accessor :reason

data/lib/sequencescape/study.rb

@@ -10,5 +10,5 @@ class Sequencescape::Study < ::Sequencescape::Api::Resource
   attribute_accessor :contaminated_human_dna, :contains_human_dna
   attribute_accessor :data_release_sort_of_study, :data_release_strategy
 
-  validates :name, :presence => true
+  validates :name, presence: true
 end

data/lib/sequencescape/submission.rb

@@ -8,9 +8,8 @@ class Sequencescape::Submission < ::Sequencescape::Api::Resource
   # TODO: use a has many, but ensure it works
   attribute_accessor :orders
 
-  has_update_action :submit!, :action => 'submit', :verb => :create, :skip_json => true
+  has_update_action :submit!, action: 'submit', verb: :create, skip_json: true
 
   attribute_reader :state
   attribute_reader :asset_group_name
-
 end

data/lib/sequencescape/tag2_layout.rb

@@ -3,8 +3,8 @@ require 'sequencescape/tag'
 
 class Sequencescape::Tag2Layout < ::Sequencescape::Api::Resource
   belongs_to :user
-  belongs_to :plate, :class_name => 'Plate'
-  belongs_to :source, :class_name => 'Asset'
-  composed_of :tag, :class_name => 'Tag'
+  belongs_to :plate, class_name: 'Plate'
+  belongs_to :source, class_name: 'Asset'
+  composed_of :tag, class_name: 'Tag'
   attribute_reader :target_well_locations
 end

data/lib/sequencescape/tag2_layout_template.rb

@@ -3,7 +3,7 @@ require 'sequencescape/tag'
 
 class Sequencescape::Tag2LayoutTemplate < ::Sequencescape::Api::Resource
   attribute_reader :name
-  composed_of :tag, :class_name => 'Tag'
+  composed_of :tag, class_name: 'Tag'
 
-  has_create_action :resource => 'tag2_layout'
+  has_create_action resource: 'tag2_layout'
 end

data/lib/sequencescape/tag_group.rb

@@ -1,4 +1,3 @@
 class Sequencescape::TagGroup < ::Sequencescape::Api::Resource
-
   attribute_accessor :name, :tags, :created_at, :updated_at
 end

data/lib/sequencescape/tag_layout.rb

@@ -3,9 +3,9 @@ require 'sequencescape/tag'
 
 class Sequencescape::TagLayout < ::Sequencescape::Api::Resource
   belongs_to :user
-  belongs_to :plate, :class_name => 'Plate'
-  composed_of :tag_group, :class_name => 'Tag::Group'
-  composed_of :tag2_group, :class_name => 'Tag::Group'
+  belongs_to :plate, class_name: 'Plate'
+  composed_of :tag_group, class_name: 'Tag::Group'
+  composed_of :tag2_group, class_name: 'Tag::Group'
 
   attribute_accessor :substitutions, :direction, :walking_by, :initial_tag, :tags_per_well
 end

data/lib/sequencescape/tag_layout_template.rb

@@ -3,11 +3,11 @@ require 'sequencescape/tag'
 
 class Sequencescape::TagLayoutTemplate < ::Sequencescape::Api::Resource
   attribute_reader :name, :direction, :walking_by
-  belongs_to :plate, :class_name => 'Plate'
-  composed_of :tag_group, :class_name => 'Tag::Group'
-  composed_of :tag2_group, :class_name => 'Tag::Group'
+  belongs_to :plate, class_name: 'Plate'
+  composed_of :tag_group, class_name: 'Tag::Group'
+  composed_of :tag2_group, class_name: 'Tag::Group'
 
-  has_create_action :resource => 'tag_layout'
+  has_create_action resource: 'tag_layout'
 
   def dual_index?
     tag2_group.present?

data/lib/sequencescape/transfer.rb

@@ -2,8 +2,8 @@ require 'sequencescape-api/resource'
 
 class Sequencescape::Transfer < ::Sequencescape::Api::Resource
   belongs_to :user
-  belongs_to :source, :class_name => 'BarcodedAsset', :disposition => :inline
-  belongs_to :destination, :class_name => 'BarcodedAsset', :disposition => :inline
+  belongs_to :source, class_name: 'BarcodedAsset', disposition: :inline
+  belongs_to :destination, class_name: 'BarcodedAsset', disposition: :inline
   attribute_reader :transfers
   attribute_accessor :targets
 end

data/lib/sequencescape/transfer_request.rb

@@ -1,11 +1,10 @@
 require 'sequencescape-api/resource'
 
 class Sequencescape::TransferRequest < ::Sequencescape::Api::Resource
-
-  belongs_to :source_asset, :class_name => 'Asset'
-  belongs_to :target_asset, :class_name => 'Asset'
-  belongs_to :submission, :class_name => 'Submission'
-  belongs_to :outer_request, :class_name => 'Request'
+  belongs_to :source_asset, class_name: 'Asset'
+  belongs_to :target_asset, class_name: 'Asset'
+  belongs_to :submission, class_name: 'Submission'
+  belongs_to :outer_request, class_name: 'Request'
 
   attribute_accessor :type, :state, :submission_id, :volume, :merge_equivalent_aliquots
 end

data/lib/sequencescape/transfer_template.rb

@@ -4,6 +4,6 @@ class Sequencescape::TransferTemplate < ::Sequencescape::Api::Resource
   attribute_reader :name
   attribute_reader :transfers
 
-  has_create_action :resource => 'transfer'
-  has_create_action :preview!, :action => :preview, :resource => 'transfer'
+  has_create_action resource: 'transfer'
+  has_create_action :preview!, action: :preview, resource: 'transfer'
 end

data/lib/sequencescape/tube.rb

@@ -14,13 +14,13 @@ class Sequencescape::Tube < ::Sequencescape::Asset
 
   attribute_accessor :closed
   attribute_accessor :concentration, :volume
-  attribute_accessor :scanned_in_date, :conversion => :to_time
+  attribute_accessor :scanned_in_date, conversion: :to_time
 
   attribute_reader :state
 
   attribute_accessor :sibling_tubes
 
-  belongs_to :purpose, :class_name => 'TubePurpose'
-  belongs_to :stock_plate, :class_name => 'Plate'
+  belongs_to :purpose, class_name: 'TubePurpose'
+  belongs_to :stock_plate, class_name: 'Plate'
   belongs_to :custom_metadatum_collection
 end

data/lib/sequencescape/tube_creation.rb

@@ -2,7 +2,7 @@ require 'sequencescape-api/resource'
 
 class Sequencescape::TubeCreation < ::Sequencescape::Api::Resource
   belongs_to :user
-  belongs_to :parent, :class_name => 'Plate'
-  belongs_to :child_purpose, :class_name => 'TubePurpose'
-  has_many :children, :class_name => 'Tube'
+  belongs_to :parent, class_name: 'Plate'
+  belongs_to :child_purpose, class_name: 'TubePurpose'
+  has_many :children, class_name: 'Tube'
 end

data/lib/sequencescape/tube_from_tube_creation.rb

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

data/lib/sequencescape/tube_purpose.rb

@@ -4,7 +4,7 @@ class Sequencescape::TubePurpose < ::Sequencescape::Api::Resource
   module TubeCreation
     def create!(attributes = nil)
       attributes ||= {}
-      attributes[:wells].delete_if { |_,v| v.blank? } if attributes.key?(:wells)
+      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))
@@ -12,8 +12,8 @@ class Sequencescape::TubePurpose < ::Sequencescape::Api::Resource
     end
   end
 
-  has_many :children, :class_name => 'TubePurpose'
-  has_many :parents, :class_name => 'TubePurpose'
+  has_many :children, class_name: 'TubePurpose'
+  has_many :parents, class_name: 'TubePurpose'
 
   has_many :tubes do
     include Sequencescape::TubePurpose::TubeCreation

data/lib/sequencescape/user.rb

@@ -5,8 +5,8 @@ class Sequencescape::User < ::Sequencescape::Api::Resource
   attribute_accessor :last_name
   attribute_accessor :barcode
 
-  #TODO make swipecard_code readonly. Can't at the moment because of a bug
-  #attribute_writer :swipecard_code
+  # TODO: make swipecard_code readonly. Can't at the moment because of a bug
+  # attribute_writer :swipecard_code
   attribute_accessor :swipecard_code
 
   attribute_reader :has_a_swipecard_code

data/lib/sequencescape/volume_update.rb

@@ -1,6 +1,6 @@
 require 'sequencescape-api/resource'
 
 class Sequencescape::VolumeUpdate < ::Sequencescape::Api::Resource
-  belongs_to :target, :class_name => 'Asset', :disposition => :inline
+  belongs_to :target, class_name: 'Asset', disposition: :inline
   attribute_accessor :volume_change, :created_by
 end

data/lib/sequencescape/well.rb

@@ -3,7 +3,6 @@ require 'sequencescape/behaviour/receptacle'
 require 'sequencescape/behaviour/state_driven'
 
 class Sequencescape::Well < ::Sequencescape::Asset
-
   include Sequencescape::Behaviour::Receptacle
   include Sequencescape::Behaviour::StateDriven
 
@@ -15,5 +14,4 @@ class Sequencescape::Well < ::Sequencescape::Asset
   def pool_id
     pool.nil? ? nil : pool['id']
   end
-
 end

data/lib/sequencescape/work_completion.rb

@@ -2,7 +2,7 @@ require 'sequencescape-api/resource'
 
 class Sequencescape::WorkCompletion < ::Sequencescape::Api::Resource
   belongs_to :user
-  belongs_to :target, :class_name => 'Asset'
+  belongs_to :target, class_name: 'Asset'
 
   # This should really be a has_many, but we'll need
   # to get assignment from arrays of strings working first.

data/sequencescape-api.gemspec

@@ -1,32 +1,33 @@
-# -*- encoding: utf-8 -*-
-$:.push File.expand_path("../lib", __FILE__)
-require "sequencescape-api/version"
+$LOAD_PATH.push File.expand_path('lib', __dir__)
+require 'sequencescape-api/version'
 
 Gem::Specification.new do |s|
-  s.name        = "sequencescape-client-api"
+  s.name        = 'sequencescape-client-api'
   s.version     = Sequencescape::Api::VERSION
   s.platform    = Gem::Platform::RUBY
-  s.authors     = ["Matthew Denner","James Glover","Eduardo Martin Rojo"]
-  s.email       = ["md12@sanger.ac.uk","james.glover@sanger.ac.uk","emr@sanger.ac.uk"]
-  s.homepage    = ""
-  s.summary     = %q{Gem for the client side of the Sequencescape API}
-  s.description = %q{Provides all of the necessary code for interacting with the Sequencescape API}
+  s.authors     = ['Matthew Denner', 'James Glover', 'Eduardo Martin Rojo']
+  s.email       = ['md12@sanger.ac.uk', 'james.glover@sanger.ac.uk', 'emr@sanger.ac.uk']
+  s.homepage    = ''
+  s.summary     = 'Gem for the client side of the Sequencescape API'
+  s.description = 'Provides all of the necessary code for interacting with the Sequencescape API'
 
-  s.rubyforge_project = "sequencescape-client-api"
+  s.rubyforge_project = 'sequencescape-client-api'
 
   s.files         = `git ls-files`.split("\n")
   s.test_files    = `git ls-files -- {test,spec,features}/*`.split("\n")
-  s.executables   = `git ls-files -- bin/*`.split("\n").map{ |f| File.basename(f) }
-  s.require_paths = ["lib"]
+  s.executables   = `git ls-files -- bin/*`.split("\n").map { |f| File.basename(f) }
+  s.require_paths = ['lib']
 
-  s.add_dependency('activesupport', '>= 4.0.0', '< 5.2')
-  s.add_dependency('activemodel', '>= 4.0.0', '< 5.2')
+  s.add_dependency('activemodel', '>= 5.0.0')
+  s.add_dependency('activesupport', '>= 5.0.0')
   s.add_dependency('i18n')
-  s.add_dependency('yajl-ruby', '>= 1.3.1')
+  s.add_dependency('yajl-ruby', '>= 1.4.1')
 
-  s.add_development_dependency('rspec', '~> 2.11.0')
   s.add_development_dependency('pry')
+  s.add_development_dependency('rake')
+  s.add_development_dependency('redcarpet')
+  s.add_development_dependency('rspec', '~> 2.11.0')
+  s.add_development_dependency('rubocop', '~> 0.84.0')
   s.add_development_dependency('webmock')
   s.add_development_dependency('yard')
-  s.add_development_dependency('redcarpet')
 end