sequencescape-client-api 0.3.5

data/lib/sequencescape/search.rb

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+require 'sequencescape-api/resource'
+
+class Sequencescape::Search < ::Sequencescape::Api::Resource
+  class BaseHandler
+    include Sequencescape::Api::BasicErrorHandling
+
+    def success(attributes)
+      raise Sequencescape::Api::Error, 'A success response from a search is unexpected'
+    end
+  end
+
+  # The response from the server contains the JSON for the resource found.  Using this we can
+  # handle the redirection by using the appropriate model based on the root element of the JSON.
+  # We don't even need to follow the redirect!
+  class SingleResultHandler < BaseHandler
+    def initialize(api)
+      @api = api
+    end
+
+    def redirection(json, &block)
+      json.delete('uuids_to_ids')
+      Sequencescape::Api::FinderMethods::FindByUuidHandler.new(@api.send(json.keys.first)).success(json)
+    end
+  end
+
+  # Wraps paginated results such that they can be navigated
+  # a step at a time.
+  class MultipleResultPaged
+    include Enumerable
+    attr_reader :objects, :size
+    def initialize(objects, size)
+      @objects = objects
+      @size = size
+    end
+
+    delegate :each, :empty?, :present?, to: :objects
+  end
+
+  # 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
+    end
+
+    def redirection(json, &block)
+      items = json['searches'].map(&method(:new))
+      size = json['size']
+      MultipleResultPaged.new(items, size)
+    end
+
+    def new(json)
+      args = [ json, false ]
+      args.unshift(@api) unless @model.is_a_proxied_model?
+      @model.new(*args)
+    end
+    private :new
+  end
+
+  def self.search_action(name)
+    line = __LINE__ + 1
+    class_eval(%Q{
+      def #{name}(criteria = {})
+        api.create(actions.#{name}, { 'search' => criteria }, SingleResultHandler.new(api))
+      end
+    }, __FILE__, line)
+  end
+
+  attribute_reader :name
+
+  search_action(:first)
+  search_action(:last)
+
+  # When performing a search for all records we need to provide the model (as in 'api.plate')
+  # that we expect to be returned.  So there is a limitation at the moment that the results can
+  # only belong to the same model hierarchy.
+  def all(model, criteria = {})
+    api.create(actions.all, { 'search' => criteria }, MultipleResultHandler.new(api, model))
+  end
+end

data/lib/sequencescape/specific_tube_creation.rb

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

data/lib/sequencescape/stamp.rb

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+require 'sequencescape-api/resource'
+
+class Sequencescape::Stamp < ::Sequencescape::Api::Resource
+
+  belongs_to :user
+  belongs_to :lot
+  belongs_to :robot
+  attribute_accessor :tip_lot, :stamp_details
+end

data/lib/sequencescape/state_change.rb

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+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
+  attribute_accessor :target_state
+  attribute_accessor :previous_state
+  attribute_accessor :reason
+  attribute_accessor :customer_accepts_responsibility
+end

data/lib/sequencescape/study.rb

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+require 'sequencescape-api/resource'
+
+class Sequencescape::Study < ::Sequencescape::Api::Resource
+  has_many :projects
+  has_many :asset_groups
+  has_many :samples
+
+  attribute_accessor :name, :abbreviation, :abstract, :description, :state, :type
+  attribute_accessor :sac_sponsor, :accession_number, :reference_genome, :ethically_approved
+  attribute_accessor :contaminated_human_dna, :contains_human_dna
+  attribute_accessor :data_release_sort_of_study, :data_release_strategy
+
+  validates :name, :presence => true
+end

data/lib/sequencescape/submission.rb

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+require 'sequencescape-api/resource'
+
+class Sequencescape::Submission < ::Sequencescape::Api::Resource
+  belongs_to :user
+  # TODO: get this working
+  # has_many   :requests
+
+  # TODO: use a has many, but ensure it works
+  attribute_accessor :orders
+
+  has_update_action :submit!, :action => 'submit', :verb => :create, :skip_json => true
+
+  attribute_reader :state
+  attribute_reader :asset_group_name
+
+end

data/lib/sequencescape/submission_pool.rb

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+require 'sequencescape-api/resource'
+
+class Sequencescape::SubmissionPool < ::Sequencescape::Api::Resource
+  attribute_reader :plates_in_submission
+  attribute_reader :used_tag2_layout_templates
+  attribute_reader :used_tag_layout_templates
+end

data/lib/sequencescape/tag.rb

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+class Sequencescape::Tag
+  include Sequencescape::Api::Composition::Target
+
+  attribute_accessor :name, :oligo, :group, :identifier
+
+  class Group
+    include Sequencescape::Api::Composition::Target
+
+    attr_accessor :actions
+
+    attribute_accessor :uuid
+    attribute_accessor :name, :tags, :created_at, :updated_at
+  end
+end

data/lib/sequencescape/tag2_layout.rb

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+require 'sequencescape-api/resource'
+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'
+  attribute_reader :target_well_locations
+end

data/lib/sequencescape/tag2_layout_template.rb

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

data/lib/sequencescape/tag_group.rb

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+class Sequencescape::TagGroup < ::Sequencescape::Api::Resource
+
+  attribute_accessor :name, :tags, :created_at, :updated_at
+end

data/lib/sequencescape/tag_layout.rb

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+require 'sequencescape-api/resource'
+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'
+
+  attribute_accessor :substitutions, :direction, :walking_by, :initial_tag
+end

data/lib/sequencescape/tag_layout_template.rb

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+require 'sequencescape-api/resource'
+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'
+
+  has_create_action :resource => 'tag_layout'
+
+  def dual_index?
+    tag2_group.present?
+  end
+end

data/lib/sequencescape/template.rb

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+require 'sequencescape-api/resource'
+require 'sequencescape/tag'
+
+class Sequencescape::Template < ::Sequencescape::Api::Resource
+  attribute_reader :name
+end

data/lib/sequencescape/transfer.rb

@@ -0,0 +1,9 @@
+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
+  attribute_reader :transfers
+  attribute_accessor :targets
+end

data/lib/sequencescape/transfer_request.rb

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+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'
+
+  attribute_accessor :type, :state, :submission_id
+
+end

data/lib/sequencescape/transfer_request_collection.rb

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+require 'sequencescape-api/resource'
+
+class Sequencescape::TransferRequestCollection < ::Sequencescape::Api::Resource
+  belongs_to :user
+  # attribute_accessor :transfer_requests
+  has_many :transfer_requests, disposition: :inline
+  has_many :target_tubes, disposition: :inline, class_name: 'Tube'
+end

data/lib/sequencescape/transfer_template.rb

@@ -0,0 +1,9 @@
+require 'sequencescape-api/resource'
+
+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'
+end

data/lib/sequencescape/tube.rb

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+require 'sequencescape/asset'
+require 'sequencescape/behaviour/receptacle'
+require 'sequencescape/behaviour/barcoded'
+require 'sequencescape/behaviour/labeled'
+require 'sequencescape/behaviour/qced'
+
+class Sequencescape::Tube < ::Sequencescape::Asset
+  include Sequencescape::Behaviour::Receptacle
+  include Sequencescape::Behaviour::Barcoded
+  include Sequencescape::Behaviour::Labeled
+  include Sequencescape::Behaviour::Qced
+
+  has_many :requests
+
+  attribute_accessor :closed
+  attribute_accessor :concentration, :volume
+  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 :custom_metadatum_collection
+end

data/lib/sequencescape/tube_creation.rb

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+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'
+end

data/lib/sequencescape/tube_from_tube_creation.rb

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+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'
+end

data/lib/sequencescape/tube_purpose.rb

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+require 'sequencescape-api/resource'
+
+class Sequencescape::TubePurpose < ::Sequencescape::Api::Resource
+  module TubeCreation
+    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 => 'TubePurpose'
+  has_many :parents, :class_name => 'TubePurpose'
+
+  has_many :tubes do
+    include Sequencescape::TubePurpose::TubeCreation
+  end
+
+  attribute_reader :name
+  attribute_writer :target_type, :type
+end

data/lib/sequencescape/user.rb

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+class Sequencescape::User < ::Sequencescape::Api::Resource
+  attribute_reader :login
+  attribute_accessor :email
+  attribute_accessor :first_name
+  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
+  attribute_accessor :swipecard_code
+
+  attribute_reader :has_a_swipecard_code
+end

data/lib/sequencescape/volume_update.rb

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

data/lib/sequencescape/well.rb

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+require 'sequencescape/asset'
+require 'sequencescape/behaviour/receptacle'
+require 'sequencescape/behaviour/state_driven'
+
+class Sequencescape::Well < ::Sequencescape::Asset
+
+  include Sequencescape::Behaviour::Receptacle
+  include Sequencescape::Behaviour::StateDriven
+
+  belongs_to :plate
+
+  attribute_accessor :location, :pool
+  attribute_accessor :initial_volume, :measured_volume, :current_volume
+
+  def pool_id
+    pool.nil? ? nil : pool['id']
+  end
+
+end

data/lib/sequencescape/work_completion.rb

@@ -0,0 +1,10 @@
+require 'sequencescape-api/resource'
+
+class Sequencescape::WorkCompletion < ::Sequencescape::Api::Resource
+  belongs_to :user
+  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.
+  attribute_accessor :submissions
+end

data/lib/sequencescape-api/actions.rb

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+module Sequencescape::Api::Actions
+  def self.extended(base)
+    base.class_eval do
+      extend ClassActionHelpers
+      extend InstanceActionHelpers
+    end
+  end
+
+  module ClassActionHelpers
+    # Defines a method that is available on the resource model itself, rather than on an instance of
+    # the resource model.
+    def has_class_create_action(*args)
+      action_module, line = Module.new, __LINE__+1
+      action_module.module_eval(%Q{
+        def initialize_class_actions(proxy)
+          super
+
+          class << proxy
+            has_create_action(#{args.map(&:inspect).join(',')})
+          end
+        end
+      }, __FILE__, line)
+
+      extend action_module
+    end
+
+    def initialize_class_actions(proxy)
+      # Does nothing by default.
+    end
+    private :initialize_class_actions
+  end
+
+  module InstanceActionHelpers
+    def has_create_action(*args)
+      options      = args.extract_options!
+      name         = args.first || :create!
+
+      action       = options[:action] || :create
+      result_class = 'self'
+      result_class = "api.#{options[:resource]}" if options[:resource]
+
+      line = __LINE__ + 1
+      class_eval(%Q{
+        def #{name}(attributes = nil)
+          url = actions.try(#{action.to_sym.inspect}) or
+            raise Sequencescape::Api::Error, "Cannot perform #{action} without an URL"
+
+          #{result_class}.new(attributes || {}, false).tap do |object|
+            object.save!(:url => url)
+          end
+        end
+      }, __FILE__, line)
+    end
+
+    def has_update_action(name, options = {})
+      api_method = options[:verb] == :create ? :create : :update
+      skip_json  = options[:skip_json]||false
+      action     = options[:action] || :update
+
+      line = __LINE__ + 1
+      class_eval(%Q{
+        def #{name}(body = nil)
+          update_from_json(body || {}, false)
+          modify!(:action => #{action.to_sym.inspect}, :http_verb => #{api_method.to_sym.inspect}, :skip_json => #{skip_json})
+        end
+      }, __FILE__, line)
+    end
+  end
+end