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

data/lib/sequencescape-api/errors.rb

@@ -8,7 +8,7 @@ module Sequencescape
       end
     end
 
-    [ :UnauthenticatedError, :ResourceNotFound ].each do |name|
+    %i[UnauthenticatedError ResourceNotFound].each do |name|
       const_set(name, Class.new(Error) { |c| c.send(:include, GeneralError) })
     end
 
@@ -30,7 +30,7 @@ module Sequencescape
         raise Sequencescape::Api::ResourceNotFound, json
       end
 
-      def redirection(json, &block)
+      def redirection(_json)
         yield(self)
       end
     end

data/lib/sequencescape-api/finder_methods.rb

@@ -3,7 +3,7 @@ require 'ostruct'
 module Sequencescape::Api::FinderMethods
   module Delegation
     def self.included(base)
-      base.with_options(:to => :all) do |all|
+      base.with_options(to: :all) do |all|
         all.delegate :each, :first, :last, :to_a, :size
         all.delegate :empty?, :blank?
         all.delegate :each_page, :first_page, :last_page
@@ -74,7 +74,7 @@ end
 
 module Sequencescape::Api::FinderMethods::Caching
   def all(reload = false)
-    @cached_all = super() if @cached_all.nil? or reload
+    @cached_all = super() if @cached_all.nil? || reload
     @cached_all
   end
 end
@@ -88,7 +88,8 @@ class Sequencescape::Api::PageOfResults
   attr_reader :size
 
   def initialize(api, json, &block)
-    @api, @ctor = api, block
+    @api = api
+    @ctor = block
     update_from_json(json)
   end
 
@@ -109,7 +110,7 @@ class Sequencescape::Api::PageOfResults
     end
   end
 
-  def each_page(&block)
+  def each_page
     walk_pages do
       yield(@objects.dup)
     end
@@ -127,9 +128,10 @@ class Sequencescape::Api::PageOfResults
 
   def walk_pages
     first_page
-    while true
+    loop do
       yield
       break if actions.next.blank?
+
       next_page
     end
   end
@@ -153,32 +155,35 @@ class Sequencescape::Api::PageOfResults
     end
   end
 
-  [ :first, :last, :previous, :next ].each do |page|
+  %i[first last previous next].each do |page|
     line = __LINE__ + 1
-    class_eval(%Q{
+    class_eval("
       def #{page}_page
         self.tap do
           api.read(actions.#{page}, UpdateHandler.new(self)) unless actions.read == actions.#{page}
           yield(@objects.dup) if block_given?
         end
       end
-    }, __FILE__, line)
+    ", __FILE__, line)
   end
   private :last_page, :next_page
 
-  def update_from_json(json)
-    json.delete('uuids_to_ids')         # Discard unwanted rubbish
+  def update_from_json(json) # rubocop:todo Metrics/MethodLength
+    json.delete('uuids_to_ids') # Discard unwanted rubbish
     actions = json.delete('actions')
     raise Sequencescape::Api::Error, 'No actions for page!' if actions.blank?
 
     if api.capabilities.size_in_pages?
       size = json.delete('size')
       raise Sequencescape::Api::Error, 'No size for page!' if size.blank?
+
       @size = size.to_i
     end
 
     raise Sequencescape::Api::Error, 'No object json in page!' if json.keys.empty?
-    @actions, @objects = OpenStruct.new(actions), json[json.keys.first].map(&@ctor)
+
+    @actions = OpenStruct.new(actions)
+    @objects = json[json.keys.first].map(&@ctor)
   end
   private :update_from_json
 end

data/lib/sequencescape-api/rails.rb

@@ -3,7 +3,7 @@ module Sequencescape::Api::Rails
   # provide a user (based on the WTSISignOn cookie) specific Sequencescape::Api instance to
   # use, accessible through `api`.
   module ApplicationController
-    def self.included(base)
+    def self.included(base) # rubocop:todo Metrics/MethodLength
       base.class_eval do
         attr_reader :api
         private :api
@@ -15,8 +15,8 @@ module Sequencescape::Api::Rails
         end
 
         # Order is important here: later ones override earlier.
-        rescue_from(::Sequencescape::Api::Error,                :with => :sequencescape_api_error_handler)
-        rescue_from(::Sequencescape::Api::UnauthenticatedError, :with => :sequencescape_api_unauthenticated_handler)
+        rescue_from(::Sequencescape::Api::Error,                with: :sequencescape_api_error_handler)
+        rescue_from(::Sequencescape::Api::UnauthenticatedError, with: :sequencescape_api_unauthenticated_handler)
       end
     end
 
@@ -26,12 +26,12 @@ module Sequencescape::Api::Rails
     private :api_class
 
     def configure_api
-      @api = api_class.new({ :cookie => cookies['WTSISignOn'] }.merge(api_connection_options))
+      @api = api_class.new({ cookie: cookies['WTSISignOn'] }.merge(api_connection_options))
     end
     private :configure_api
 
     def api_connection_options
-      { }
+      {}
     end
     private :api_connection_options
 
@@ -43,7 +43,7 @@ module Sequencescape::Api::Rails
 
     def sequencescape_api_unauthenticated_handler(exception)
       Rails.logger.error "#{exception}, #{exception.backtrace}"
-      raise StandardError, "You are not authenticated; please visit the WTSI login page"
+      raise StandardError, 'You are not authenticated; please visit the WTSI login page'
     end
     private :sequencescape_api_unauthenticated_handler
   end
@@ -57,7 +57,7 @@ module Sequencescape::Api::Rails
     def self.included(base)
       base.class_eval do
         attr_protected :remote_resource, :uuid
-        validates_presence_of :uuid, :allow_blank => false
+        validates_presence_of :uuid, allow_blank: false
         before_save :save_remote_resource
       end
     end
@@ -80,6 +80,7 @@ module Sequencescape::Api::Rails
     def save_remote_resource
       return true if @remote_resource.nil?
       return true unless @remote_resource.can_save?
+
       self[:uuid] = @remote_resource
       @remote_resource.save
     end

data/lib/sequencescape-api/resource/active_model.rb

@@ -12,6 +12,6 @@ module Sequencescape::Api::Resource::ActiveModel
   end
 
   def persisted?
-    not self.uuid.nil?
+    !uuid.nil?
   end
 end

data/lib/sequencescape-api/resource/attribute_groups.rb

@@ -7,7 +7,7 @@ module Sequencescape::Api::Resource::Groups
     end
 
     def attribute_group_json(options)
-      attribute_groups.each_with_object({}) do |(k,v), agj|
+      attribute_groups.each_with_object({}) do |(k, v), agj|
         agj[k.to_s] = v.send(:as_json_for_update, options) if v.changed?
       end
     end
@@ -28,7 +28,7 @@ module Sequencescape::Api::Resource::Groups
   end
 
   module Json
-    def as_json_for_update(options)
+    def as_json_for_update(options) # rubocop:todo Metrics/MethodLength
       super.tap do |json|
         begin
           if options[:root]
@@ -64,14 +64,18 @@ class Sequencescape::Api::Resource::Groups::Proxy
   module InstanceMethods
     def self.included(base)
       base.class_eval do
-        attr_reader :attributes
-        private :attributes
+        private
+
+        def attributes
+          @_attributes_
+        end
       end
     end
 
     def initialize(owner, attributes = {})
-      @owner, @attributes = owner, {}
-      attributes.each { |k,v| send(:"#{k}=", v) if respond_to?(:"#{k}=", :include_private_methods) }
+      @owner = owner
+      @_attributes_ = {}
+      attributes.each { |k, v| send(:"#{k}=", v) if respond_to?(:"#{k}=", :include_private_methods) }
     end
 
     def as_json_for_update(options)
@@ -82,7 +86,7 @@ class Sequencescape::Api::Resource::Groups::Proxy
     private :as_json_for_update
 
     def clear_changed_attributes
-      changed_attributes.clear
+      clear_changes_information
     end
     private :clear_changed_attributes
   end

data/lib/sequencescape-api/resource/attributes.rb

@@ -5,7 +5,7 @@ module Sequencescape::Api::Resource::Attributes
   def self.extended(base)
     base.class_eval do
       include InstanceMethods
-      class_attribute :defined_attributes, :instance_writer => false
+      class_attribute :defined_attributes, instance_writer: false
       self.defined_attributes = Set.new
     end
   end
@@ -20,16 +20,16 @@ module Sequencescape::Api::Resource::Attributes
     end
   end
 
-  def generate_attribute_reader(*names)
+  def generate_attribute_reader(*names) # rubocop:todo Metrics/MethodLength
     options    = names.extract_options!
     conversion = options[:conversion].blank? ? nil : "try(#{options[:conversion].to_sym.inspect})"
 
     names.each do |name|
       defined_attributes << name.to_sym
-      converted = [ "#{name}_before_type_cast", conversion ].compact.join('.')
+      converted = ["#{name}_before_type_cast", conversion].compact.join('.')
 
       line = __LINE__ + 1
-      class_eval(%Q{
+      class_eval("
         def #{name}
           #{converted}
         end
@@ -37,25 +37,25 @@ module Sequencescape::Api::Resource::Attributes
         def #{name}_before_type_cast
           attributes[#{name.to_s.inspect}]
         end
-      }, __FILE__, line)
+      ", __FILE__, line)
     end
     extend_attribute_methods(names)
   end
   private :generate_attribute_reader
 
-  def generate_attribute_writer(*names)
+  def generate_attribute_writer(*names) # rubocop:todo Metrics/MethodLength
     options = names.extract_options!
 
     names.each do |name|
       defined_attributes << name.to_sym
 
       line = __LINE__ + 1
-      class_eval(%Q{
+      class_eval("
         def #{name}=(value)
           #{name}_will_change! if not attributes.key?(#{name.to_s.inspect}) or #{name} != value
           attributes[#{name.to_s.inspect}] = value
         end
-      }, __FILE__, line)
+      ", __FILE__, line)
     end
     extend_attribute_methods(names)
   end

data/lib/sequencescape-api/resource/instance_methods.rb

@@ -1,24 +1,32 @@
 module Sequencescape::Api::Resource::InstanceMethods
-  def self.included(base)
+  def self.included(base) # rubocop:todo Metrics/MethodLength
     base.class_eval do
-      attr_reader :api, :actions, :attributes, :uuid
-      private :api, :actions, :attributes
+      attr_reader :api, :actions, :uuid
+      private :api, :actions
       alias_method(:model, :class)
       alias_method(:id, :uuid)
 
-      delegate :hash, :to => :uuid
-      delegate :read_timeout, :to => :api
+      delegate :hash, to: :uuid
+      delegate :read_timeout, to: :api
 
-      attribute_accessor :created_at, :updated_at, :conversion => :to_time
+      attribute_accessor :created_at, :updated_at, conversion: :to_time
+
+      private
+
+      def attributes
+        @_attributes_
+      end
     end
   end
 
   def eql?(object_or_proxy)
     return false unless object_or_proxy.respond_to?(:uuid)
-    self.uuid.eql?(object_or_proxy.uuid)
+
+    uuid.eql?(object_or_proxy.uuid)
   end
 
-  def initialize(api, json = nil, wrapped = false)
-    @api, @attributes = api, {}
+  def initialize(api, _json = nil, _wrapped = false)
+    @api = api
+    @_attributes_ = {}
   end
 end

data/lib/sequencescape-api/resource/json.rb

@@ -7,11 +7,11 @@ module Sequencescape::Api::Resource::Json
 
   module ClassMethods
     def self.extended(base)
-      base.delegate :json_root, :to => 'self.class'
+      base.delegate :json_root, to: 'self.class'
     end
 
     def json_root
-      self.name.demodulize.underscore
+      name.demodulize.underscore
     end
   end
 
@@ -19,7 +19,8 @@ module Sequencescape::Api::Resource::Json
     include Sequencescape::Api::BasicErrorHandling
 
     def initialize(api, owner)
-      @api, @owner = api, owner
+      @api = api
+      @owner = owner
     end
 
     attr_reader :api
@@ -39,11 +40,11 @@ module Sequencescape::Api::Resource::Json
 
   # Coerces the current object instance to another class.
   def coerce_to(klazz)
-    api.read_uuid(self.uuid, CoercionHandler.new(api, klazz))
+    api.read_uuid(uuid, CoercionHandler.new(api, klazz))
   end
 
   def as_json(options = nil)
-    options = { :action => :create, :root => true }.merge(options || {})
+    options = { action: :create, root: true }.merge(options || {})
     send(:"as_json_for_#{options[:action]}", options)
   end
 
@@ -57,28 +58,28 @@ module Sequencescape::Api::Resource::Json
   private :as_json_for_create
 
   # Returns the appropriate JSON for when we are updating a resource.
-  def as_json_for_update(options)
+  def as_json_for_update(options) # rubocop:todo Metrics/MethodLength
     if must_output_full_json?(options)
-      json = { }
-      json['uuid'] = uuid if options[:uuid] and uuid.present?
+      json = {}
+      json['uuid'] = uuid if options[:uuid] && uuid.present?
 
       json.merge!(attributes_for_json(options))
-      json.merge!(associations_for_json(options.merge(:root => false)))
+      json.merge!(associations_for_json(options.merge(root: false)))
 
       return json unless options[:root]
+
       { json_root => json }
     elsif options[:root]
       # We are the root element so we must output something!
-      { json_root => { } }
-    else
-      # We are not a root element, we haven't been changed, so we might as well not exist!
+      { json_root => {} }
+    else # We are not a root element, we haven't been changed, so we might as well not exist!
       nil
     end
   end
   private :as_json_for_update
 
   def unwrapped_json(json)
-    json[(json.keys - [ 'uuids_to_ids' ]).first]
+    json[(json.keys - ['uuids_to_ids']).first]
   end
   private :unwrapped_json
 
@@ -88,13 +89,14 @@ module Sequencescape::Api::Resource::Json
 
   def attributes_for_json(options)
     attributes_to_send_to_server(options).tap do |changed_attributes|
-      [ 'created_at', 'updated_at' ].map(&changed_attributes.method(:delete))
+      %w[created_at updated_at].map(&changed_attributes.method(:delete))
     end
   end
   private :attributes_for_json
 
   def attributes_to_send_to_server(options)
-    return attributes if options[:force] or (options[:action] == :create)
+    return attributes if options[:force] || (options[:action] == :create)
+
     changes.keys.each_with_object({}) { |k, attributes| attributes[k.to_s] = send(k) }
   end
   private :attributes_to_send_to_server
@@ -102,6 +104,7 @@ module Sequencescape::Api::Resource::Json
   def associations_for_json(options)
     associations.each_with_object({}) do |(k, v), associations|
       next unless must_output_full_json?(options, v)
+
       associations[k.to_s] = v.as_json(options)
     end
   end

data/lib/sequencescape-api/resource/modifications.rb

@@ -38,32 +38,33 @@ module Sequencescape::Api::Resource::Modifications
   def initialize(api, json = nil, wrapped = false)
     super
     update_from_json(json, wrapped)
-    changed_attributes.clear
+    clear_changes_information
   end
 
   def update_attributes!(attributes)
-    changed_attributes.clear
+    clear_changes_information
     update_from_json(attributes, false)
-    modify!(:action => :update)
+    modify!(action: :update)
   end
   alias update! update_attributes!
 
   def save!(options = nil)
     action = persisted? ? :update : :create
-    modify!((options || {}).merge({ :action => action }))
+    modify!((options || {}).merge({ action: action }))
   end
 
-  def modify!(options)
-    raise Sequencescape::Api::Error, "No actions exist" if options[:url].nil? and actions.nil?
+  # rubocop:todo Metrics/MethodLength
+  def modify!(options) # rubocop:todo Metrics/CyclomaticComplexity
+    raise Sequencescape::Api::Error, 'No actions exist' if options[:url].nil? && actions.nil?
 
     action    = options[:action]
-    skip_json = options[:skip_json]||false
+    skip_json = options[:skip_json] || false
     http_verb = options[:http_verb] || options[:action]
     url       = options[:url]
     url     ||= (actions.send(action) or raise Sequencescape::Api::Error, "Cannot perform #{action}")
-    raise Sequencescape::Api::Error, "Cannot perform modification without a URL" if url.blank?
+    raise Sequencescape::Api::Error, 'Cannot perform modification without a URL' if url.blank?
 
-    self.tap do
+    tap do
       run_validations! or raise Sequencescape::Api::ResourceInvalid, self
 
       object = skip_json ? {} : self
@@ -75,9 +76,10 @@ module Sequencescape::Api::Resource::Modifications
         Sequencescape::Api::ModifyingHandler.new(self)
       )
 
-      changed_attributes.clear
+      clear_changes_information
     end
   end
+  # rubocop:enable Metrics/MethodLength
   private :modify!
 
   def update_from_json(json, wrapped = false)
@@ -92,7 +94,8 @@ module Sequencescape::Api::Resource::Modifications
     when name.to_s == 'actions'                     then update_actions(value)
     when name.to_s == 'uuid'                        then @uuid = (value || @uuid)
     when respond_to?(:"#{name}=", :include_private) then send(:"#{name}=", value)
-    else # TODO: Maybe we need debug logging in here at some point!
+    else
+      debug_log("Unrecognized attribute #{name}")
     end
   end
   private :update_attribute
@@ -108,4 +111,10 @@ module Sequencescape::Api::Resource::Modifications
     @actions = actions_from_attributes.nil? ? actions_before_update : OpenStruct.new(actions_from_attributes)
   end
   private :update_actions
+
+  private
+
+  def debug_log(message)
+    Rails.loggger.debug(message) if defined?(Rails)
+  end
 end