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

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

data/spec/sequencescape-api/associations_spec.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 require 'spec_helper'
 
 describe 'Various associations' do
@@ -51,7 +53,7 @@ describe 'Various associations' do
       stub_request_from('retrieve-model') { response('model-a-instance') }
       stub_request_from('create-via-has-many') { response('model-b-instance') }
 
-      subject { api.model_a.find('UUID').model_bs.create!() }
+      subject { api.model_a.find('UUID').model_bs.create! }
 
       its(:class) { should == Unauthorised::ModelB }
     end
@@ -62,7 +64,7 @@ describe 'Various associations' do
 
     let(:resource) { api.model_b.find('UUID') }
 
-    [ :model_a, :model_by_simple_name, :model_by_full_name ].each do |association_name|
+    %i[model_a model_by_simple_name model_by_full_name].each do |association_name|
       context "expressed as #{association_name.inspect}" do
         stub_request_and_response('belongs-to-association')
 

data/spec/sequencescape-api/finding_methods_spec.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 require 'spec_helper'
 
 describe 'Finding a resource instance' do
@@ -9,7 +11,7 @@ describe 'Finding a resource instance' do
     stub_request_from('retrieve-model') { response('resource-not-found') }
 
     it 'raises an exception' do
-      lambda { subject }.should raise_error(Sequencescape::Api::ResourceNotFound)
+      -> { subject }.should raise_error(Sequencescape::Api::ResourceNotFound)
     end
   end
 

data/spec/sequencescape-api/modifications_spec.rb

@@ -1,18 +1,20 @@
+# frozen_string_literal: true
+
 require 'spec_helper'
 
 shared_examples_for 'errors on both client and server' do |action, request_contract|
   context 'may be invalid on the client side' do
     it 'raises an error' do
       lambda do
-        target.__send__(action, :attribute_validated_at_client => 'please error')
+        target.__send__(action, attribute_validated_at_client: 'please error')
       end.should raise_error(Sequencescape::Api::ResourceInvalid)
     end
 
     it 'includes the error on the field' do
       begin
-        target.__send__(action, :attribute_validated_at_client => 'please error')
-      rescue Sequencescape::Api::ResourceInvalid => exception
-        exception.resource.errors[:attribute_validated_at_client].should == [ 'cannot be set' ]
+        target.__send__(action, attribute_validated_at_client: 'please error')
+      rescue Sequencescape::Api::ResourceInvalid => e
+        e.resource.errors[:attribute_validated_at_client].should == ['cannot be set']
       end
     end
   end
@@ -22,15 +24,15 @@ shared_examples_for 'errors on both client and server' do |action, request_contr
 
     it 'raises an error' do
       lambda do
-        target.__send__(action, :attribute_validated_at_server => 'please error')
+        target.__send__(action, attribute_validated_at_server: 'please error')
       end.should raise_error(Sequencescape::Api::ResourceInvalid)
     end
 
     it 'includes the error on the field' do
       begin
-        target.__send__(action, :attribute_validated_at_server => 'please error')
-      rescue Sequencescape::Api::ResourceInvalid => exception
-        exception.resource.errors[:attribute_validated_at_server].should == [ 'cannot be set' ]
+        target.__send__(action, attribute_validated_at_server: 'please error')
+      rescue Sequencescape::Api::ResourceInvalid => e
+        e.resource.errors[:attribute_validated_at_server].should == ['cannot be set']
       end
     end
   end
@@ -49,7 +51,7 @@ describe 'Creating a resource' do
     stub_request_from('create-model-c') { response('model-c-instance-created') }
 
     subject do
-      target.create!(:changes_during_update => 'sent from client', :remains_same_during_update => 'from JSON')
+      target.create!(changes_during_update: 'sent from client', remains_same_during_update: 'from JSON')
     end
 
     its(:changes_during_update)      { should == 'set during create' }
@@ -65,7 +67,7 @@ describe 'Creating a resource' do
 
       it 'takes an array of objects and converts them to UUID'
       it 'assumes an array of strings are UUIDs' do
-        target.create!(:model_bs => ['model-b-uuids'])
+        target.create!(model_bs: ['model-b-uuids'])
       end
       it 'raises if not given an enumerable'
     end
@@ -75,7 +77,7 @@ describe 'Creating a resource' do
 
       it 'takes an array of objects and converts them to UUID'
       it 'assumes an array of strings are UUIDs' do
-        target.create!(:model_bs => [{ "test_attribute" => "test_value" }])
+        target.create!(model_bs: [{ 'test_attribute' => 'test_value' }])
       end
       it 'raises if not given an enumerable'
     end
@@ -85,7 +87,7 @@ describe 'Creating a resource' do
 
       it 'takes an array of objects and converts them to UUID'
       it 'assumes an array of strings are UUIDs' do
-        target.create!(:model_as => ['model-a-uuids'])
+        target.create!(model_as: ['model-a-uuids'])
       end
       it 'raises if not given an enumerable'
     end
@@ -120,9 +122,9 @@ describe 'Updating a resource' do
 
     before(:each) do
       subject.update_attributes!(
-        :changes_during_update => 'sent from client',
-        :remains_same_during_update => 'from JSON',
-        :write_only => 'has been set'
+        changes_during_update: 'sent from client',
+        remains_same_during_update: 'from JSON',
+        write_only: 'has been set'
       )
     end
 
@@ -166,4 +168,3 @@ describe 'Updating a resource through an association' do
     it 'handles individual attribute changes'
   end
 end
-

data/spec/sequencescape-api/root_spec.rb

@@ -1,12 +1,14 @@
+# frozen_string_literal: true
+
 require 'spec_helper'
 
 describe 'Handling authentication issues' do
   stub_request_from('retrieve-root-with-an-unauthorised-client') { response('client-fails-authentication') }
 
-  subject { Sequencescape::Api.new(:url => 'http://localhost:3000/', :cookie => 'single-sign-on-cookie') }
+  subject { Sequencescape::Api.new(url: 'http://localhost:3000/', cookie: 'single-sign-on-cookie') }
 
   it 'raises an exception' do
-    lambda { subject }.should raise_error(Sequencescape::Api::UnauthenticatedError)
+    -> { subject }.should raise_error(Sequencescape::Api::UnauthenticatedError)
   end
 end
 
@@ -15,7 +17,7 @@ describe 'Retrieving the root URL' do
     is_working_as_an_unauthorised_client
 
     context 'with no namespace' do
-      subject { Sequencescape::Api.new(:url => 'http://localhost:3000/', :cookie => 'single-sign-on-cookie') }
+      subject { Sequencescape::Api.new(url: 'http://localhost:3000/', cookie: 'single-sign-on-cookie') }
 
       Unauthorised::MODELS_THROUGH_API.each do |model|
         it "provides the #{model} through the API instance" do
@@ -24,12 +26,15 @@ describe 'Retrieving the root URL' do
 
         it "errors because Sequencescape::#{model.to_s.classify} is not defined" do
           # Note: Using a regex as > Ruby 2.3 'DidYouMean' changes the error message slightly.
-          lambda { subject.send(model.to_sym) }.should raise_error(NameError, /uninitialized constant Sequencescape::#{model.to_s.classify}/)
+          lambda {
+            subject.send(model.to_sym)
+          }.should raise_error(NameError,
+                               /uninitialized constant Sequencescape::#{model.to_s.classify}/)
         end
       end
     end
 
-    context "with a specified namespace" do
+    context 'with a specified namespace' do
       Unauthorised::MODELS_THROUGH_API.each do |model|
         context do
           stub_request_and_response("unauthorised-#{model.to_s.dasherize}-list")
@@ -49,7 +54,7 @@ describe 'Retrieving the root URL' do
 
     subject { api }
 
-    [ :model_c, :model_d ].each do |model|
+    %i[model_c model_d].each do |model|
       it "provides the #{model} through the API instance" do
         subject.should respond_to(model.to_sym)
       end

data/spec/spec_helper.rb

@@ -1,8 +1,10 @@
+# frozen_string_literal: true
+
 require 'sequencescape-api'
 require 'sequencescape'
 
 # Make sure our support files can be loaded when required
-$:.push(File.expand_path(File.join(File.dirname(__FILE__), 'support')))
+$LOAD_PATH.push(File.expand_path(File.join(File.dirname(__FILE__), 'support')))
 require 'contract_helper'
 require 'namespaces'
 require 'shared_examples'

data/spec/support/contract_helper.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 # Fake the web connections so we don't trash anything
 require 'webmock/rspec'
 
@@ -21,13 +23,16 @@ module ContractHelper
       \g<verb>\s+\g<path>\s+HTTP/1.1\g<eol>
       \g<headers>\g<eol>
       (\g<eol>\g<body>?)?
-    }mx
+    }mx.freeze
 
     def request(contract_name)
       contract(contract_name) do |file|
-        match = REQUEST_REGEXP.match(file.read) or raise StandardError, "Invalidly formatted request in #{contract_name.inspect}"
+        match = REQUEST_REGEXP.match(file.read)
+
+        raise StandardError, "Invalidly formatted request in #{contract_name.inspect}" if match.nil?
 
-        @http_verb, @url   = match[:verb].downcase.to_sym, "http://localhost:3000#{match[:path]}"
+        @http_verb = match[:verb].downcase.to_sym
+        @url = "http://localhost:3000#{match[:path]}"
         @conditions = {}
         @conditions[:headers] = Hash[*match[:headers].split(/\r?\n/).map { |l| l.split(':') }.flatten.map(&:strip)]
         @conditions[:body] = Yajl::Encoder.encode(Yajl::Parser.parse(match[:body])) unless match[:body].blank?
@@ -40,11 +45,12 @@ module ContractHelper
       end
     end
 
-    def contract(contract_name, &block)
+    def contract(contract_name)
       path = @root.dup
       until path.empty?
         filename = File.join(path, 'contracts', "#{contract_name}.txt")
         return File.open(filename, 'r') { |file| yield(file) } if File.file?(filename)
+
         path.pop
       end
       raise StandardError, "Cannot find contract #{filename.inspect} anywhere within #{@root.inspect}"
@@ -74,7 +80,7 @@ module ContractHelper
 
   module ClassMethods
     def stub_request_from(request_filename, &block)
-      stubbed_request = StubRequestBuilder.new(File.join(File.dirname(__FILE__), %w{.. sequencescape-api contracts}))
+      stubbed_request = StubRequestBuilder.new(File.join(File.dirname(__FILE__), %w[.. sequencescape-api contracts]))
       stubbed_request.request(request_filename)
       stubbed_request.instance_eval(&block)
       stubbed_request.inject_into(self)
@@ -85,11 +91,13 @@ module ContractHelper
     end
 
     def is_working_as_an_unauthorised_client
-      stub_request_from('retrieve-root-with-an-unauthorised-client') { response('root-response-for-unauthorised-client') }
+      stub_request_from('retrieve-root-with-an-unauthorised-client') do
+        response('root-response-for-unauthorised-client')
+      end
       let(:api) do
         Sequencescape::Api.new(
-          :url => 'http://localhost:3000/', :cookie => 'single-sign-on-cookie',
-          :namespace => Unauthorised
+          url: 'http://localhost:3000/', cookie: 'single-sign-on-cookie',
+          namespace: Unauthorised
         )
       end
     end
@@ -99,8 +107,8 @@ module ContractHelper
 
       let(:api) do
         Sequencescape::Api.new(
-          :url => 'http://localhost:3000/', :cookie => 'single-sign-on-cookie',
-          :authorisation => 'authorised!', :namespace => Authenticated
+          url: 'http://localhost:3000/', cookie: 'single-sign-on-cookie',
+          authorisation: 'authorised!', namespace: Authenticated
         )
       end
     end

data/spec/support/namespaces.rb

@@ -1,9 +1,11 @@
+# frozen_string_literal: true
+
 module Unauthorised
-  MODELS_THROUGH_API = [ :model_a, :model_b, :model_c ]
+  MODELS_THROUGH_API = %i[model_a model_b model_c].freeze
 
   class ModelA < Sequencescape::Api::Resource
     module LotCreator
-      def create!(attributes=nil)
+      def create!(attributes = nil)
         attributes ||= {}
         new({}, false).tap do |lot|
           api.create(actions.create, { 'model_b' => attributes }, Sequencescape::Api::ModifyingHandler.new(lot))
@@ -24,14 +26,14 @@ module Unauthorised
 
   class ModelB < Sequencescape::Api::Resource
     belongs_to :model_a
-    belongs_to :model_by_simple_name, :class_name => 'ModelA'
-    belongs_to :model_by_full_name, :class_name => 'Nested::Model'
-    belongs_to :model_with_early_data, :class_name => 'ModelA'
+    belongs_to :model_by_simple_name, class_name: 'ModelA'
+    belongs_to :model_by_full_name, class_name: 'Nested::Model'
+    belongs_to :model_with_early_data, class_name: 'ModelA'
     attribute_accessor :test_attribute
   end
 
   class ModelC < Sequencescape::Api::Resource
-    has_many :model_bs, :disposition => :inline
+    has_many :model_bs, disposition: :inline
     has_many :model_as
 
     attribute_accessor :attribute_validated_at_client, :attribute_validated_at_server
@@ -56,12 +58,10 @@ module Unauthorised
 end
 
 module Authenticated
-  MODELS_THROUGH_API = [ :model_c, :model_d ]
+  MODELS_THROUGH_API = %i[model_c model_d].freeze
 
   class ModelC < Sequencescape::Api::Resource
-
   end
   class ModelD < Sequencescape::Api::Resource
-
   end
 end

data/spec/support/shared_examples.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 shared_examples_for 'a paged result' do
   it 'physically contains 3 items' do
     subject.map(&:inspect).size.should == 3

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: sequencescape-client-api
 version: !ruby/object:Gem::Version
-  version: 0.3.7
+  version: 0.4.0.pre.rc2
 platform: ruby
 authors:
 - Matthew Denner
@@ -10,48 +10,36 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-02-19 00:00:00.000000000 Z
+date: 2020-05-28 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
-  name: activesupport
+  name: activemodel
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: 4.0.0
-    - - "<"
-      - !ruby/object:Gem::Version
-        version: '5.2'
+        version: 5.0.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: 4.0.0
-    - - "<"
-      - !ruby/object:Gem::Version
-        version: '5.2'
+        version: 5.0.0
 - !ruby/object:Gem::Dependency
-  name: activemodel
+  name: activesupport
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: 4.0.0
-    - - "<"
-      - !ruby/object:Gem::Version
-        version: '5.2'
+        version: 5.0.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: 4.0.0
-    - - "<"
-      - !ruby/object:Gem::Version
-        version: '5.2'
+        version: 5.0.0
 - !ruby/object:Gem::Dependency
   name: i18n
   requirement: !ruby/object:Gem::Requirement
@@ -72,30 +60,30 @@ dependencies:
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: 1.3.1
+        version: 1.4.1
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: 1.3.1
+        version: 1.4.1
 - !ruby/object:Gem::Dependency
-  name: rspec
+  name: pry
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ">="
       - !ruby/object:Gem::Version
-        version: 2.11.0
+        version: '0'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ">="
       - !ruby/object:Gem::Version
-        version: 2.11.0
+        version: '0'
 - !ruby/object:Gem::Dependency
-  name: pry
+  name: rake
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
@@ -109,7 +97,7 @@ dependencies:
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
-  name: webmock
+  name: redcarpet
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
@@ -123,7 +111,35 @@ dependencies:
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
-  name: yard
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 2.11.0
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 2.11.0
+- !ruby/object:Gem::Dependency
+  name: rubocop
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.84.0
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.84.0
+- !ruby/object:Gem::Dependency
+  name: webmock
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
@@ -137,7 +153,7 @@ dependencies:
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
-  name: redcarpet
+  name: yard
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
@@ -162,7 +178,9 @@ extra_rdoc_files: []
 files:
 - ".gitignore"
 - ".rspec"
-- ".rvmrc"
+- ".rubocop.yml"
+- ".rubocop_todo.yml"
+- ".ruby-version"
 - ".yardoc/checksums"
 - ".yardoc/complete"
 - ".yardoc/object_types"
@@ -374,6 +392,7 @@ files:
 - lib/sequencescape/bulk_transfer.rb
 - lib/sequencescape/comment.rb
 - lib/sequencescape/custom_metadatum_collection.rb
+- lib/sequencescape/extraction_attribute.rb
 - lib/sequencescape/lane.rb
 - lib/sequencescape/library_event.rb
 - lib/sequencescape/library_tube.rb
@@ -485,12 +504,11 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
-  - - ">="
+  - - ">"
     - !ruby/object:Gem::Version
-      version: '0'
+      version: 1.3.1
 requirements: []
-rubyforge_project: sequencescape-client-api
-rubygems_version: 2.6.14
+rubygems_version: 3.0.8
 signing_key: 
 specification_version: 4
 summary: Gem for the client side of the Sequencescape API