sequencescape-client-api 0.4.3 → 0.5.0.pre.rc1

checksums.yaml

@@ -1,7 +1,7 @@
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data/.rubocop.yml

@@ -22,23 +22,29 @@ Naming/FileName:
     - 'lib/sequencescape-api.rb'
 
 # Pending Cops
-Layout/EmptyLinesAroundAttributeAccessor:
+Lint/DuplicateBranch: # (new in 1.3)
   Enabled: true
-Layout/SpaceAroundMethodCallOperator:
+Lint/DuplicateRegexpCharacterClassElement: # (new in 1.1)
   Enabled: true
-Lint/DeprecatedOpenSSLConstant:
+Lint/EmptyBlock: # (new in 1.1)
   Enabled: true
-Lint/RaiseException:
+Lint/EmptyClass: # (new in 1.3)
   Enabled: true
-Lint/StructNewOverride:
+Lint/NoReturnInBeginEndBlocks: # (new in 1.2)
   Enabled: true
-Style/ExponentialNotation:
+Lint/ToEnumArguments: # (new in 1.1)
   Enabled: true
-Style/HashEachMethods:
+Lint/UnmodifiedReduceAccumulator: # (new in 1.1)
   Enabled: true
-Style/HashTransformKeys:
+Style/ArgumentsForwarding: # (new in 1.1)
   Enabled: true
-Style/HashTransformValues:
+Style/CollectionCompact: # (new in 1.2)
   Enabled: true
-Style/SlicingWithRange:
+Style/DocumentDynamicEvalDefinition: # (new in 1.1)
+  Enabled: true
+Style/NegatedIfElseCondition: # (new in 1.2)
+  Enabled: true
+Style/NilLambda: # (new in 1.3)
+  Enabled: true
+Style/SwapValues: # (new in 1.1)
   Enabled: true

data/.rubocop_todo.yml

@@ -1,11 +1,29 @@
 # This configuration was generated by
 # `rubocop --auto-gen-config --exclude-limit 15000`
-# on 2020-05-28 09:58:56 +0100 using RuboCop version 0.84.0.
+# on 2020-11-20 12:14:23 UTC using RuboCop version 1.3.1.
 # The point is for the user to remove these configuration records
 # one by one as the offenses are removed from the code base.
 # Note that changes in the inspected code, or installation of new
 # versions of RuboCop, may require this file to be generated again.
 
+# Offense count: 4
+Lint/DuplicateBranch:
+  Exclude:
+    - 'lib/sequencescape-api/associations/belongs_to.rb'
+    - 'lib/sequencescape-api/connection_factory/actions.rb'
+
+# Offense count: 3
+Lint/MissingSuper:
+  Exclude:
+    - 'lib/sequencescape-api/associations/belongs_to.rb'
+    - 'lib/sequencescape-api/resource_model_proxy.rb'
+    - 'lib/sequencescape/search.rb'
+
+# Offense count: 1
+Lint/MixedRegexpCaptureTypes:
+  Exclude:
+    - 'spec/support/contract_helper.rb'
+
 # Offense count: 2
 Lint/ShadowingOuterLocalVariable:
   Exclude:
@@ -28,28 +46,34 @@ Lint/Void:
   Exclude:
     - 'spec/sequencescape-api/associations_spec.rb'
 
-# Offense count: 10
+# Offense count: 7
 # Configuration parameters: IgnoredMethods.
 Metrics/AbcSize:
-  Max: 25
+  Max: 26
 
 # Offense count: 8
-# Configuration parameters: CountComments, ExcludedMethods.
+# Configuration parameters: CountComments, CountAsOne, ExcludedMethods.
 # ExcludedMethods: refine
 Metrics/BlockLength:
   Max: 65
 
 # Offense count: 1
-# Configuration parameters: CountComments.
+# Configuration parameters: IgnoredMethods.
+Metrics/CyclomaticComplexity:
+  Max: 8
+
+# Offense count: 1
+# Configuration parameters: CountComments, CountAsOne.
 Metrics/ModuleLength:
   Max: 120
 
-# Offense count: 1
+# Offense count: 2
 # Configuration parameters: IgnoredMethods.
 Metrics/PerceivedComplexity:
-  Max: 9
+  Max: 10
 
 # Offense count: 1
+# Cop supports --auto-correct.
 Naming/BinaryOperatorParameterName:
   Exclude:
     - 'lib/sequencescape-api/resource/instance_methods.rb'
@@ -71,18 +95,23 @@ Naming/PredicateName:
     - 'lib/sequencescape-api/resource/attributes.rb'
     - 'lib/sequencescape-api/resource_model_proxy.rb'
 
-# Offense count: 1
-# Configuration parameters: EnforcedStyle, AllowModifiersOnSymbols.
-# SupportedStyles: inline, group
-Style/AccessModifierDeclarations:
-  Exclude:
-    - 'lib/sequencescape-api/resource/attributes.rb'
-
 # Offense count: 1
 Style/BeginBlock:
   Exclude:
     - 'lib/sequencescape-api/connection_factory/actions.rb'
 
+# Offense count: 11
+Style/DocumentDynamicEvalDefinition:
+  Exclude:
+    - 'lib/sequencescape-api/actions.rb'
+    - 'lib/sequencescape-api/associations.rb'
+    - 'lib/sequencescape-api/composition.rb'
+    - 'lib/sequencescape-api/finder_methods.rb'
+    - 'lib/sequencescape-api/resource/attributes.rb'
+    - 'lib/sequencescape/batch.rb'
+    - 'lib/sequencescape/behaviour/state_driven.rb'
+    - 'lib/sequencescape/search.rb'
+
 # Offense count: 138
 Style/Documentation:
   Exclude:
@@ -214,6 +243,12 @@ Style/EvalWithLocation:
     - 'lib/sequencescape/behaviour/state_driven.rb'
     - 'lib/sequencescape/search.rb'
 
+# Offense count: 1
+# Cop supports --auto-correct.
+Style/ExplicitBlockArgument:
+  Exclude:
+    - 'spec/support/contract_helper.rb'
+
 # Offense count: 104
 # Cop supports --auto-correct.
 # Configuration parameters: EnforcedStyle.
@@ -326,13 +361,18 @@ Style/FrozenStringLiteralComment:
     - 'sequencescape-api.gemspec'
 
 # Offense count: 2
-Style/MethodMissingSuper:
+Style/MissingRespondToMissing:
   Exclude:
     - 'lib/sequencescape-api/associations/belongs_to.rb'
-    - 'lib/sequencescape-api/resource_model_proxy.rb'
+    - 'lib/sequencescape-api/core.rb'
 
-# Offense count: 2
-Style/MissingRespondToMissing:
+# Offense count: 6
+# Configuration parameters: AllowedMethods.
+# AllowedMethods: respond_to_missing?
+Style/OptionalBooleanParameter:
   Exclude:
     - 'lib/sequencescape-api/associations/belongs_to.rb'
     - 'lib/sequencescape-api/core.rb'
+    - 'lib/sequencescape-api/finder_methods.rb'
+    - 'lib/sequencescape-api/resource/instance_methods.rb'
+    - 'lib/sequencescape-api/resource/modifications.rb'

data/README.markdown

@@ -10,8 +10,9 @@ Version Guides
 - 0.2.x Supports older versions of Rails.
 - 0.3.x Supports Rails 3.2.x to 5.1.x
 - 0.4.x Supports Rails 5.0 and up
+- 0.5.x Supports Rails 5.0 and up, drops yajl in favour of multi-json
 
-- master currently corresponds to 0.4.x
+- master currently corresponds to 0.5.x
 
 Rails 6 appears to be supported judging by Specs, but haven't used it in anger
 yet.

data/lib/sequencescape-api/connection_factory/actions.rb

@@ -1,5 +1,5 @@
 require 'net/http'
-require 'yajl'
+require 'multi_json'
 
 # PINCHED FROM https://gist.github.com/736721
 BEGIN {
@@ -48,7 +48,7 @@ module Sequencescape::Api::ConnectionFactory::Actions
   end
 
   # rubocop:todo Metrics/MethodLength
-  def create(url, body, handler) # rubocop:todo Metrics/CyclomaticComplexity
+  def create(url, body, handler)
     perform(:post, url, jsonify(body, action: :create)) do |response|
       case response
       when Net::HTTPCreated             then handler.success(parse_json_from(response))
@@ -64,7 +64,7 @@ module Sequencescape::Api::ConnectionFactory::Actions
   # rubocop:enable Metrics/MethodLength
 
   # rubocop:todo Metrics/MethodLength
-  def create_from_file(url, file, filename, content_type, handler) # rubocop:todo Metrics/CyclomaticComplexity
+  def create_from_file(url, file, filename, content_type, handler)
     perform_for_file(:post, url, file, filename, content_type) do |response|
       case response
       when Net::HTTPCreated             then handler.success(parse_json_from(response))
@@ -113,7 +113,7 @@ module Sequencescape::Api::ConnectionFactory::Actions
       unless body.nil?
         request.content_type = 'application/json'
         # request.body         = body.to_json
-        request.body         = Yajl::Encoder.encode(body)
+        request.body         = MultiJson.dump(body)
       end
       yield(connection.request(request))
     end
@@ -146,7 +146,7 @@ module Sequencescape::Api::ConnectionFactory::Actions
   def parse_json_from(response)
     raise ServerError, 'server returned non-JSON content' unless response.content_type == 'application/json'
 
-    Yajl::Parser.parse(StringIO.new(response.body))
+    MultiJson.load(StringIO.new(response.body))
   end
   private :parse_json_from
 

data/lib/sequencescape-api/finder_methods.rb

@@ -82,11 +82,9 @@ end
 class Sequencescape::Api::PageOfResults
   include Enumerable
 
-  attr_reader :api, :actions
+  attr_reader :api, :actions, :size
   private :api, :actions
 
-  attr_reader :size
-
   def initialize(api, json, &block)
     @api = api
     @ctor = block

data/lib/sequencescape-api/version.rb

@@ -1,5 +1,5 @@
 module Sequencescape
   class Api
-    VERSION = '0.4.3'.freeze
+    VERSION = '0.5.0-rc1'.freeze
   end
 end

data/lib/sequencescape/order.rb

@@ -9,5 +9,6 @@ class Sequencescape::Order < ::Sequencescape::Api::Resource
   # It does, but we don't care for now.
   # has_many :request_types
 
-  attr_accessor :request_options
+  attribute_accessor :request_options
+  attribute_writer :autodetect_studies_projects
 end

data/sequencescape-api.gemspec

@@ -10,6 +10,7 @@ Gem::Specification.new do |s|
   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.required_ruby_version = '> 2.4'
 
   s.rubyforge_project = 'sequencescape-client-api'
 
@@ -18,16 +19,27 @@ Gem::Specification.new do |s|
   s.executables   = `git ls-files -- bin/*`.split("\n").map { |f| File.basename(f) }
   s.require_paths = ['lib']
 
+  s.post_install_message = <<~POST_INSTALL
+    sequencescape-client-api has dropped 'yajl-ruby' in favour of 'multi_json',
+    https://rubygems.org/gems/multi_json. This will automatically pick the
+    fastest json encoder in your Gemfile, falling back to the default encoder.
+
+    For best performance you are strongly encouraged to add a custom json
+    encoder to your project. eg. bundle install oj.
+  POST_INSTALL
+
   s.add_dependency('activemodel', '>= 5.0.0')
   s.add_dependency('activesupport', '>= 5.0.0')
   s.add_dependency('i18n')
-  s.add_dependency('yajl-ruby', '>= 1.4.1')
+  s.add_dependency('multi_json')
 
   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('rubocop', '~> 1.3.1')
   s.add_development_dependency('webmock')
   s.add_development_dependency('yard')
+  # Add a json encoder for development
+  s.add_development_dependency('oj')
 end

data/spec/sequencescape-api/root_spec.rb

@@ -25,7 +25,7 @@ describe 'Retrieving the root URL' do
         end
 
         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.
+          # NOTE: Using a regex as > Ruby 2.3 'DidYouMean' changes the error message slightly.
           lambda {
             subject.send(model.to_sym)
           }.should raise_error(NameError,

data/spec/support/contract_helper.rb

@@ -35,7 +35,7 @@ module ContractHelper
         @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?
+        @conditions[:body] = MultiJson.dump(MultiJson.load(match[:body])) unless match[:body].blank?
       end
     end
 

metadata

@@ -1,16 +1,16 @@
 --- !ruby/object:Gem::Specification
 name: sequencescape-client-api
 version: !ruby/object:Gem::Version
-  version: 0.4.3
+  version: 0.5.0.pre.rc1
 platform: ruby
 authors:
 - Matthew Denner
 - James Glover
 - Eduardo Martin Rojo
-autorequire:
+autorequire: 
 bindir: bin
 cert_chain: []
-date: 2020-11-11 00:00:00.000000000 Z
+date: 2020-11-20 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: activemodel
@@ -55,19 +55,19 @@ dependencies:
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
-  name: yajl-ruby
+  name: multi_json
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: 1.4.1
+        version: '0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: 1.4.1
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: pry
   requirement: !ruby/object:Gem::Requirement
@@ -130,14 +130,14 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 0.84.0
+        version: 1.3.1
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 0.84.0
+        version: 1.3.1
 - !ruby/object:Gem::Dependency
   name: webmock
   requirement: !ruby/object:Gem::Requirement
@@ -166,6 +166,20 @@ dependencies:
     - - ">="
       - !ruby/object:Gem::Version
         version: '0'
+- !ruby/object:Gem::Dependency
+  name: oj
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
 description: Provides all of the necessary code for interacting with the Sequencescape
   API
 email:
@@ -493,23 +507,29 @@ files:
 homepage: ''
 licenses: []
 metadata: {}
-post_install_message:
+post_install_message: |
+  sequencescape-client-api has dropped 'yajl-ruby' in favour of 'multi_json',
+  https://rubygems.org/gems/multi_json. This will automatically pick the
+  fastest json encoder in your Gemfile, falling back to the default encoder.
+
+  For best performance you are strongly encouraged to add a custom json
+  encoder to your project. eg. bundle install oj.
 rdoc_options: []
 require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
-  - - ">="
+  - - ">"
     - !ruby/object:Gem::Version
-      version: '0'
+      version: '2.4'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
-  - - ">="
+  - - ">"
     - !ruby/object:Gem::Version
-      version: '0'
+      version: 1.3.1
 requirements: []
-rubygems_version: 3.0.8
-signing_key:
+rubygems_version: 3.1.4
+signing_key: 
 specification_version: 4
 summary: Gem for the client side of the Sequencescape API
 test_files: