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

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: dc5c9f8ff1555f7d9c65631bc73adc64bc5cbdc9
+SHA256:
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+  data.tar.gz: 54607236fa8c9f57130090e07d34c36073174f583f15bfacc2a08f9727ee354c
 SHA512:
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data/.rubocop.yml

@@ -0,0 +1,44 @@
+inherit_from: .rubocop_todo.yml
+
+# The behaviour of RuboCop can be controlled via the .rubocop.yml
+# configuration file. It makes it possible to enable/disable
+# certain cops (checks) and to alter their behaviour if they accept
+# any parameters. The file can be placed either in your home
+# directory or in some project directory.
+#
+# RuboCop will start looking for the configuration file in the directory
+# where the inspected file is and continue its way up to the root directory.
+#
+# See https://github.com/rubocop-hq/rubocop/blob/master/manual/configuration.md
+AllCops:
+  TargetRubyVersion: 2.4
+Style/ClassAndModuleChildren:
+  Enabled: false
+Layout/LineLength:
+  Max: 120
+  AutoCorrect: true
+Naming/FileName:
+  Exclude:
+    - 'lib/sequencescape-api.rb'
+
+# Pending Cops
+Layout/EmptyLinesAroundAttributeAccessor:
+  Enabled: true
+Layout/SpaceAroundMethodCallOperator:
+  Enabled: true
+Lint/DeprecatedOpenSSLConstant:
+  Enabled: true
+Lint/RaiseException:
+  Enabled: true
+Lint/StructNewOverride:
+  Enabled: true
+Style/ExponentialNotation:
+  Enabled: true
+Style/HashEachMethods:
+  Enabled: true
+Style/HashTransformKeys:
+  Enabled: true
+Style/HashTransformValues:
+  Enabled: true
+Style/SlicingWithRange:
+  Enabled: true

data/.rubocop_todo.yml

@@ -0,0 +1,338 @@
+# 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.
+# 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: 2
+Lint/ShadowingOuterLocalVariable:
+  Exclude:
+    - 'lib/sequencescape-api/associations/has_many.rb'
+    - 'lib/sequencescape-api/core_ext/hash.rb'
+
+# Offense count: 7
+Lint/UselessAssignment:
+  Exclude:
+    - 'lib/sequencescape-api/associations/belongs_to.rb'
+    - 'lib/sequencescape-api/connection_factory/actions.rb'
+    - 'lib/sequencescape-api/core.rb'
+    - 'lib/sequencescape-api/resource/attributes.rb'
+    - 'lib/sequencescape/behaviour/qced.rb'
+    - 'lib/sequencescape/plate/pooling.rb'
+
+# Offense count: 1
+# Configuration parameters: CheckForMethodsWithNoSideEffects.
+Lint/Void:
+  Exclude:
+    - 'spec/sequencescape-api/associations_spec.rb'
+
+# Offense count: 10
+# Configuration parameters: IgnoredMethods.
+Metrics/AbcSize:
+  Max: 25
+
+# Offense count: 8
+# Configuration parameters: CountComments, ExcludedMethods.
+# ExcludedMethods: refine
+Metrics/BlockLength:
+  Max: 65
+
+# Offense count: 1
+# Configuration parameters: CountComments.
+Metrics/ModuleLength:
+  Max: 120
+
+# Offense count: 1
+# Configuration parameters: IgnoredMethods.
+Metrics/PerceivedComplexity:
+  Max: 9
+
+# Offense count: 1
+Naming/BinaryOperatorParameterName:
+  Exclude:
+    - 'lib/sequencescape-api/resource/instance_methods.rb'
+
+# Offense count: 9
+# Configuration parameters: NamePrefix, ForbiddenPrefixes, AllowedMethods, MethodDefinitionMacros.
+# NamePrefix: is_, has_, have_
+# ForbiddenPrefixes: is_, has_, have_
+# AllowedMethods: is_a?
+# MethodDefinitionMacros: define_method, define_singleton_method
+Naming/PredicateName:
+  Exclude:
+    - 'spec/**/*'
+    - 'lib/sequencescape-api/actions.rb'
+    - 'lib/sequencescape-api/associations.rb'
+    - 'lib/sequencescape-api/associations/belongs_to.rb'
+    - 'lib/sequencescape-api/associations/has_many.rb'
+    - 'lib/sequencescape-api/resource.rb'
+    - '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: 138
+Style/Documentation:
+  Exclude:
+    - 'spec/**/*'
+    - 'test/**/*'
+    - 'lib/sequencescape-api/actions.rb'
+    - 'lib/sequencescape-api/associations.rb'
+    - 'lib/sequencescape-api/associations/base.rb'
+    - 'lib/sequencescape-api/associations/base/instance_methods.rb'
+    - 'lib/sequencescape-api/associations/belongs_to.rb'
+    - 'lib/sequencescape-api/associations/has_many.rb'
+    - 'lib/sequencescape-api/associations/has_many/json.rb'
+    - 'lib/sequencescape-api/associations/has_many/validation.rb'
+    - 'lib/sequencescape-api/capabilities.rb'
+    - 'lib/sequencescape-api/composition.rb'
+    - 'lib/sequencescape-api/connection_factory.rb'
+    - 'lib/sequencescape-api/connection_factory/actions.rb'
+    - 'lib/sequencescape-api/connection_factory/helpers.rb'
+    - 'lib/sequencescape-api/core.rb'
+    - 'lib/sequencescape-api/core_ext/array.rb'
+    - 'lib/sequencescape-api/core_ext/hash.rb'
+    - 'lib/sequencescape-api/error_handling.rb'
+    - 'lib/sequencescape-api/errors.rb'
+    - 'lib/sequencescape-api/finder_methods.rb'
+    - 'lib/sequencescape-api/resource.rb'
+    - 'lib/sequencescape-api/resource/attribute_groups.rb'
+    - 'lib/sequencescape-api/resource/attributes.rb'
+    - 'lib/sequencescape-api/resource/instance_methods.rb'
+    - 'lib/sequencescape-api/resource/json.rb'
+    - 'lib/sequencescape-api/resource/modifications.rb'
+    - 'lib/sequencescape.rb'
+    - 'lib/sequencescape/asset.rb'
+    - 'lib/sequencescape/asset_audit.rb'
+    - 'lib/sequencescape/asset_group.rb'
+    - 'lib/sequencescape/bait_library.rb'
+    - 'lib/sequencescape/bait_library_layout.rb'
+    - 'lib/sequencescape/barcode_printer.rb'
+    - 'lib/sequencescape/barcoded_asset.rb'
+    - 'lib/sequencescape/batch.rb'
+    - 'lib/sequencescape/behaviour/barcoded.rb'
+    - 'lib/sequencescape/behaviour/labeled.rb'
+    - 'lib/sequencescape/behaviour/qced.rb'
+    - 'lib/sequencescape/behaviour/receptacle.rb'
+    - 'lib/sequencescape/behaviour/state_driven.rb'
+    - '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'
+    - 'lib/sequencescape/lot.rb'
+    - 'lib/sequencescape/lot_type.rb'
+    - 'lib/sequencescape/multiplexed_library_tube.rb'
+    - 'lib/sequencescape/order.rb'
+    - 'lib/sequencescape/order_template.rb'
+    - 'lib/sequencescape/pipeline.rb'
+    - 'lib/sequencescape/plate.rb'
+    - 'lib/sequencescape/plate/pooling.rb'
+    - 'lib/sequencescape/plate/well_structure.rb'
+    - 'lib/sequencescape/plate_conversion.rb'
+    - 'lib/sequencescape/plate_creation.rb'
+    - 'lib/sequencescape/plate_purpose.rb'
+    - 'lib/sequencescape/plate_template.rb'
+    - 'lib/sequencescape/pooled_plate_creation.rb'
+    - 'lib/sequencescape/project.rb'
+    - 'lib/sequencescape/qc_decision.rb'
+    - 'lib/sequencescape/qc_file.rb'
+    - 'lib/sequencescape/qcable.rb'
+    - 'lib/sequencescape/qcable_creator.rb'
+    - 'lib/sequencescape/request.rb'
+    - 'lib/sequencescape/robot.rb'
+    - 'lib/sequencescape/sample.rb'
+    - 'lib/sequencescape/sample_tube.rb'
+    - 'lib/sequencescape/search.rb'
+    - 'lib/sequencescape/specific_tube_creation.rb'
+    - 'lib/sequencescape/stamp.rb'
+    - 'lib/sequencescape/state_change.rb'
+    - 'lib/sequencescape/study.rb'
+    - 'lib/sequencescape/submission.rb'
+    - 'lib/sequencescape/submission_pool.rb'
+    - 'lib/sequencescape/tag.rb'
+    - 'lib/sequencescape/tag2_layout.rb'
+    - 'lib/sequencescape/tag2_layout_template.rb'
+    - 'lib/sequencescape/tag_group.rb'
+    - 'lib/sequencescape/tag_layout.rb'
+    - 'lib/sequencescape/tag_layout_template.rb'
+    - 'lib/sequencescape/template.rb'
+    - 'lib/sequencescape/transfer.rb'
+    - 'lib/sequencescape/transfer_request.rb'
+    - 'lib/sequencescape/transfer_request_collection.rb'
+    - 'lib/sequencescape/transfer_template.rb'
+    - 'lib/sequencescape/tube.rb'
+    - 'lib/sequencescape/tube_creation.rb'
+    - 'lib/sequencescape/tube_from_tube_creation.rb'
+    - 'lib/sequencescape/tube_purpose.rb'
+    - 'lib/sequencescape/user.rb'
+    - 'lib/sequencescape/volume_update.rb'
+    - 'lib/sequencescape/well.rb'
+    - 'lib/sequencescape/work_completion.rb'
+
+# Offense count: 6
+# Cop supports --auto-correct.
+Style/EmptyCaseCondition:
+  Exclude:
+    - 'lib/sequencescape-api/associations/base/instance_methods.rb'
+    - 'lib/sequencescape-api/associations/belongs_to.rb'
+    - 'lib/sequencescape-api/associations/has_many.rb'
+    - 'lib/sequencescape-api/connection_factory/actions.rb'
+    - 'lib/sequencescape-api/resource/modifications.rb'
+
+# Offense count: 1
+# Cop supports --auto-correct.
+# Configuration parameters: EnforcedStyle.
+# SupportedStyles: empty, nil, both
+Style/EmptyElse:
+  Exclude:
+    - 'lib/sequencescape-api/resource/json.rb'
+
+# Offense count: 11
+Style/EvalWithLocation:
+  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: 104
+# Cop supports --auto-correct.
+# Configuration parameters: EnforcedStyle.
+# SupportedStyles: always, always_true, never
+Style/FrozenStringLiteralComment:
+  Exclude:
+    - 'Gemfile'
+    - 'Rakefile'
+    - 'lib/sequencescape-api.rb'
+    - 'lib/sequencescape-api/actions.rb'
+    - 'lib/sequencescape-api/associations.rb'
+    - 'lib/sequencescape-api/associations/base.rb'
+    - 'lib/sequencescape-api/associations/base/instance_methods.rb'
+    - 'lib/sequencescape-api/associations/belongs_to.rb'
+    - 'lib/sequencescape-api/associations/has_many.rb'
+    - 'lib/sequencescape-api/associations/has_many/json.rb'
+    - 'lib/sequencescape-api/associations/has_many/validation.rb'
+    - 'lib/sequencescape-api/capabilities.rb'
+    - 'lib/sequencescape-api/composition.rb'
+    - 'lib/sequencescape-api/connection_factory.rb'
+    - 'lib/sequencescape-api/connection_factory/actions.rb'
+    - 'lib/sequencescape-api/connection_factory/helpers.rb'
+    - 'lib/sequencescape-api/core.rb'
+    - 'lib/sequencescape-api/core_ext.rb'
+    - 'lib/sequencescape-api/core_ext/array.rb'
+    - 'lib/sequencescape-api/core_ext/hash.rb'
+    - 'lib/sequencescape-api/error_handling.rb'
+    - 'lib/sequencescape-api/errors.rb'
+    - 'lib/sequencescape-api/finder_methods.rb'
+    - 'lib/sequencescape-api/rails.rb'
+    - 'lib/sequencescape-api/resource.rb'
+    - 'lib/sequencescape-api/resource/active_model.rb'
+    - 'lib/sequencescape-api/resource/attribute_groups.rb'
+    - 'lib/sequencescape-api/resource/attributes.rb'
+    - 'lib/sequencescape-api/resource/instance_methods.rb'
+    - 'lib/sequencescape-api/resource/json.rb'
+    - 'lib/sequencescape-api/resource/modifications.rb'
+    - 'lib/sequencescape-api/resource_model_proxy.rb'
+    - 'lib/sequencescape-api/version.rb'
+    - 'lib/sequencescape.rb'
+    - 'lib/sequencescape/asset.rb'
+    - 'lib/sequencescape/asset_audit.rb'
+    - 'lib/sequencescape/asset_group.rb'
+    - 'lib/sequencescape/bait_library.rb'
+    - 'lib/sequencescape/bait_library_layout.rb'
+    - 'lib/sequencescape/barcode_printer.rb'
+    - 'lib/sequencescape/barcoded_asset.rb'
+    - 'lib/sequencescape/batch.rb'
+    - 'lib/sequencescape/behaviour/barcoded.rb'
+    - 'lib/sequencescape/behaviour/labeled.rb'
+    - 'lib/sequencescape/behaviour/qced.rb'
+    - 'lib/sequencescape/behaviour/receptacle.rb'
+    - 'lib/sequencescape/behaviour/state_driven.rb'
+    - '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'
+    - 'lib/sequencescape/lot.rb'
+    - 'lib/sequencescape/lot_type.rb'
+    - 'lib/sequencescape/multiplexed_library_tube.rb'
+    - 'lib/sequencescape/order.rb'
+    - 'lib/sequencescape/order_template.rb'
+    - 'lib/sequencescape/pipeline.rb'
+    - 'lib/sequencescape/plate.rb'
+    - 'lib/sequencescape/plate/pooling.rb'
+    - 'lib/sequencescape/plate/well_structure.rb'
+    - 'lib/sequencescape/plate_conversion.rb'
+    - 'lib/sequencescape/plate_creation.rb'
+    - 'lib/sequencescape/plate_purpose.rb'
+    - 'lib/sequencescape/plate_template.rb'
+    - 'lib/sequencescape/pooled_plate_creation.rb'
+    - 'lib/sequencescape/project.rb'
+    - 'lib/sequencescape/qc_decision.rb'
+    - 'lib/sequencescape/qc_file.rb'
+    - 'lib/sequencescape/qcable.rb'
+    - 'lib/sequencescape/qcable_creator.rb'
+    - 'lib/sequencescape/request.rb'
+    - 'lib/sequencescape/robot.rb'
+    - 'lib/sequencescape/sample.rb'
+    - 'lib/sequencescape/sample_tube.rb'
+    - 'lib/sequencescape/search.rb'
+    - 'lib/sequencescape/specific_tube_creation.rb'
+    - 'lib/sequencescape/stamp.rb'
+    - 'lib/sequencescape/state_change.rb'
+    - 'lib/sequencescape/study.rb'
+    - 'lib/sequencescape/submission.rb'
+    - 'lib/sequencescape/submission_pool.rb'
+    - 'lib/sequencescape/tag.rb'
+    - 'lib/sequencescape/tag2_layout.rb'
+    - 'lib/sequencescape/tag2_layout_template.rb'
+    - 'lib/sequencescape/tag_group.rb'
+    - 'lib/sequencescape/tag_layout.rb'
+    - 'lib/sequencescape/tag_layout_template.rb'
+    - 'lib/sequencescape/template.rb'
+    - 'lib/sequencescape/transfer.rb'
+    - 'lib/sequencescape/transfer_request.rb'
+    - 'lib/sequencescape/transfer_request_collection.rb'
+    - 'lib/sequencescape/transfer_template.rb'
+    - 'lib/sequencescape/tube.rb'
+    - 'lib/sequencescape/tube_creation.rb'
+    - 'lib/sequencescape/tube_from_tube_creation.rb'
+    - 'lib/sequencescape/tube_purpose.rb'
+    - 'lib/sequencescape/user.rb'
+    - 'lib/sequencescape/volume_update.rb'
+    - 'lib/sequencescape/well.rb'
+    - 'lib/sequencescape/work_completion.rb'
+    - 'sequencescape-api.gemspec'
+
+# Offense count: 2
+Style/MethodMissingSuper:
+  Exclude:
+    - 'lib/sequencescape-api/associations/belongs_to.rb'
+    - 'lib/sequencescape-api/resource_model_proxy.rb'
+
+# Offense count: 2
+Style/MissingRespondToMissing:
+  Exclude:
+    - 'lib/sequencescape-api/associations/belongs_to.rb'
+    - 'lib/sequencescape-api/core.rb'

data/.ruby-version

@@ -0,0 +1 @@
+ruby-2.5.8

data/Gemfile

@@ -1,4 +1,4 @@
-source "http://rubygems.org"
+source 'http://rubygems.org'
 
 # Specify your gem's dependencies in sequencescape-api.gemspec
 gemspec

data/README.markdown

@@ -1,4 +1,17 @@
 Sequencescape Client API
 ========================
+
 This is the Ruby client library for the Sequencescape API.
 Documentation can be found [on the wiki](https://github.com/sanger/sequencescape-client-api/wiki).
+
+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
+
+- master currently corresponds to 0.4.x
+
+Rails 6 appears to be supported judging by Specs, but haven't used it in anger
+yet.

data/lib/sequencescape-api.rb

@@ -13,4 +13,4 @@ require 'sequencescape-api/resource'
 require 'sequencescape-api/rails'
 
 # Ensure that the I18n stuff has been properly configured
-I18n.config.load_path << File.expand_path(File.join(File.dirname(__FILE__), %w{sequencescape-api locale en.yml}))
+I18n.config.load_path << File.expand_path(File.join(File.dirname(__FILE__), %w[sequencescape-api locale en.yml]))

data/lib/sequencescape-api/actions.rb

@@ -9,9 +9,10 @@ module Sequencescape::Api::Actions
   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 has_class_create_action(*args) # rubocop:todo Metrics/MethodLength
+      action_module = Module.new
+      line = __LINE__ + 1
+      action_module.module_eval(%{
         def initialize_class_actions(proxy)
           super
 
@@ -31,7 +32,7 @@ module Sequencescape::Api::Actions
   end
 
   module InstanceActionHelpers
-    def has_create_action(*args)
+    def has_create_action(*args) # rubocop:todo Metrics/MethodLength
       options      = args.extract_options!
       name         = args.first || :create!
 
@@ -40,7 +41,7 @@ module Sequencescape::Api::Actions
       result_class = "api.#{options[:resource]}" if options[:resource]
 
       line = __LINE__ + 1
-      class_eval(%Q{
+      class_eval(%{
         def #{name}(attributes = nil)
           url = actions.try(#{action.to_sym.inspect}) or
             raise Sequencescape::Api::Error, "Cannot perform #{action} without an URL"
@@ -54,14 +55,14 @@ module Sequencescape::Api::Actions
 
     def has_update_action(name, options = {})
       api_method = options[:verb] == :create ? :create : :update
-      skip_json  = options[:skip_json]||false
+      skip_json  = options[:skip_json] || false
       action     = options[:action] || :update
 
       line = __LINE__ + 1
-      class_eval(%Q{
+      class_eval(%{
         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})
+          modify!(action: #{action.to_sym.inspect}, http_verb: #{api_method.to_sym.inspect}, skip_json: #{skip_json})
         end
       }, __FILE__, line)
     end