DPL-274 - ONT - remove existing code

.github/workflows/asset_dispatch.yml

@@ -26,7 +26,6 @@ jobs:
           cp config/database.yml.example config/database.yml
           cp config/mailer.yml.example config/mailer.yml
           cp config/bunny.yml.example config/bunny.yml
-          cp config/env_constants.yml.example config/env_constants.yml
 
       - name: Compile Build
         run: ./compile-build

.github/workflows/automated_release_and_build.yml

@@ -30,7 +30,6 @@ jobs:
           cp config/database.yml.example config/database.yml
           cp config/mailer.yml.example config/mailer.yml
           cp config/bunny.yml.example config/bunny.yml
-          cp config/env_constants.yml.example config/env_constants.yml
 
       - name: Compile Build
         run: ./compile-build

.github/workflows/ruby.yml

@@ -41,7 +41,6 @@ jobs:
         cp config/database.yml.example config/database.yml
         cp config/mailer.yml.example config/mailer.yml
         cp config/bunny.yml.example config/bunny.yml
-        cp config/env_constants.yml.example config/env_constants.yml
         bundle exec rake db:reset
     - name: Run tests
       env:

.gitignore

@@ -32,7 +32,6 @@
 config/database.yml
 config/mailer.yml
 config/bunny.yml
-config/env_constants.yml
 
 release.tar.gz
 

.rubocop.yml

@@ -1,27 +1,26 @@
-require: rubocop-rails
+inherit_from: .rubocop_todo.yml
+
+require:
+  - rubocop-rails
+  - rubocop-rspec
 
 AllCops:
   NewCops: enable
   Exclude:
     - db/schema.rb
     - db/seeds.rb
     - db/migrate/*
-    # Travis installs gems in the vendor directory, which causes rubocop to try
+    # GitHub actions installs gems in the vendor directory, which causes rubocop to try
     # and cop our gems. We don't want it to.
     - vendor/**/*
-    - 'test/**/*'
-    - 'spec/**/*'
     - 'config/routes.rb'
     - 'config/initializers/secret_token.rb'
     - 'config/initializers/backtrace_silencers.rb'
     - 'config/environments/*'
     - 'bin/*'
     - 'config/application.rb'
     - 'config/initializers/content_security_policy.rb'
-    # Exclude auto-generated GraphQL classes
-    - 'app/controllers/graphql_controller.rb'
-    - 'app/graphql/mutations/base_*'
-    - 'app/graphql/types/base_*'
+    - 'config/initializers/new_framework_defaults_7_0.rb'
 
 # The cop is meant to enforce conventions regarding variables containing numbers
 # However in 0.43.0 it is bugged. Both changed on master and disabled by default
@@ -49,6 +48,9 @@ Layout/LineLength:
   Max: 100
   Exclude:
     - 'lib/tasks/*'
+    # TODO: I have tried to add this to rubocop todo but it is causing all sorts of issues
+    # The maximum line length is 157.
+    - 'spec/**/*'
 
 Metrics/MethodLength:
   Max: 12
@@ -117,11 +119,6 @@ Style/RedundantFetchBlock:
 Style/CaseEquality:
   Exclude:
     - 'db/migrate/*'
-    - 'config/initializers/01_proc.rb'
-
-Rails/SkipsModelValidations:
-  Exclude:
-    - 'app/models/ont/plate_with_samples_factory.rb'
 
 Rails/EnvironmentVariableAccess:
   AllowReads: true

.rubocop_todo.yml

@@ -0,0 +1,142 @@
+# I addded this as spec was not being rubocopped. Due to the size of the task this is best
+# left until a later date.
+# This configuration was generated by
+# `rubocop --auto-gen-config`
+# on 2022-05-05 13:28:31 UTC using RuboCop version 1.28.2.
+# 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
+# Configuration parameters: IgnoredMethods.
+Lint/AmbiguousBlockAssociation:
+  Exclude:
+    - 'spec/pipelines/pipelines_spec.rb'
+    - 'spec/requests/v1/pacbio/libraries_spec.rb'
+
+# Offense count: 1
+# Configuration parameters: AllowComments, AllowEmptyLambdas.
+Lint/EmptyBlock:
+  Exclude:
+    - 'spec/factories/saphyr/runs.rb'
+
+# Offense count: 2
+Lint/ShadowingOuterLocalVariable:
+  Exclude:
+    - 'spec/requests/v1/pacbio/plates_spec.rb'
+
+# Offense count: 6
+Lint/UselessAssignment:
+  Exclude:
+    - 'spec/messages/message_spec.rb'
+    - 'spec/models/pacbio/run_spec.rb'
+    - 'spec/models/sample_spec.rb'
+    - 'spec/models/saphyr/run_spec.rb'
+    - 'spec/requests/v1/saphyr/runs_spec.rb'
+    - 'spec/support/tube_material.rb'
+
+# Offense count: 1
+# Configuration parameters: IgnoredMethods, CountRepeatedAttributes.
+Metrics/AbcSize:
+  Max: 32
+
+# Offense count: 2
+RSpec/AnyInstance:
+  Exclude:
+    - 'spec/models/pacbio/run_spec.rb'
+    - 'spec/support/read_only.rb'
+
+# Offense count: 194
+# Configuration parameters: Prefixes.
+# Prefixes: when, with, without
+RSpec/ContextWording:
+  Enabled: false
+
+# Offense count: 71
+# Configuration parameters: CountAsOne.
+RSpec/ExampleLength:
+  Max: 52
+
+# Offense count: 1
+# Configuration parameters: Include, CustomTransform, IgnoreMethods, SpecSuffixOnly.
+# Include: **/*_spec*rb*, **/spec/**/*
+RSpec/FilePath:
+  Exclude:
+    - 'spec/models/pacbio/well_pool.spec.rb'
+
+# Offense count: 1
+RSpec/IdenticalEqualityAssertion:
+  Exclude:
+    - 'spec/requests/v1/saphyr/chips_spec.rb'
+
+# Offense count: 52
+# Configuration parameters: AssignmentOnly.
+RSpec/InstanceVariable:
+  Exclude:
+    - 'spec/models/pacbio/library_factory_spec.rb'
+    - 'spec/requests/v1/pacbio/runs_spec.rb'
+    - 'spec/requests/v1/saphyr/runs_spec.rb'
+
+# Offense count: 18
+RSpec/LetSetup:
+  Exclude:
+    - 'spec/models/plate_spec.rb'
+    - 'spec/models/tube_spec.rb'
+    - 'spec/requests/v1/pacbio/libraries_spec.rb'
+    - 'spec/requests/v1/pacbio/pools_spec.rb'
+    - 'spec/requests/v1/pacbio/runs/plates_spec.rb'
+    - 'spec/requests/v1/pacbio/runs/wells_spec.rb'
+    - 'spec/requests/v1/pacbio/runs_spec.rb'
+    - 'spec/requests/v1/pacbio/tag_sets_spec.rb'
+    - 'spec/requests/v1/saphyr/libraries_spec.rb'
+    - 'spec/requests/v1/saphyr/runs_spec.rb'
+    - 'spec/support/tubes.rb'
+
+# Offense count: 25
+# Configuration parameters: .
+# SupportedStyles: have_received, receive
+RSpec/MessageSpies:
+  EnforcedStyle: receive
+
+# Offense count: 148
+RSpec/MultipleExpectations:
+  Max: 16
+
+# Offense count: 68
+# Configuration parameters: AllowSubject.
+RSpec/MultipleMemoizedHelpers:
+  Max: 14
+
+# Offense count: 64
+RSpec/NestedGroups:
+  Max: 6
+
+# Offense count: 4
+RSpec/RepeatedDescription:
+  Exclude:
+    - 'spec/models/sample_spec.rb'
+    - 'spec/pipelines/ont/message_spec.rb'
+
+# Offense count: 2
+RSpec/RepeatedExample:
+  Exclude:
+    - 'spec/models/sample_spec.rb'
+
+# Offense count: 5
+# Configuration parameters: IgnoreNameless, IgnoreSymbolicNames.
+RSpec/VerifiedDoubles:
+  Exclude:
+    - 'spec/messages/broker_spec.rb'
+
+# Offense count: 2
+Style/OpenStructUse:
+  Exclude:
+    - 'spec/messages/message_spec.rb'
+
+# Offense count: 1
+# Configuration parameters: AllowedMethods.
+# AllowedMethods: respond_to_missing?
+Style/OptionalBooleanParameter:
+  Exclude:
+    - 'spec/support/read_only.rb'

Gemfile

@@ -8,16 +8,13 @@ ruby '2.7.3'
 gem 'bootsnap', '>= 1.1.0', require: false # Reduces boot times through caching
 gem 'bunny'
 gem 'exception_notification'
-gem 'graphql'
-gem 'graphql-client'
-gem 'graphql-docs'
 # 0.10.5 Results in MySQL syntax error on several tests when run against a MySQL
 # There is a 'monkey patch' for this in config/intializers/jsonapi_resources:15-63
 gem 'jsonapi-resources'
 gem 'mysql2'
 gem 'puma', '~> 4.3' # Use Puma as the app server
 gem 'rack-cors' # Use Rack CORS for handling CORS, making cross-origin AJAX possible
-gem 'rails', '~> 6.0.4.1'
+gem 'rails', '~> 7.0.2.3'
 
 group :development do
   gem 'listen', '>= 3.0.5', '< 3.2'
@@ -37,7 +34,8 @@ group :development, :test do
   gem 'pry-rails'
   gem 'rspec-rails'
   gem 'rubocop', require: false
-  gem 'rubocop-rails'
+  gem 'rubocop-rails', require: false
+  gem 'rubocop-rspec', require: false
   gem 'shoulda-matchers'
   gem 'sqlite3'
 end