upgrade to ruby 3.1.4 (#160)

* upgrade to ruby 3.1.4

* update the rubocop ruby version

* bump google protobuf gem version up

* disable rubocop style

* remove dockerfile entry

* disable rubocop check

* appease our rubocop overlords

* rework error serializer due to deprecation warning

* fix spec

* fix spec

* fix spec

* fix specs. fix json serialization. upgrade postrank gem.

* bump the vcr gem version up

* configure passenger

---------

Co-authored-by: Wendel Fabian Chinsamy <[email protected]>

.github/workflows/ci.yml

@@ -57,10 +57,10 @@ jobs:
       JWT_PUBLIC_KEY: ${{ secrets.JWT_PUBLIC_KEY }}
     steps:
       - uses: actions/checkout@v3
-      - name: Set up Ruby 2.6
+      - name: Set up Ruby 3.1.4
         uses: ruby/setup-ruby@v1
         with:
-          ruby-version: 2.6
+          ruby-version: 3.1.4
       - uses: actions/cache@v2
         with:
           path: vendor/bundle

.rubocop.yml

@@ -5,7 +5,7 @@ require:
   - rubocop-rspec
 
 AllCops:
-  TargetRubyVersion: 2.6
+  TargetRubyVersion: 3.1
   # RuboCop has a bunch of cops enabled by default. This setting tells RuboCop
   # to ignore them, so only the ones explicitly set in this file are enabled.
   DisabledByDefault: true
@@ -89,7 +89,7 @@ Layout/EmptyLinesAroundModuleBody:
 
 # Use Ruby >= 1.9 syntax for hashes. Prefer { a: :b } over { :a => :b }.
 Style/HashSyntax:
-  Enabled: true
+  Enabled: false
 
 Layout/FirstArgumentIndentation:
   Enabled: true

Dockerfile

@@ -1,4 +1,4 @@
-FROM phusion/passenger-full:2.0.0
+FROM phusion/passenger-full:2.5.1
 LABEL maintainer="[email protected]"
 
 # Set correct environment variables
@@ -15,8 +15,8 @@ RUN groupmod -g 1000 app
 # Use baseimage-docker's init process
 CMD ["/sbin/my_init"]
 
-# Use Ruby 2.6.8
-RUN bash -lc 'rvm --default use ruby-2.6.8'
+# Use Ruby 3.1.4
+RUN bash -lc 'rvm --default use ruby-3.1.4'
 
 # Set debconf to run non-interactively
 RUN echo 'debconf debconf/frontend select Noninteractive' | debconf-set-selections

Gemfile

@@ -14,7 +14,10 @@ gem "aws-sdk-sqs", "~> 1.23", ">= 1.23.1"
 gem "base32-crockford-checksum", "~> 0.2.3"
 gem "config", "~> 2.2", ">= 2.2.1"
 gem "dotenv", "~> 2.7", ">= 2.7.5"
-gem "fast_jsonapi", "~> 1.5"
+# IMPORTANT!!!
+# We have monkey patched this gem -> config/initializers/serialization_core.rb
+# Please check this before upgrading/downgrading versions
+gem "jsonapi-serializer", "~> 2.2"
 gem "flipper", "~> 0.17.2"
 gem "flipper-active_support_cache_store"
 gem "flipper-api"
@@ -24,7 +27,7 @@ gem "nilify_blanks", "~> 1.3"
 gem "oj", ">= 2.8.3"
 gem "oj_mimic_json", "~> 1.0", ">= 1.0.1"
 gem "orcid_client", "~> 0.11.0"
-gem "postrank-uri", "~> 1.0", ">= 1.0.24"
+gem "postrank-uri", "~> 1.1"
 gem "pwqgen.rb", "~> 0.1.0"
 gem "rake", "~> 12.0"
 gem "sentry-raven", "~> 2.13"
@@ -66,7 +69,7 @@ gem "elasticsearch", "~> 7.1.0"
 gem "elasticsearch-model", "~> 7.0", require: "elasticsearch/model"
 gem "elasticsearch-rails", "~> 7.0"
 gem "faraday_middleware-aws-sigv4", "~> 0.2.4"
-gem "google-protobuf", "3.10.0.rc.1"
+gem "google-protobuf", "3.19.6"
 gem "graphql", "~> 1.9", ">= 1.9.16"
 gem "graphql-batch", "~> 0.4.1"
 gem "graphql-cache", "~> 0.6.0"
@@ -102,7 +105,6 @@ group :development do
   gem "spring"
   gem "spring-commands-rspec"
   gem "spring-watcher-listen", "~> 2.0.0"
-  # gem "httplog", "~> 1.0"
 end
 
 group :test do
@@ -117,7 +119,7 @@ group :test do
   gem "shoulda-matchers", "~> 4.1", ">= 4.1.2"
   gem "simplecov", "~> 0.17.1"
   gem "test-prof", "~> 0.10.2"
-  gem "vcr", "~> 3.0.3"
+  gem "vcr", "~> 6.2"
   gem "webmock", "~> 3.1"
   gem "with_env", "~> 1.1"
 end

Gemfile.lock

@@ -289,8 +289,6 @@ GEM
     faraday_middleware-aws-sigv4 (0.2.4)
       aws-sigv4 (~> 1.0)
       faraday (>= 0.9)
-    fast_jsonapi (1.5)
-      activesupport (>= 4.2)
     ferrum (0.11)
       addressable (~> 2.5)
       cliver (~> 0.3)
@@ -318,7 +316,7 @@ GEM
       rchardet (~> 1.8)
     globalid (1.2.1)
       activesupport (>= 6.1)
-    google-protobuf (3.10.0.rc.1)
+    google-protobuf (3.19.6)
     graphql (1.12.16)
     graphql-batch (0.4.3)
       graphql (>= 1.3, < 2)
@@ -352,6 +350,8 @@ GEM
       json-ld (~> 3.2)
       rdf (~> 3.2)
     jsonapi-renderer (0.2.2)
+    jsonapi-serializer (2.2.0)
+      activesupport (>= 4.2)
     jsonlint (0.3.0)
       oj (~> 3)
       optimist (~> 3)
@@ -372,10 +372,9 @@ GEM
     launchy (2.5.0)
       addressable (~> 2.7)
     link_header (0.0.8)
-    listen (3.1.5)
+    listen (3.0.8)
       rb-fsevent (~> 0.9, >= 0.9.4)
       rb-inotify (~> 0.9, >= 0.9.7)
-      ruby_dep (~> 1.2)
     lograge (0.11.2)
       actionpack (>= 4)
       activesupport (>= 4)
@@ -479,12 +478,12 @@ GEM
     parallel (1.22.1)
     parser (3.1.2.1)
       ast (~> 2.4.1)
-    postrank-uri (1.0.24)
+    postrank-uri (1.1)
       addressable (>= 2.4.0)
       nokogiri (>= 1.8.0)
-      public_suffix (>= 2.0.0, < 2.1)
+      public_suffix (>= 4.0.0, < 5)
     promise.rb (0.7.4)
-    public_suffix (2.0.5)
+    public_suffix (4.0.7)
     pwqgen.rb (0.1.0)
       docopt (~> 0.5)
       sysrandom
@@ -615,7 +614,6 @@ GEM
     ruby-enum (0.9.0)
       i18n
     ruby-progressbar (1.11.0)
-    ruby_dep (1.5.0)
     ruby_dig (0.0.2)
     scanf (1.0.0)
     sentry-raven (2.13.0)
@@ -675,7 +673,7 @@ GEM
     unicode_utils (1.4.0)
     validates_email_format_of (1.6.3)
       i18n
-    vcr (3.0.3)
+    vcr (6.2.0)
     warden (1.2.9)
       rack (>= 2.0.9)
     webmock (3.14.0)
@@ -725,21 +723,21 @@ DEPENDENCIES
   email_spec (~> 2.2)
   factory_bot_rails (~> 4.8, >= 4.8.2)
   faraday_middleware-aws-sigv4 (~> 0.2.4)
-  fast_jsonapi (~> 1.5)
   flipper (~> 0.17.2)
   flipper-active_support_cache_store
   flipper-api
   flipper-redis
   flipper-ui
   git (~> 1.5)
-  google-protobuf (= 3.10.0.rc.1)
+  google-protobuf (= 3.19.6)
   graphql (~> 1.9, >= 1.9.16)
   graphql-batch (~> 0.4.1)
   graphql-cache (~> 0.6.0)
   graphql-errors (~> 0.4.0)
   gravtastic (~> 3.2, >= 3.2.6)
   hashdiff (>= 1.0.0.beta1, < 2.0.0)
   hashie
+  jsonapi-serializer (~> 2.2)
   jwt (~> 2.2, >= 2.2.1)
   kaminari (~> 1.2)
   listen (>= 3.0.5, < 3.2)
@@ -762,7 +760,7 @@ DEPENDENCIES
   omniauth-orcid (~> 2.0)
   omniauth-rails_csrf_protection (~> 1.0)
   orcid_client (~> 0.11.0)
-  postrank-uri (~> 1.0, >= 1.0.24)
+  postrank-uri (~> 1.1)
   pwqgen.rb (~> 0.1.0)
   rack-cors (~> 1.0)
   rack-jwt
@@ -795,9 +793,9 @@ DEPENDENCIES
   tzinfo-data (~> 1.2019, >= 1.2019.3)
   uglifier (~> 2.7, >= 2.7.2)
   validates_email_format_of (~> 1.6, >= 1.6.3)
-  vcr (~> 3.0.3)
+  vcr (~> 6.2)
   webmock (~> 3.1)
   with_env (~> 1.1)
 
 BUNDLED WITH
-   2.4.22
+   2.4.22

app/controllers/claims_controller.rb

@@ -12,7 +12,7 @@ def show
     options[:include] = @include
     options[:is_collection] = false
 
-    render json: ClaimSerializer.new(@claim, options).serialized_json, status: :ok
+    render json: ClaimSerializer.new(@claim, options).serializable_hash.to_json, status: :ok
   end
 
   def index
@@ -84,9 +84,9 @@ def index
 
       fields = fields_from_params(params)
       if fields
-        render json: ClaimSerializer.new(response.results, options.merge(fields: fields)).serialized_json, status: :ok
+        render json: ClaimSerializer.new(response.results, options.merge(fields: fields)).serializable_hash.to_json, status: :ok
       else
-        render json: ClaimSerializer.new(response.results, options).serialized_json, status: :ok
+        render json: ClaimSerializer.new(response.results, options).serializable_hash.to_json, status: :ok
       end
     rescue Elasticsearch::Transport::Transport::Errors::BadRequest => e
       Raven.capture_exception(e)
@@ -112,13 +112,12 @@ def create
     end
 
     if @claim.save
-
       @claim.queue_claim_job
 
       options = {}
       options[:include] = @include
       options[:is_collection] = false
-      render json: ClaimSerializer.new(@claim, options).serialized_json, status: :accepted
+      render json: ClaimSerializer.new(@claim, options).serializable_hash.to_json, status: :accepted
     else
       logger.error @claim.errors.inspect
       render json: serialize_errors(@claim.errors), include: @include, status: :unprocessable_entity
@@ -137,7 +136,7 @@ def destroy
         options = {}
         options[:include] = @include
         options[:is_collection] = false
-        render json: ClaimSerializer.new(@claim, options).serialized_json, status: :accepted
+        render json: ClaimSerializer.new(@claim, options).serializable_hash.to_json, status: :accepted
       else
         logger.error @claim.errors.inspect
         render json: serialize_errors(@claim.errors), include: @include, status: :unprocessable_entity

app/controllers/concerns/error_serializable.rb

@@ -4,20 +4,25 @@ module ErrorSerializable
   extend ActiveSupport::Concern
 
   included do
-    def serialize_errors(errors)
+    def serialize_errors(errors, options = {})
       return nil if errors.nil?
 
-      arr = Array.wrap(errors).reduce([]) do |sum, err|
-        source = err.keys.first
+      errors_arr = []
 
-        Array.wrap(err.values.first).each do |title|
-          sum << { source: source, title: title.is_a?(String) ? title.capitalize : title.to_s }
+      errors.each do |err|
+        unless errors_arr.any? { |e| e[:source] == err.attribute }
+          new_err = { source: err.attribute, title: capitalize_error_message(err) }
+          new_err[:uid] = options[:uid] if options[:uid].present?
+          errors_arr << new_err
         end
-
-        sum
       end
 
-      { errors: arr }.to_json
+      { errors: errors_arr }.to_json
     end
   end
+
+  private
+    def capitalize_error_message(error)
+      error.message.sub(/^./, &:upcase)
+    end
 end

app/controllers/users_controller.rb

@@ -30,7 +30,7 @@ def show
     options[:is_collection] = false
     options[:params] = { current_ability: current_ability }
 
-    render json: UserSerializer.new(@user, options).serialized_json, status: :ok
+    render json: UserSerializer.new(@user, options).serializable_hash.to_json, status: :ok
   end
 
   def index
@@ -78,9 +78,9 @@ def index
 
       fields = fields_from_params(params)
       if fields
-        render json: UserSerializer.new(response.results, options.merge(fields: fields)).serialized_json, status: :ok
+        render json: UserSerializer.new(response.results, options.merge(fields: fields)).serializable_hash.to_json, status: :ok
       else
-        render json: UserSerializer.new(response.results, options).serialized_json, status: :ok
+        render json: UserSerializer.new(response.results, options).serializable_hash.to_json, status: :ok
       end
     rescue Elasticsearch::Transport::Transport::Errors::BadRequest => e
       Raven.capture_exception(e)
@@ -98,7 +98,7 @@ def create
     if @user.save
       options = {}
       options[:is_collection] = false
-      render json: UserSerializer.new(@user, options).serialized_json, status: :created
+      render json: UserSerializer.new(@user, options).serializable_hash.to_json, status: :created
     else
       logger.error @user.errors.inspect
       render json: serialize_errors(@user.errors), status: :unprocessable_entity
@@ -122,7 +122,7 @@ def update
     if @user.save
       options = {}
       options[:is_collection] = false
-      render json: UserSerializer.new(@user, options).serialized_json, status: status
+      render json: UserSerializer.new(@user, options).serializable_hash.to_json, status: status
     else
       logger.error @user.errors.inspect
       render json: serialize_errors(@user.errors), status: :unprocessable_entity

app/serializers/claim_serializer.rb

@@ -1,7 +1,7 @@
 # frozen_string_literal: true
 
 class ClaimSerializer
-  include FastJsonapi::ObjectSerializer
+  include JSONAPI::Serializer
   set_key_transform :camel_lower
   set_type :claims
   set_id :uuid

app/serializers/user_serializer.rb

@@ -1,7 +1,7 @@
 # frozen_string_literal: true
 
 class UserSerializer
-  include FastJsonapi::ObjectSerializer
+  include JSONAPI::Serializer
   set_key_transform :camel_lower
   set_type :users
   set_id :uid

config/initializers/constants.rb

@@ -20,10 +20,10 @@
 
 # Format used for DOI validation
 # The prefix is 10.x where x is 4-5 digits. The suffix can be anything, but can"t be left off
-DOI_FORMAT = %r(\A10\.\d{4,5}/.+).freeze
+DOI_FORMAT = %r(\A10\.\d{4,5}/.+)
 
 # Format used for URL validation
-URL_FORMAT = %r(\A(http|https|ftp):\/\/[a-z0-9]+([\-\.]{1}[a-z0-9]+)*\.[a-z]{2,5}(([0-9]{1,5})?\/.*)?\z).freeze
+URL_FORMAT = %r(\A(http|https|ftp):\/\/[a-z0-9]+([\-\.]{1}[a-z0-9]+)*\.[a-z]{2,5}(([0-9]{1,5})?\/.*)?\z)
 
 # Form queue options
 QUEUE_OPTIONS = ["high", "default", "low"].freeze