upgrade to ruby 3.1.4

.github/workflows/deploy.yml

@@ -17,10 +17,10 @@ jobs:
       ELASTIC_PASSWORD: ${{ secrets.RE3DATA_ES_PASSWORD }}
     steps:
       - uses: actions/checkout@v2
-      - name: Set up Ruby 2.7
+      - name: Set up Ruby 3.1.4
         uses: actions/setup-ruby@v1
         with:
-          ruby-version: '2.7.6'
+          ruby-version: '3.1.4'
       - uses: actions/cache@v2
         with:
           path: vendor/bundle

.github/workflows/pull_request.yml

@@ -13,10 +13,10 @@ jobs:
           - 11211/tcp
     steps:
       - uses: actions/checkout@v2
-      - name: Set up Ruby 2.7
+      - name: Set up Ruby 3.1.4
         uses: actions/setup-ruby@v1
         with:
-          ruby-version: '2.7.6'
+          ruby-version: '3.1.4'
       - uses: actions/cache@v2
         with:
           path: vendor/bundle

.github/workflows/release.yml

@@ -17,10 +17,10 @@ jobs:
       ELASTIC_PASSWORD: ${{ secrets.RE3DATA_ES_PASSWORD }}
     steps:
       - uses: actions/checkout@v2
-      - name: Set up Ruby 2.7
+      - name: Set up Ruby 3.1.4
         uses: actions/setup-ruby@v1
         with:
-          ruby-version: '2.7.6'
+          ruby-version: '3.1.4'
       - uses: actions/cache@v2
         with:
           path: vendor/bundle

.rubocop.yml

@@ -3,7 +3,7 @@ inherit_from: .rubocop_todo.yml
 # from https://github.com/rails/rails/blob/master/.rubocop.yml
 
 AllCops:
-  TargetRubyVersion: 2.5
+  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

Dockerfile

@@ -1,4 +1,4 @@
-FROM phusion/passenger-full:2.3.0
+FROM phusion/passenger-full:2.5.1
 LABEL maintainer="tech@datacite.org"
 
 # Set correct environment variables.
@@ -10,8 +10,8 @@ RUN usermod -a -G docker_env app
 # Use baseimage-docker's init process.
 CMD ["/sbin/my_init"]
 
-# Install Ruby 2.7.6
-RUN bash -lc 'rvm --default use ruby-2.7.6'
+# Install Ruby 3.1.4
+RUN bash -lc 'rvm --default use ruby-3.1.4'
 
 # Update installed APT packages
 RUN apt-get update -y -o Dpkg::Options::="--force-confold" && \
@@ -41,7 +41,7 @@ RUN mkdir -p /home/app/webapp/tmp/pids && \
 # Install Ruby gems
 WORKDIR /home/app/webapp
 RUN gem update --system && \
-    gem install bundler:2.3.20 && \
+    gem install bundler:2.5.6 && \
     /sbin/setuser app bundle config set --local path 'vendor/bundle' && \
     /sbin/setuser app bundle install
 

Gemfile

@@ -7,7 +7,7 @@ gem "dalli", "~> 2.7.6"
 gem 'lograge', '~> 0.5'
 gem 'sentry-raven', '~> 2.9'
 gem 'active_model_serializers', '~> 0.10.0'
-gem 'fast_jsonapi', '~> 1.3'
+gem 'jsonapi-serializer', '~> 2.2'
 gem 'kaminari', '~> 1.2'
 gem 'elasticsearch', '~> 1.1', '>= 1.1.3'
 gem 'elasticsearch-model', '~> 0.1.9', require: 'elasticsearch/model'
@@ -35,19 +35,19 @@ group :development, :test do
 end
 
 group :development do
-  gem 'listen', '>= 3.0.5', '< 3.2'
-  gem 'spring'
-  gem 'spring-watcher-listen', '~> 2.0.0'
+  gem 'listen', '~> 3.9'
+  gem 'spring', '~> 4.1', '>= 4.1.3'
   gem 'spring-commands-rspec'
+  gem 'spring-watcher-listen', '~> 2.1'
   # gem 'httplog', '~> 1.0'
 end
 
 group :test do
   gem 'capybara'
   gem 'webmock', '~> 3.1'
-  gem 'vcr', '~> 3.0.3'
+  gem 'vcr', '~> 6.1'
   gem 'codeclimate-test-reporter', '~> 1.0.0'
   gem 'simplecov'
   gem 'shoulda-matchers', '~> 3.1'
   gem 'elasticsearch-extensions'
-end
+end

Gemfile.lock

@@ -152,9 +152,7 @@ GEM
       faraday
     faraday_middleware (0.14.0)
       faraday (>= 0.7.4, < 1.0)
-    fast_jsonapi (1.5)
-      activesupport (>= 4.2)
-    ffi (1.15.5)
+    ffi (1.16.3)
     git (1.12.0)
       addressable (~> 2.8)
       rchardet (~> 1.8)
@@ -174,6 +172,8 @@ GEM
     ice_nine (0.11.2)
     json (2.6.2)
     jsonapi-renderer (0.2.2)
+    jsonapi-serializer (2.2.0)
+      activesupport (>= 4.2)
     kaminari (1.2.2)
       activesupport (>= 4.1.0)
       kaminari-actionview (= 1.2.2)
@@ -186,10 +186,9 @@ GEM
       activerecord
       kaminari-core (= 1.2.2)
     kaminari-core (1.2.2)
-    listen (3.1.5)
-      rb-fsevent (~> 0.9, >= 0.9.4)
-      rb-inotify (~> 0.9, >= 0.9.7)
-      ruby_dep (~> 1.2)
+    listen (3.9.0)
+      rb-fsevent (~> 0.10, >= 0.10.3)
+      rb-inotify (~> 0.9, >= 0.9.10)
     lograge (0.12.0)
       actionpack (>= 4)
       activesupport (>= 4)
@@ -265,7 +264,7 @@ GEM
       thor (~> 1.0)
     rainbow (3.1.1)
     rake (13.0.6)
-    rb-fsevent (0.11.1)
+    rb-fsevent (0.11.2)
     rb-inotify (0.10.1)
       ffi (~> 1.0)
     rchardet (1.8.0)
@@ -305,7 +304,6 @@ GEM
     rubocop-performance (1.3.0)
       rubocop (>= 0.68.0)
     ruby-progressbar (1.11.0)
-    ruby_dep (1.5.0)
     sentry-raven (2.13.0)
       faraday (>= 0.7.6, < 1.0)
     shoulda-matchers (3.1.3)
@@ -315,12 +313,12 @@ GEM
       json (>= 1.8, < 3)
       simplecov-html (~> 0.10.0)
     simplecov-html (0.10.2)
-    spring (2.1.1)
+    spring (4.2.1)
     spring-commands-rspec (1.0.4)
       spring (>= 0.9.1)
-    spring-watcher-listen (2.0.1)
+    spring-watcher-listen (2.1.0)
       listen (>= 2.7, < 4.0)
-      spring (>= 1.2, < 3.0)
+      spring (>= 4)
     sprockets (4.1.1)
       concurrent-ruby (~> 1.0)
       rack (> 1, < 3)
@@ -333,7 +331,7 @@ GEM
     tzinfo (2.0.5)
       concurrent-ruby (~> 1.0)
     unicode-display_width (2.2.0)
-    vcr (3.0.3)
+    vcr (6.2.0)
     virtus (2.0.0)
       axiom-types (~> 0.1)
       coercible (~> 1.0)
@@ -369,15 +367,15 @@ DEPENDENCIES
   elasticsearch-model (~> 0.1.9)
   elasticsearch-persistence (~> 0.1.9)
   elasticsearch-rails (~> 0.1.9)
-  fast_jsonapi (~> 1.3)
   git (~> 1.5)
   google-protobuf (~> 3.0)
   graphql (~> 1.9, >= 1.9.4)
   graphql-batch (~> 0.4.0)
   graphql-cache (~> 0.6.0)!
   graphql-errors (~> 0.3.0)
+  jsonapi-serializer (~> 2.2)
   kaminari (~> 1.2)
-  listen (>= 3.0.5, < 3.2)
+  listen (~> 3.9)
   lograge (~> 0.5)
   maremma (>= 4.1)
   rack-cors (~> 1.0)
@@ -388,11 +386,11 @@ DEPENDENCIES
   sentry-raven (~> 2.9)
   shoulda-matchers (~> 3.1)
   simplecov
-  spring
+  spring (~> 4.1, >= 4.1.3)
   spring-commands-rspec
-  spring-watcher-listen (~> 2.0.0)
-  vcr (~> 3.0.3)
+  spring-watcher-listen (~> 2.1)
+  vcr (~> 6.1)
   webmock (~> 3.1)
 
 BUNDLED WITH
-   2.3.20
+   2.5.6

app/controllers/re3data_controller.rb

@@ -12,7 +12,7 @@ def index
            end
 
     page = params[:page] || {}
-    if page[:size].present? 
+    if page[:size].present?
       page[:size] = [page[:size].to_i, 1000].min
       max_number = page[:size] > 0 ? 10000/page[:size] : 1
     else
@@ -26,11 +26,11 @@ def index
     elsif params[:ids].present?
       response = Repository.find_by_id(params[:ids], page: page, sort: sort)
     else
-      response = Repository.query(params[:query], 
-        page: page, 
-        sort: sort, 
+      response = Repository.query(params[:query],
+        page: page,
+        sort: sort,
         subject: params[:subject],
-        open: params[:open], 
+        open: params[:open],
         certified: params[:certified],
         pid: params[:pid],
         software: params[:software],
@@ -59,7 +59,7 @@ def index
       }.compact
     options[:is_collection] = true
 
-    render json: Re3dataSerializer.new(@repositories, options).serialized_json, status: :ok
+    render json: Re3dataSerializer.new(@repositories, options).serializable_hash.to_json, status: :ok
   rescue Elasticsearch::Transport::Transport::Errors::LengthRequired
     render json: []
   end
@@ -68,7 +68,7 @@ def show
     options = {}
     options[:is_collection] = false
 
-    render json: Re3dataSerializer.new(@repository, options).serialized_json, status: :ok
+    render json: Re3dataSerializer.new(@repository, options).serializable_hash.to_json, status: :ok
   end
 
   def suggest

app/serializers/re3data_serializer.rb

@@ -1,10 +1,10 @@
 class Re3dataSerializer
-  include FastJsonapi::ObjectSerializer
+  include JSONAPI::Serializer
   set_key_transform :camel_lower
   set_type :re3data
 
-  attributes :re3data_id, :repositoryName, :repositoryUrl, :repositoryContacts, :description, :repositoryLanguages, :certificates, :types, 
-    :additionalNames, :subjects, :contentTypes, :providerTypes, 
+  attributes :re3data_id, :repositoryName, :repositoryUrl, :repositoryContacts, :description, :repositoryLanguages, :certificates, :types,
+    :additionalNames, :subjects, :contentTypes, :providerTypes,
     :keywords, :institutions, :dataAccesses, :dataUploads, :dataUploadLicenses, :pidSystems,
     :apis, :pidSystems, :software, :startDate, :endDate, :created, :updated
 
@@ -23,4 +23,4 @@ class Re3dataSerializer
   attribute :updated do |object|
     object.updated.strftime("%FT%TZ")
   end
-end
+end

config/initializers/serialization_core.rb

@@ -0,0 +1,52 @@
+# frozen_string_literal: true
+
+# Monkey patch for jsonapi-serializer gem
+
+module FastJsonapi
+  module SerializationCore
+    class_methods do
+      def get_included_records(record, includes_list, known_included_objects, fieldsets, params = {})
+        return unless includes_list.present?
+        return [] unless relationships_to_serialize
+
+        includes_list = parse_includes_list(includes_list)
+
+        includes_list.each_with_object([]) do |include_item, included_records|
+          relationship_item = relationships_to_serialize[include_item.first]
+
+          next unless relationship_item&.include_relationship?(record, params)
+
+          associated_objects = relationship_item.fetch_associated_object(record, params)
+
+          if associated_objects.is_a?(Elasticsearch::Model::HashWrapper)
+            associated_objects = OpenStruct.new(associated_objects)
+          end
+
+          included_objects = Array(associated_objects)
+
+          next if included_objects.empty?
+
+          static_serializer = relationship_item.static_serializer
+          static_record_type = relationship_item.static_record_type
+
+          included_objects.each do |inc_obj|
+            serializer = static_serializer || relationship_item.serializer_for(inc_obj, params)
+            record_type = static_record_type || serializer.record_type
+
+            if include_item.last.any?
+              serializer_records = serializer.get_included_records(inc_obj, include_item.last, known_included_objects, fieldsets, params)
+              included_records.concat(serializer_records) unless serializer_records.empty?
+            end
+
+            code = "#{record_type}_#{serializer.id_from_record(inc_obj, params)}"
+            next if known_included_objects.include?(code)
+
+            known_included_objects << code
+
+            included_records << serializer.record_hash(inc_obj, fieldsets[record_type], includes_list, params)
+          end
+        end
+      end
+    end
+  end
+end

docker-compose.local.yml

@@ -0,0 +1,5 @@
+version: "2.1"
+
+services:
+  web:
+    build: .