Add support for Ruby 4 [Traction]

.github/workflows/ruby.yml

@@ -2,78 +2,38 @@ name: CI
 
 on:
   push:
-    branches: [ 'master', 'release-0-8', 'release-0-9', 'release-0-10' ]
+    branches: ["master"]
   pull_request:
-    branches: ['**']
+    branches: ["**"]
 
 jobs:
   tests:
     runs-on: ubuntu-latest
-    services:
-      postgres:
-        image: postgres
-        env:
-          POSTGRES_PASSWORD: password
-          POSTGRES_DB: test
-        options: >-
-          --health-cmd pg_isready
-          --health-interval 10s
-          --health-timeout 5s
-          --health-retries 5
-        ports:
-          - 5432:5432
     strategy:
       fail-fast: false
       matrix:
         ruby:
-          - 2.6
-          - 2.7
-          - '3.0'
-          - 3.1
-          - 3.2
+          - "3.2"
+          - "3.3"
+          - "3.4"
+          - "4.0"
         rails:
-          - 7.0.4
-          - 6.1.7
-          - 6.0.6
-          - 5.2.8.1
-          - 5.1.7
+          - "7.1"
+          - "7.2"
+          - "8.0"
+          - "8.1"
         database_url:
-          - postgresql://postgres:password@localhost:5432/test
           - sqlite3:test_db
-        exclude:
-          - ruby: 3.2
-            rails: 6.0.6
-          - ruby: 3.2
-            rails: 5.2.8.1
-          - ruby: 3.2
-            rails: 5.1.7
-          - ruby: 3.1
-            rails: 6.0.6
-          - ruby: 3.1
-            rails: 5.2.8.1
-          - ruby: 3.1
-            rails: 5.1.7
-          - ruby: '3.0'
-            rails: 6.0.6
-          - ruby: '3.0'
-            rails: 5.2.8.1
-          - ruby: '3.0'
-            rails: 5.1.7
-          - ruby: 2.6
-            rails: 7.0.4
-          - database_url: postgresql://postgres:password@localhost:5432/test
-            rails: 5.1.7
     env:
       RAILS_VERSION: ${{ matrix.rails }}
       DATABASE_URL: ${{ matrix.database_url }}
     name: Ruby ${{ matrix.ruby }} Rails ${{ matrix.rails }} DB ${{ matrix.database_url }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v7
       - name: Set up Ruby
         uses: ruby/setup-ruby@v1
         with:
           ruby-version: ${{ matrix.ruby }}
-      - name: Install dependencies
-        run: bundle install --jobs 4 --retry 3
+          bundler-cache: true
       - name: Run tests
         run: bundle exec rake test

.gitignore

@@ -21,5 +21,6 @@ coverage
 test/log
 test_db
 test_db-journal
+test/test_db-*
 .idea
 *.iml

CONTRIBUTING.md

@@ -0,0 +1,30 @@
+# Contributing
+
+All contributions to this project are subject to the [MIT License](https://foss-haas.mit-license.org/). By submitting a contribution, you agree to license your work under these terms.
+
+## Contribution Process
+
+### 1. Issue First
+
+All contributions from outside the core team require an **Issue First** approach. Before submitting a pull request (PR), you must:
+
+- Open an issue in the repository.
+- Ensure the issue includes:
+  - **Clear problem statement:** Describe the issue or feature request.
+  - **Reproduction steps:** If reporting a bug, provide steps to reproduce it.
+  - **Proposed approach:** Outline your suggested solution or implementation.
+  - **Why this change matters:** Explain the impact or necessity of the change.
+- Tag `@sanger/psd-developers` in the issue to bring it to the attention of a maintainer.
+- Wait for the issue to be assigned or approved by a maintainer.
+
+### 2. Pull Request
+
+Once your issue is approved:
+
+- Fork the repository and create a branch for your changes.
+- Submit a PR referencing the approved issue.
+- Ensure your code adheres to the project's coding standards and passes all tests.
+
+### 3. Review
+
+Maintainers will review your PR. Address any feedback before merging.

Gemfile

@@ -7,23 +7,22 @@ platforms :jruby do
 end
 
 version = ENV['RAILS_VERSION'] || 'default'
+# If version is like 'x.y' add a '.0' to make it 'x.y.0' for correct resolution
+version = "#{version}.0" if version =~ /^\d+\.\d+$/
 
 platforms :ruby do
   gem 'pg'
-
-  if version.start_with?('4.2', '5.0')
-    gem 'sqlite3', '~> 1.3.13'
-  else
-    gem 'sqlite3', '~> 1.4'
-  end
+  gem 'mysql2'
+  gem 'sqlite3'
+  gem 'csv'
 end
 
 case version
 when 'master'
   gem 'railties', { git: 'https://github.com/rails/rails.git' }
   gem 'arel', { git: 'https://github.com/rails/arel.git' }
 when 'default'
-  gem 'railties', '>= 6.0'
+  gem 'railties', '~> 8.1.0'
 else
   gem 'railties', "~> #{version}"
-end
+end

README.md

@@ -1,6 +1,4 @@
-# JSONAPI::Resources [![Gem Version](https://badge.fury.io/rb/jsonapi-resources.svg)](https://badge.fury.io/rb/jsonapi-resources) [![Build Status](https://secure.travis-ci.org/cerebris/jsonapi-resources.svg?branch=master)](http://travis-ci.org/cerebris/jsonapi-resources) [![Code Climate](https://codeclimate.com/github/cerebris/jsonapi-resources/badges/gpa.svg)](https://codeclimate.com/github/cerebris/jsonapi-resources)
-
-[![Join the chat at https://gitter.im/cerebris/jsonapi-resources](https://badges.gitter.im/Join%20Chat.svg)](https://gitter.im/cerebris/jsonapi-resources?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
+# JSONAPI::Resources (Sanger fork)
 
 `JSONAPI::Resources`, or "JR", provides a framework for developing an API server that complies with the
 [JSON:API](http://jsonapi.org/) specification.
@@ -13,7 +11,7 @@ backed by ActiveRecord models or by custom objects.
 
 ## Documentation
 
-Full documentation can be found at [http://jsonapi-resources.com](http://jsonapi-resources.com), including the [v0.10 alpha Guide](http://jsonapi-resources.com/v0.10/guide/) specific to this version. 
+Full documentation can be found at [http://jsonapi-resources.com](http://jsonapi-resources.com), including the [v0.10 alpha Guide](http://jsonapi-resources.com/v0.10/guide/) specific to this version.
 
 ## Demo App
 
@@ -22,54 +20,74 @@ We have a simple demo app, called [Peeps](https://github.com/cerebris/peeps), av
 ## Client Libraries
 
 JSON:API maintains a (non-verified) listing of [client libraries](http://jsonapi.org/implementations/#client-libraries)
-which *should* be compatible with JSON:API compliant server implementations such as JR.
+which _should_ be compatible with JSON:API compliant server implementations such as JR.
 
 ## Installation
 
 Add JR to your application's `Gemfile`:
 
-``` 
+```
 gem 'jsonapi-resources'
 ```
 
 And then execute:
 
-```bash 
+```bash
 bundle
 ```
 
 Or install it yourself as:
 
-```bash 
+```bash
 gem install jsonapi-resources
 ```
 
 **For further usage see the [v0.10 alpha Guide](http://jsonapi-resources.com/v0.10/guide/)**
 
-## Contributing
+## Sanger-specific release process
+
+There are two versions of the gem which we use for production. The version 1 series has unique customisations and is used by Sequencescape. The version 2 series is a more generic version which is used by Traction.
+
+The aim is to support the 3 most recent Rails versions for each series to allow for seamless upgrades between releases.
 
-1. Submit an issue describing any new features you wish it add or the bug you intend to fix
-1. Fork it ( http://github.com/cerebris/jsonapi-resources/fork )
-1. Create your feature branch (`git checkout -b my-new-feature`)
-1. Run the full test suite (`rake test`)
-1. Fix any failing tests
-1. Commit your changes (`git commit -am 'Add some feature'`)
-1. Push to the branch (`git push origin my-new-feature`)
-1. Create a new Pull Request
+Check which versions we have published at https://rubygems.org/gems/sanger-jsonapi-resources
 
-## Did you find a bug?
+### For version 1 series
 
-* **Ensure the bug was not already reported** by searching on GitHub under [Issues](https://github.com/cerebris/jsonapi-resources/issues).
+- Create a branch from **develop**, apply fixes.
+- Change version number in `lib/jsonapi/resources/version.rb` . This file is read by the gemspec during publication.
+- Test Sequencescape with the gem from the branch.
+- Merge the branch into develop.
+- Create a release from the develop branch with the new version number as the tag. Set Release label to _None_.
+<!-- list separator -->
+- Checkout the newly-created tag on develop.
+- Execute `bundle install` to ensure the gemspec is up to date.
+- Execute `gem build jsonapi-resources.gemspec` which builds sanger-jsonapi-resources-0.1.x.gem in this case.
+- Execute `gem push sanger-jsonapi-resources-0.1.x.gem` which publishes the gem.
 
-* If you're unable to find an open issue addressing the problem, [open a new one](https://github.com/cerebris/jsonapi-resources/issues/new). 
-Be sure to include a **title and clear description**, as much relevant information as possible, 
-and a **code sample** or an **executable test case** demonstrating the expected behavior that is not occurring.
+### For version 2 series
 
-* If possible, use the relevant bug report templates to create the issue. 
-Simply copy the content of the appropriate template into a .rb file, make the necessary changes to demonstrate the issue, 
-and **paste the content into the issue description or attach as a file**:
-  * [**Rails 5** issues](https://github.com/cerebris/jsonapi-resources/blob/master/lib/bug_report_templates/rails_5_master.rb)
+- Create a branch from **master**, apply fixes.
+- Change version number in `lib/jsonapi/resources/version.rb` . This file is read by the gemspec during publication.
+- Test Traction with the gem from the branch.
+- Merge the branch into master.
+- Create a release from the master branch with the new version number as the tag. Set Release label to _Latest_.
+<!-- list separator -->
+- Checkout the newly-created tag on master.
+- Execute `bundle install` to ensure the gemspec is up to date.
+- Execute `gem build jsonapi-resources.gemspec` which builds sanger-jsonapi-resources-0.2.x.gem in this case.
+- Execute `gem push sanger-jsonapi-resources-0.2.x.gem` which publishes the gem.
+
+### Publication
+
+You will be notified by email for each. You will also receive one email for API key setup. The first push will ask email and password for the account, which are in KeePass (search for "gem").
+
+> [!NOTE]
+> The email and password for gem publication is a recent addition to the credentials database. Pull latest changes in the credentials repo.
+
+## Contributing
 
+See CONTRIBUTING.md for details.
 
 ## License
 

Rakefile

@@ -1,13 +1,20 @@
 #!/usr/bin/env rake
 require 'bundler/gem_tasks'
+require 'fileutils'
 require 'rake/testtask'
 
+task :remove_test_db do
+  FileUtils.rm_f(File.expand_path('test/test_db', __dir__))
+end
+
 Rake::TestTask.new do |t|
-  t.verbose = true
+  t.verbose = false
   t.warning = false
   t.test_files = FileList['test/**/*_test.rb']
 end
 
+Rake::Task[:test].enhance([:remove_test_db])
+
 task default: [:test]
 
 desc 'Run benchmarks'

jsonapi-resources.gemspec

@@ -4,30 +4,33 @@ $LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
 require 'jsonapi/resources/version'
 
 Gem::Specification.new do |spec|
-  spec.name          = 'jsonapi-resources'
+  spec.name          = 'sanger-jsonapi-resources'
   spec.version       = JSONAPI::Resources::VERSION
-  spec.authors       = ['Dan Gebhardt', 'Larry Gebhardt']
-  spec.email         = ['dan@cerebris.com', 'larry@cerebris.com']
+  spec.authors       = ['PSD Team - Wellcome Trust Sanger Institute']
+  spec.email         = ['psd@sanger.ac.uk']
   spec.summary       = 'Easily support JSON API in Rails.'
-  spec.description   = 'A resource-centric approach to implementing the controllers, routes, and serializers needed to support the JSON API spec.'
-  spec.homepage      = 'https://github.com/cerebris/jsonapi-resources'
+  spec.description   = 'Forked from jsonapi-resources. A resource-centric approach to implementing the controllers, routes, and serializers needed to support the JSON API spec.'
+  spec.homepage      = 'https://github.com/sanger/jsonapi-resources'
   spec.license       = 'MIT'
 
   spec.files         = Dir.glob("{bin,lib}/**/*") + %w(LICENSE.txt README.md)
   spec.executables   = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
   spec.test_files    = spec.files.grep(%r{^(test|spec|features)/})
   spec.require_paths = ['lib']
-  spec.required_ruby_version = '>= 2.3'
+  spec.required_ruby_version = '>= 3.2'
 
   spec.add_development_dependency 'bundler', '>= 1.17'
   spec.add_development_dependency 'rake'
-  spec.add_development_dependency 'minitest', '~> 5.10', '!= 5.10.2'
+  spec.add_development_dependency 'minitest'
+  spec.add_development_dependency 'minitest-mock'
   spec.add_development_dependency 'minitest-spec-rails'
+  spec.add_development_dependency 'minitest-reporters'
   spec.add_development_dependency 'simplecov'
   spec.add_development_dependency 'pry'
   spec.add_development_dependency 'concurrent-ruby-ext'
   spec.add_development_dependency 'database_cleaner'
-  spec.add_dependency 'activerecord', '>= 5.1'
-  spec.add_dependency 'railties', '>= 5.1'
+  spec.add_dependency 'activerecord', '>= 7.1', '< 9.0' # versions 7.1, 7.2, 8.0, 8.1, and above, but not 9.0
+  spec.add_dependency 'railties', '>= 7.1', '< 9.0' # versions 7.1, 7.2, 8.0, 8.1, and above, but not 9.0
+  spec.add_dependency 'rack', '~> 3.0'
   spec.add_dependency 'concurrent-ruby'
 end

lib/generators/jsonapi/controller_generator.rb

@@ -1,3 +1,4 @@
+require 'rails/generators'
 module Jsonapi
   class ControllerGenerator < Rails::Generators::NamedBase
     source_root File.expand_path('../templates', __FILE__)

lib/generators/jsonapi/resource_generator.rb

@@ -1,3 +1,4 @@
+require 'rails/generators'
 module Jsonapi
   class ResourceGenerator < Rails::Generators::NamedBase
     source_root File.expand_path('../templates', __FILE__)

lib/jsonapi/active_relation_resource.rb

@@ -666,10 +666,14 @@ def find_related_polymorphic_fragments(source_fragments, relationship, options,
             end
 
             relation_position = relation_positions[row[2].downcase.pluralize]
-            model_fields = relation_position[:model_fields]
-            cache_field = relation_position[:cache_field]
-            cache_offset = relation_position[:cache_offset]
-            field_offset = relation_position[:field_offset]
+            if relation_position
+              model_fields = relation_position[:model_fields]
+              cache_field = relation_position[:cache_field]
+              cache_offset = relation_position[:cache_offset]
+              field_offset = relation_position[:field_offset]
+            else
+              next # Skip processing if relation_position is nil
+            end
 
             if cache_field
               related_fragments[rid].cache = cast_to_attribute_type(row[cache_offset], cache_field[:type])

lib/jsonapi/acts_as_resource_controller.rb

@@ -1,7 +1,7 @@
 # frozen_string_literal: true
 
 require 'csv'
-
+require_relative 'compatibility_helper'
 module JSONAPI
   module ActsAsResourceController
     MEDIA_TYPE_MATCHER = /.+".+"[^,]*|[^,]+/
@@ -63,16 +63,16 @@ def index_related_resources
 
     def get_related_resource
       # :nocov:
-    ActiveSupport::Deprecation.warn "In #{self.class.name} you exposed a `get_related_resource`"\
-                                      " action. Please use `show_related_resource` instead."
+      JSONAPI::CompatibilityHelper.deprecation_warn("In #{self.class.name} you exposed a `get_related_resource`"\
+                                      " action. Please use `show_related_resource` instead.")
       show_related_resource
       # :nocov:
     end
 
     def get_related_resources
       # :nocov:
-      ActiveSupport::Deprecation.warn "In #{self.class.name} you exposed a `get_related_resources`"\
-                                      " action. Please use `index_related_resources` instead."
+      JSONAPI::CompatibilityHelper.deprecation_warn("In #{self.class.name} you exposed a `get_related_resources`"\
+                                      " action. Please use `index_related_resources` instead.")
       index_related_resources
       # :nocov:
     end