Merge branch 'develop' into depfu/update/graphql-1.12.12

.ruby-version

@@ -1 +1 @@
-2.6.3
+2.7.3

Gemfile

@@ -3,15 +3,19 @@
 source 'https://rubygems.org'
 git_source(:github) { |repo| "https://github.com/#{repo}.git" }
 
-ruby '2.6.3'
+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'
-gem 'jsonapi-resources', '~> 0.9.10'
+# Pinned to 0.10.4 pending fix of
+# https://github.com/cerebris/jsonapi-resources/issues/1369
+# Results in MySQL syntax error on several tests when run against a MySQL
+# (Not SQL lite) database
+gem 'jsonapi-resources', '= 0.10.4'
 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
@@ -33,6 +37,7 @@ end
 
 group :development, :test do
   gem 'byebug', platforms: %i[mri mingw x64_mingw]
+  gem 'pry-rails'
   gem 'rspec-rails'
   gem 'rubocop', require: false
   gem 'shoulda-matchers'

Gemfile.lock

@@ -61,10 +61,12 @@ GEM
     bootsnap (1.7.5)
       msgpack (~> 1.0)
     builder (3.2.4)
-    bunny (2.17.0)
+    bunny (2.18.0)
       amq-protocol (~> 2.3, >= 2.3.1)
+      sorted_set (~> 1, >= 1.0.2)
     byebug (11.1.3)
     choice (0.2.0)
+    coderay (1.1.3)
     commonmarker (0.21.0)
       ruby-enum (~> 0.5)
     concurrent-ruby (1.1.8)
@@ -109,7 +111,7 @@ GEM
       nokogiri (>= 1.4)
     i18n (1.8.10)
       concurrent-ruby (~> 1.0)
-    jsonapi-resources (0.9.11)
+    jsonapi-resources (0.10.4)
       activerecord (>= 4.1)
       concurrent-ruby
       railties (>= 4.1)
@@ -130,12 +132,17 @@ GEM
     msgpack (1.4.2)
     mysql2 (0.5.3)
     nio4r (2.5.7)
-    nokogiri (1.11.5)
+    nokogiri (1.11.6)
       mini_portile2 (~> 2.5.0)
       racc (~> 1.4)
     parallel (1.20.1)
     parser (3.0.1.1)
       ast (~> 2.4.1)
+    pry (0.14.1)
+      coderay (~> 1.1)
+      method_source (~> 1.0)
+    pry-rails (0.3.9)
+      pry (>= 0.10.4)
     puma (4.3.8)
       nio4r (~> 2.0)
     racc (1.5.2)
@@ -180,6 +187,7 @@ GEM
     rb-fsevent (0.10.3)
     rb-inotify (0.10.1)
       ffi (~> 1.0)
+    rbtree (0.4.4)
     regexp_parser (2.1.1)
     rexml (3.2.5)
     rspec-core (3.10.1)
@@ -225,8 +233,12 @@ GEM
     sass-listen (4.0.0)
       rb-fsevent (~> 0.9, >= 0.9.4)
       rb-inotify (~> 0.9, >= 0.9.7)
+    set (1.0.1)
     shoulda-matchers (4.5.1)
       activesupport (>= 4.2.0)
+    sorted_set (1.0.3)
+      rbtree
+      set (~> 1.0)
     spring (2.1.1)
     spring-watcher-listen (2.0.1)
       listen (>= 2.7, < 4.0)
@@ -263,9 +275,10 @@ DEPENDENCIES
   graphql
   graphql-client
   graphql-docs
-  jsonapi-resources (~> 0.9.10)
+  jsonapi-resources (= 0.10.4)
   listen (>= 3.0.5, < 3.2)
   mysql2
+  pry-rails
   puma (~> 4.3)
   rack-cors
   rails (~> 6.0.3.1)
@@ -280,7 +293,7 @@ DEPENDENCIES
   yard
 
 RUBY VERSION
-   ruby 2.6.3p62
+   ruby 2.7.3p183
 
 BUNDLED WITH
    2.1.4

README.md

@@ -14,12 +14,18 @@ Rails app which exposes a RESTful API.
 
 ## Installation
 
-1. Install using: `bundle install`
-1. Remove the `.example` from the config files in `config` folder
+1. Run `bin/setup`
+
+This will:
+
+- Run bundle install
+- Create copies of any .example files
+- Create the database
 
 ## Database setup
 
-To create the database for a fresh install: `bundle exec rails db:setup`
+The database should have been generated as part of the installation step above.
+If you need to create the database afresh: `bundle exec rails db:setup`.
 
 To create a set of enzymes (needed for saphyr dummy runs): `bundle exec rails enzymes:create`
 
@@ -29,7 +35,7 @@ To fetch tags from SS: `bundle exec rails tags:fetch`
 
 To update tags for an ONT plate which has tags wrongly assigned by row rather than column: `BARCODES=barcode1,barcode2... bundle exec rails tags:reorder`
 
-To create pacbio dummy runs: `bundle exec rails pacbio_runs:create`
+To create pacbio dummy runs: `bundle exec rails pacbio_data:create`
 
 To create saphyr dummy runs: `bundle exec rails saphyr_runs:create`
 
@@ -98,6 +104,6 @@ This documentation can be updated by running the following commands:
 On merging a pull request into develop, a release will be created with the tag/name `<branch>/<timestamp>`
 
 #### PROD
-Update `.release-version` with major/minor/patch. On merging a pull request into master, a release will be created with the release version as the tag/name 
+Update `.release-version` with major/minor/patch. On merging a pull request into master, a release will be created with the release version as the tag/name
 
 See Confluence for further information

app/controllers/application_controller.rb

@@ -1,6 +1,31 @@
 # frozen_string_literal: true
 
 # ApplicationController
-class ApplicationController < JSONAPI::ResourceController
+class ApplicationController < ActionController::Base
+  include JSONAPI::ActsAsResourceController
   skip_before_action :verify_authenticity_token
+
+  on_server_error :send_exception_notification
+
+  def self.send_exception_notification(exception)
+    ExceptionNotifier.notify_exception(exception)
+  end
+
+  private
+
+  # Caution: Using this approach for a 'create' action is not strictly JSON API
+  # compliant.
+  def serialize_array(array)
+    {
+      data: array.map do |r|
+        JSONAPI::ResourceSerializer.new(r.class).object_hash(r, {})
+      end
+    }
+  end
+
+  # Where possible try to use the default json api resources actions, as
+  # they will correctly ensure parameters such as include are properly processed
+  def serialize_resource(resource)
+    { data: JSONAPI::ResourceSerializer.new(resource.class).object_hash(resource, {}) }
+  end
 end

app/controllers/v1/pacbio/libraries_controller.rb

@@ -8,8 +8,7 @@ def create
         @library_factory = ::Pacbio::LibraryFactory.new(params_names)
         if @library_factory.save
           @resources = LibraryResource.new(@library_factory.library, nil)
-          body = JSONAPI::ResourceSerializer.new(LibraryResource).serialize_to_hash(@resources)
-          render json: body, status: :created
+          render json: serialize_resource(@resources), status: :created
         else
           render json: { data: { errors: @library_factory.errors.messages } },
                  status: :unprocessable_entity
@@ -66,9 +65,7 @@ def tag_param_names(params)
       end
 
       def render_json(status)
-        render json:
-           JSONAPI::ResourceSerializer.new(LibraryResource)
-                                      .serialize_to_hash(LibraryResource.new(@library, nil)),
+        render json: serialize_resource(LibraryResource.new(@library, nil)),
                status: status
       end
     end

app/controllers/v1/pacbio/plates_controller.rb

@@ -4,11 +4,19 @@ module V1
   module Pacbio
     # PlatesController
     class PlatesController < ApplicationController
+      # This endpoint is not strictly JSON API compliant:
+      # https://jsonapi.org/format/#crud-creating
+      #   A resource can be created by sending a POST request to a URL that represents a collection
+      #   of resources. The request MUST include a single resource object as primary data. The
+      #   resource object MUST contain at least a type member.
+      #
+      # Here we may return multiple libraries. To be compliant I think it would need to return a
+      # library_collection (or similar), but it doesn't sound like we'd need to provide an id.
       def create
         @plate_creator = ::Pacbio::PlateCreator.new(plates_params)
         if @plate_creator.save!
           @plates = @plate_creator.plates.map { |plate| PlateResource.new(plate, nil) }
-          body = JSONAPI::ResourceSerializer.new(PlateResource).serialize_to_hash(@plates)
+          body = serialize_array(@plates)
           render json: body, status: :created
         else
           render json: { data: { errors: @plate_creator.errors.messages } },

app/controllers/v1/pacbio/request_library_controller.rb

@@ -23,10 +23,8 @@ def request_library_update_params
       end
 
       def render_json(status)
-        render json:
-            JSONAPI::ResourceSerializer.new(RequestLibraryResource)
-                                       .serialize_to_hash(RequestLibraryResource
-                                       .new(@request_library, nil)), status: status
+        resource = RequestLibraryResource.new(@request_library, nil)
+        render json: serialize_resource(resource), status: status
       end
     end
   end

app/controllers/v1/pacbio/runs/plates_controller.rb

@@ -40,9 +40,7 @@ def plate
         end
 
         def render_json(status)
-          render json:
-             JSONAPI::ResourceSerializer.new(PlateResource)
-                                        .serialize_to_hash(PlateResource.new(@plate, nil)),
+          render json: serialize_resource(PlateResource.new(@plate, nil)),
                  status: status
         end
       end

app/controllers/v1/pacbio/runs/wells_controller.rb

@@ -44,7 +44,7 @@ def body
           resources = @well_factory.wells.map do |well_factory|
             WellResource.new(::Pacbio::Well.find(well_factory.id), nil)
           end
-          JSONAPI::ResourceSerializer.new(WellResource).serialize_to_hash(resources)
+          serialize_array(resources)
         end
 
         def publish_message
@@ -105,9 +105,7 @@ def well
         end
 
         def render_json(status)
-          render json:
-           JSONAPI::ResourceSerializer.new(WellResource)
-                                      .serialize_to_hash(WellResource.new(@well, nil)),
+          render json: serialize_resource(WellResource.new(@well, nil)),
                  status: status
         end
       end

app/controllers/v1/pacbio/runs_controller.rb

@@ -54,9 +54,7 @@ def params_names
       end
 
       def render_json(status)
-        render json:
-         JSONAPI::ResourceSerializer.new(RunResource)
-                                    .serialize_to_hash(RunResource.new(@run, nil)), status: status
+        render json: serialize_resource(RunResource.new(@run, nil)), status: status
       end
     end
   end

app/controllers/v1/saphyr/chips_controller.rb

@@ -41,10 +41,7 @@ def chip
       end
 
       def render_json(status)
-        render json:
-           JSONAPI::ResourceSerializer.new(ChipResource)
-                                      .serialize_to_hash(ChipResource.new(chip, nil)),
-               status: status
+        render json: serialize_resource(ChipResource.new(chip, nil)), status: status
       end
     end
   end

app/controllers/v1/saphyr/flowcells_controller.rb

@@ -10,9 +10,7 @@ def create
         @flowcell = ::Saphyr::Flowcell.new(params_names)
         if @flowcell.save
           Messages.publish(@flowcell, Pipelines.saphyr.message)
-          render json:
-            JSONAPI::ResourceSerializer.new(FlowcellResource)
-                                       .serialize_to_hash(FlowcellResource.new(flowcell, nil)),
+          render json: serialize_resource(FlowcellResource.new(flowcell, nil)),
                  status: :created
         else
           render json: { data: { errors: @flowcell.errors.messages } },
@@ -23,9 +21,7 @@ def create
       def update
         flowcell.update(library: library)
         Messages.publish(flowcell, Pipelines.saphyr.message)
-        render json:
-          JSONAPI::ResourceSerializer.new(FlowcellResource)
-                                     .serialize_to_hash(FlowcellResource.new(flowcell, nil)),
+        render json: serialize_resource(FlowcellResource.new(flowcell, nil)),
                status: :ok
       rescue StandardError => e
         render json: { data: { errors: e.message } }, status: :unprocessable_entity

app/controllers/v1/saphyr/libraries_controller.rb

@@ -6,11 +6,19 @@ module Saphyr
     class LibrariesController < ApplicationController
       before_action :current_library, only: [:destroy]
 
+      # This endpoint is not strictly JSON API compliant:
+      # https://jsonapi.org/format/#crud-creating
+      #   A resource can be created by sending a POST request to a URL that represents a collection
+      #   of resources. The request MUST include a single resource object as primary data. The
+      #   resource object MUST contain at least a type member.
+      #
+      # Here we may return multiple libraries. To be compliant I think it would need to return a
+      # library_collection (or similar), but it doesn't sound like we'd need to provide an id.
       def create
         @library_factory = ::Saphyr::LibraryFactory.new(params_names)
         if @library_factory.save
           @resources = @library_factory.libraries.map { |lib| LibraryResource.new(lib, nil) }
-          body = JSONAPI::ResourceSerializer.new(LibraryResource).serialize_to_hash(@resources)
+          body = serialize_array(@resources)
           render json: body, status: :created
         else
           render json: { data: { errors: @library_factory.errors.messages } },

app/controllers/v1/saphyr/runs_controller.rb

@@ -41,9 +41,7 @@ def params_names
       end
 
       def render_json(status)
-        render json:
-         JSONAPI::ResourceSerializer.new(RunResource)
-                                    .serialize_to_hash(RunResource.new(run, nil)),
+        render json: serialize_resource(RunResource.new(run, nil)),
                status: status
       end
     end

app/controllers/v1/tags_controller.rb

@@ -38,9 +38,7 @@ def tag
     end
 
     def render_json(status)
-      render json:
-       JSONAPI::ResourceSerializer.new(TagResource)
-                                  .serialize_to_hash(TagResource.new(@tag, nil)), status: status
+      render json: serialize_resource(TagResource.new(@tag, nil)), status: status
     end
   end
 end