Merge pull request #306 from sanger/develop

Dependency updates and added net-imap and net-pop gem

.release-version

@@ -1 +1 @@
-3.5.0
+3.6.0

Gemfile

@@ -7,6 +7,8 @@ gem 'mysql2'
 # Use SCSS for stylesheets
 gem 'sass-rails', '~> 6.0'
 
+gem 'net-imap', require: false
+gem 'net-pop', require: false
 gem 'net-smtp'
 
 # Use jquery as the JavaScript library

Gemfile.lock

@@ -91,6 +91,7 @@ GEM
       activerecord (>= 5.a)
       database_cleaner-core (~> 2.0.0)
     database_cleaner-core (2.0.1)
+    date (3.3.3)
     diff-lcs (1.5.0)
     docile (1.4.0)
     erubi (1.12.0)
@@ -126,7 +127,12 @@ GEM
     mini_mime (1.1.2)
     mini_portile2 (2.8.1)
     minitest (5.18.0)
-    mysql2 (0.5.4)
+    mysql2 (0.5.5)
+    net-imap (0.3.4)
+      date
+      net-protocol
+    net-pop (0.1.2)
+      net-protocol
     net-protocol (0.2.1)
       timeout
     net-smtp (0.3.3)
@@ -138,13 +144,12 @@ GEM
     parallel (1.22.1)
     parser (3.2.1.1)
       ast (~> 2.4.1)
-    pry (0.14.1)
+    pry (0.14.2)
       coderay (~> 1.1)
       method_source (~> 1.0)
     psych (4.0.4)
       stringio
     public_suffix (5.0.1)
-      nio4r (~> 2.0)
     puma (6.1.1)
       nio4r (~> 2.0)
     racc (1.6.2)
@@ -204,7 +209,7 @@ GEM
       rspec-mocks (~> 3.5.0)
       rspec-support (~> 3.5.0)
     rspec-support (3.5.0)
-    rubocop (1.48.0)
+    rubocop (1.48.1)
       json (~> 2.3)
       parallel (~> 1.10)
       parser (>= 3.2.0.0)
@@ -221,10 +226,10 @@ GEM
     rubocop-performance (1.16.0)
       rubocop (>= 1.7.0, < 2.0)
       rubocop-ast (>= 0.4.0)
-    rubocop-rails (2.15.1)
+    rubocop-rails (2.18.0)
       activesupport (>= 4.2.0)
       rack (>= 1.1)
-      rubocop (>= 1.7.0, < 2.0)
+      rubocop (>= 1.33.0, < 2.0)
     rubocop-rspec (2.19.0)
       rubocop (~> 1.33)
       rubocop-capybara (~> 2.17)
@@ -252,7 +257,7 @@ GEM
       simplecov_json_formatter (~> 0.1)
     simplecov-html (0.12.3)
     simplecov_json_formatter (0.1.4)
-    spring (4.0.0)
+    spring (4.1.1)
     sprockets (3.7.2)
       concurrent-ruby (~> 1.0)
       rack (> 1, < 3)
@@ -304,6 +309,8 @@ DEPENDENCIES
   jquery-rails
   launchy
   mysql2
+  net-imap
+  net-pop
   net-smtp
   pry
   puma

app/controllers/assets_controller.rb

@@ -1,6 +1,16 @@
 require './app/presenters/asset/index'
 
 class AssetsController < ApplicationController
+  def index
+    if params[:state].nil? && params[:identifier].nil?
+      redirect_to('/assets?state=in_progress')
+    else
+      assets = Asset.in_state(state)
+                    .with_identifier(params[:identifier])
+      @presenter = Presenter::AssetPresenter::Index.new(assets, search, state)
+    end
+  end
+
   # Assets updater creates new events for assets and moves assets to the next state
   def update
     if assets_provided
@@ -13,16 +23,6 @@ def update
     end
   end
 
-  def index
-    if params[:state].nil? && params[:identifier].nil?
-      redirect_to('/assets?state=in_progress')
-    else
-      assets = Asset.in_state(state)
-                    .with_identifier(params[:identifier])
-      @presenter = Presenter::AssetPresenter::Index.new(assets, search, state)
-    end
-  end
-
   private
 
   def state

app/controllers/batches_controller.rb

@@ -4,12 +4,35 @@
 class BatchesController < ApplicationController
   before_action :batch, only: %i[show update remove]
 
+  def show
+    @presenter = Presenter::BatchPresenter::Show.new(batch)
+  end
+
   def new
     @presenter = Presenter::BatchPresenter::New.new
   end
 
-  def show
-    @presenter = Presenter::BatchPresenter::Show.new(batch)
+  def create
+    batch_creator = Batch::Creator.new(
+      study: params[:study],
+      project: params[:project],
+      workflow:,
+      pipeline_destination:,
+      begun_at: params[:begun_at],
+      cost_code:,
+      asset_type:,
+      assets:,
+      comment: params[:comment]
+    )
+    if batch_creator.valid?
+      batch = batch_creator.create!
+      @presenter = Presenter::BatchPresenter::Show.new(batch)
+      flash[:notice] = I18n.t('batches.success.created')
+      redirect_to("/batches/#{@presenter.id}")
+    else
+      flash[:error] = batch_creator.errors.full_messages.join('; ')
+      redirect_back(fallback_location: root_path)
+    end
   end
 
   def update
@@ -40,29 +63,6 @@ def destroy
     redirect_to('/batches/new')
   end
 
-  def create
-    batch_creator = Batch::Creator.new(
-      study: params[:study],
-      project: params[:project],
-      workflow:,
-      pipeline_destination:,
-      begun_at: params[:begun_at],
-      cost_code:,
-      asset_type:,
-      assets:,
-      comment: params[:comment]
-    )
-    if batch_creator.valid?
-      batch = batch_creator.create!
-      @presenter = Presenter::BatchPresenter::Show.new(batch)
-      flash[:notice] = I18n.t('batches.success.created')
-      redirect_to("/batches/#{@presenter.id}")
-    else
-      flash[:error] = batch_creator.errors.full_messages.join('; ')
-      redirect_back(fallback_location: root_path)
-    end
-  end
-
   private
 
   def workflow

app/controllers/reports_controller.rb

@@ -2,6 +2,8 @@
 require './app/presenters/report/show'
 
 class ReportsController < ApplicationController
+  def show; end
+
   def new
     @presenter = Presenter::ReportPresenter::New.new
   end
@@ -18,8 +20,6 @@ def create
     end
   end
 
-  def show; end
-
   def csv
     send_data params[:csv_file_content],
               type: 'text/csv',

app/controllers/workflows_controller.rb

@@ -3,6 +3,10 @@
 class WorkflowsController < ApplicationController
   include InitialState
 
+  def show
+    @presenter = Presenter::WorkflowPresenter::Show.new(workflow)
+  end
+
   def create
     @workflow = Workflow.new(workflow_params)
     if @workflow.save
@@ -14,10 +18,6 @@ def create
     end
   end
 
-  def show
-    @presenter = Presenter::WorkflowPresenter::Show.new(workflow)
-  end
-
   def update
     workflow.assign_attributes(workflow_params)
     if workflow.save

lib/deployed_version.rb

@@ -84,7 +84,7 @@ def execute_command(cmd)
     end
 
     def read_file(filename)
-      File.open(Rails.root.join(filename), 'r', &:readline)
+      Rails.root.join(filename).open('r', &:readline)
     rescue Errno::ENOENT, EOFError
       ''
     end