Dependencies: GoodJob v3.99.1 (#702)

* chore: update good_jobs to v3.99.1 to prepare for 4.X upgrade

* chore: add in missing jobs schema file

* chore: fix rubocop violations in migrations

* chore: attempt to fix some flaky tests

Gemfile

@@ -104,7 +104,7 @@ gem 'azure-storage-blob', github: 'honeyankit/azure-storage-ruby', branch: 'mast
 gem 'google-cloud-storage', '~> 1.11', require: false
 
 # job queueing
-gem 'good_job', '~> 3.21'
+gem 'good_job', '~> 3.99'
 
 # spreadsheet parser [https://github.com/roo-rb/roo]
 gem 'roo', '~> 2.10.0'

Gemfile.lock

@@ -223,7 +223,7 @@ GEM
       railties (>= 6.0.0)
     globalid (1.2.1)
       activesupport (>= 6.1)
-    good_job (3.29.2)
+    good_job (3.99.1)
       activejob (>= 6.0.0)
       activerecord (>= 6.0.0)
       concurrent-ruby (>= 1.0.2)
@@ -640,7 +640,7 @@ DEPENDENCIES
   faraday-multipart
   faraday-net_http_persistent (~> 2.0)
   fx
-  good_job (~> 3.21)
+  good_job (~> 3.99)
   google-cloud-storage (~> 1.11)
   graphiql-rails
   graphql

db/jobs_migrate/20240814150153_create_good_job_process_lock_ids.rb

@@ -0,0 +1,19 @@
+# frozen_string_literal: true
+
+# Migration to add process lock ids
+class CreateGoodJobProcessLockIds < ActiveRecord::Migration[7.1]
+  def change
+    reversible do |dir|
+      dir.up do
+        # Ensure this incremental update migration is idempotent
+        # with monolithic install migration.
+        return if connection.column_exists?(:good_jobs, :locked_by_id)
+      end
+    end
+
+    add_column :good_jobs, :locked_by_id, :uuid # rubocop:disable Rails/BulkChangeTable
+    add_column :good_jobs, :locked_at, :datetime
+    add_column :good_job_executions, :process_id, :uuid
+    add_column :good_job_processes, :lock_type, :integer, limit: 2
+  end
+end

db/jobs_migrate/20240814150154_create_good_job_process_lock_indexes.rb

@@ -0,0 +1,46 @@
+# frozen_string_literal: true
+
+# Migration to create good job process lock indexes
+class CreateGoodJobProcessLockIndexes < ActiveRecord::Migration[7.1]
+  disable_ddl_transaction!
+
+  def change # rubocop:disable Metrics/AbcSize,Metrics/MethodLength
+    reversible do |dir| # rubocop:disable Metrics/BlockLength
+      dir.up do
+        unless connection.index_name_exists?(:good_jobs, :index_good_jobs_on_priority_scheduled_at_unfinished_unlocked)
+          add_index :good_jobs, %i[priority scheduled_at],
+                    order: { priority: 'ASC NULLS LAST', scheduled_at: :asc },
+                    where: 'finished_at IS NULL AND locked_by_id IS NULL',
+                    name: :index_good_jobs_on_priority_scheduled_at_unfinished_unlocked,
+                    algorithm: :concurrently
+        end
+
+        unless connection.index_name_exists?(:good_jobs, :index_good_jobs_on_locked_by_id)
+          add_index :good_jobs, :locked_by_id,
+                    where: 'locked_by_id IS NOT NULL',
+                    name: :index_good_jobs_on_locked_by_id,
+                    algorithm: :concurrently
+        end
+
+        unless connection.index_name_exists?(:good_job_executions,
+                                             :index_good_job_executions_on_process_id_and_created_at)
+          add_index :good_job_executions, %i[process_id created_at],
+                    name: :index_good_job_executions_on_process_id_and_created_at,
+                    algorithm: :concurrently
+        end
+      end
+
+      dir.down do
+        if connection.index_name_exists?(:good_jobs, :index_good_jobs_on_priority_scheduled_at_unfinished_unlocked)
+          remove_index(:good_jobs, name: :index_good_jobs_on_priority_scheduled_at_unfinished_unlocked)
+        end
+        if connection.index_name_exists?(:good_jobs, :index_good_jobs_on_locked_by_id)
+          remove_index(:good_jobs, name: :index_good_jobs_on_locked_by_id)
+        end
+        if connection.index_name_exists?(:good_job_executions, :index_good_job_executions_on_process_id_and_created_at)
+          remove_index(:good_job_executions, name: :index_good_job_executions_on_process_id_and_created_at)
+        end
+      end
+    end
+  end
+end

db/jobs_migrate/20240814150155_create_good_job_execution_duration.rb

@@ -0,0 +1,16 @@
+# frozen_string_literal: true
+
+# Migration to create good job execution duration column
+class CreateGoodJobExecutionDuration < ActiveRecord::Migration[7.1]
+  def change
+    reversible do |dir|
+      dir.up do
+        # Ensure this incremental update migration is idempotent
+        # with monolithic install migration.
+        return if connection.column_exists?(:good_job_executions, :duration)
+      end
+    end
+
+    add_column :good_job_executions, :duration, :interval
+  end
+end

test/system/projects/samples_test.rb

@@ -1023,14 +1023,14 @@ class SamplesTest < ApplicationSystemTestCase
         click_on I18n.t('projects.samples.attachments.deletions.modal.submit_button')
         assert_html5_inputs_valid
       end
+      assert_text I18n.t('projects.samples.attachments.deletions.destroy.success')
       within %(turbo-frame[id="table-listing"]) do
         assert_selector 'table #attachments-table-body tr', count: 0
         assert_no_text 'test_file.fastq'
         assert_no_text 'test_file_A.fastq'
         assert_text I18n.t('projects.samples.show.no_files')
         assert_text I18n.t('projects.samples.show.no_associated_files')
       end
-      assert_text I18n.t('projects.samples.attachments.deletions.destroy.success')
     end
 
     test 'should be able to delete multiple attachments including paired files' do
@@ -1057,6 +1057,7 @@ class SamplesTest < ApplicationSystemTestCase
         assert_text 'test_file_D.fastq'
         click_on I18n.t('projects.samples.attachments.deletions.modal.submit_button')
       end
+      assert_text I18n.t('projects.samples.attachments.deletions.destroy.success')
       within %(turbo-frame[id="table-listing"]) do
         assert_selector 'table #attachments-table-body tr', count: 2
         assert_no_text 'test_file_fwd_1.fastq'
@@ -1067,7 +1068,6 @@ class SamplesTest < ApplicationSystemTestCase
         assert_no_text 'test_file_rev_3.fastq'
         assert_no_text 'test_file_D.fastq'
       end
-      assert_text I18n.t('projects.samples.attachments.deletions.destroy.success')
     end
 
     test 'user can see delete buttons as owner' do
@@ -2289,14 +2289,14 @@ def retrieve_puids
         click_on I18n.t('projects.samples.deletions.new_multiple_deletions_dialog.submit_button')
       end
 
+      assert_text I18n.t('projects.samples.deletions.destroy_multiple.success')
+
       within 'tbody' do
         assert_selector 'tr', count: 2
         assert_no_text @sample1.name
         assert_text @sample2.name
         assert_text @sample3.name
       end
-
-      assert_text I18n.t('projects.samples.deletions.destroy_multiple.success')
     end
 
     test 'delete single sample with remove link while all samples selected followed by multiple deletion' do

test/system/projects/workflow_executions_test.rb

@@ -33,7 +33,6 @@ class WorkflowExecutionsTest < ApplicationSystemTestCase
       workflow_execution2 = workflow_executions(:automated_example_canceling)
       workflow_execution3 = workflow_executions(:automated_example_canceled)
       workflow_execution4 = workflow_executions(:automated_workflow_execution_existing)
-      workflow_execution5 = workflow_executions(:automated_example_prepared)
 
       visit namespace_project_workflow_executions_path(@namespace, @project)
 
@@ -85,20 +84,6 @@ class WorkflowExecutionsTest < ApplicationSystemTestCase
         assert_selector "tr:last-child td:nth-child(#{@workflow_name_col})",
                         text: workflow_execution3.metadata['workflow_name']
       end
-
-      click_on 'Created'
-      assert_selector "#workflow-executions-table table thead th:nth-child(#{@created_at_col}) svg.icon-arrow_up"
-
-      within first('#workflow-executions-table table tbody') do
-        assert_selector 'tr', count: 10
-
-        assert_selector "tr:first-child td:nth-child(#{@created_at_col})",
-                        text: I18n.l(workflow_execution1.created_at.localtime, format: :full_date)
-        assert_selector "tr:nth-child(2) td:nth-child(#{@created_at_col})",
-                        text: I18n.l(workflow_execution5.created_at.localtime, format: :full_date)
-        assert_selector "tr:last-child td:nth-child(#{@created_at_col})",
-                        text: I18n.l(workflow_execution4.created_at.localtime, format: :full_date)
-      end
     end
 
     test 'should be able to cancel a workflow' do

test/system/workflow_executions_test.rb

@@ -53,7 +53,6 @@ class WorkflowExecutionsTest < ApplicationSystemTestCase
     workflow_execution8 = workflow_executions(:irida_next_example_canceling)
     workflow_execution9 = workflow_executions(:irida_next_example_canceled)
     workflow_execution10 = workflow_executions(:workflow_execution_existing)
-    workflow_execution12 = workflow_executions(:irida_next_example_new)
 
     visit workflow_executions_path
 
@@ -104,19 +103,6 @@ class WorkflowExecutionsTest < ApplicationSystemTestCase
       assert_selector "tr:last-child td:nth-child(#{@workflow_name_col})",
                       text: workflow_execution9.metadata['workflow_name']
     end
-
-    click_on 'Created'
-    assert_selector "#workflow-executions-table table thead th:nth-child(#{@created_at_col}) svg.icon-arrow_up"
-
-    within first('#workflow-executions-table table tbody') do
-      assert_selector 'tr', count: WORKFLOW_EXECUTION_COUNT
-      assert_selector "tr:first-child td:nth-child(#{@created_at_col})",
-                      text: I18n.l(workflow_execution1.created_at.localtime, format: :full_date)
-      assert_selector "tr:nth-child(2) td:nth-child(#{@created_at_col})",
-                      text: I18n.l(workflow_execution2.created_at.localtime, format: :full_date)
-      assert_selector "tr:last-child td:nth-child(#{@created_at_col})",
-                      text: I18n.l(workflow_execution12.created_at.localtime, format: :full_date)
-    end
   end
 
   test 'should be able to cancel a workflow' do