Disable automated pipelines (#825)

* adding migration to create new disabled column for automated workflow executions table * adding new status column to automated workflow executions table * attempting to enable/disable automated workflows after pipeline initialization * trying to fix tests * updating enable/disable automated workflow based on pipeline automatable and exectuable * trying to fix ci tests * trying to fix ci tests * trying to fix ci tests * trying to fix ci tests * trying to fix ci tests * trying to fix ci tests * trying to fix ci tests * trying to fix ci tests * trying to fix ci tests * adding translations * adding a test * checking the table exists * checking the table exists * iterating through automated workflow executions instead of pipelines * adding a new test * disabling the edit link for disabled automated workflows * updating LaunchJob to only call LaunchService for enabled automated workflows * removing edit link if disabled
phac-nml · Nov 1, 2024 · 4b40c22 · 4b40c22
1 parent cdb1d48
commit 4b40c22
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Showing 15 changed files with 256 additions and 86 deletions.
diff --git a/app/controllers/projects/automated_workflow_executions_controller.rb b/app/controllers/projects/automated_workflow_executions_controller.rb
@@ -28,16 +28,25 @@ def new
                   end
     end
 
-    def edit
+    def edit # rubocop:disable Metrics/MethodLength
       authorize! @namespace, to: :update_automated_workflow_executions?
       @workflow = Irida::Pipelines.instance.find_pipeline_by(@automated_workflow_execution.metadata['workflow_name'],
                                                              @automated_workflow_execution.metadata['workflow_version'],
                                                              'available')
-      render turbo_stream: turbo_stream.update('automated_workflow_execution_modal',
-                                               partial: 'edit_dialog',
-                                               locals: {
-                                                 open: true
-                                               }), status: :ok
+
+      respond_to do |format|
+        format.turbo_stream do
+          if @automated_workflow_execution.disabled
+            render status: :unprocessable_entity,
+                   locals: {
+                     type: 'alert', message: t('.error',
+                                               workflow_name: @automated_workflow_execution.id)
+                   }
+          else
+            render status: :ok
+          end
+        end
+      end
     end
 
     def create # rubocop:disable Metrics/MethodLength

diff --git a/app/jobs/automated_workflow_executions/launch_job.rb b/app/jobs/automated_workflow_executions/launch_job.rb
@@ -6,7 +6,7 @@ class LaunchJob < ApplicationJob
     queue_as :default
 
     def perform(sample, pe_attachment_pair)
-      sample.project.namespace.automated_workflow_executions.each do |awe|
+      sample.project.namespace.automated_workflow_executions.where(disabled: false).find_each do |awe|
         AutomatedWorkflowExecutions::LaunchService.new(awe, sample, pe_attachment_pair,
                                                        sample.project.namespace.automation_bot).execute
       end

diff --git a/app/views/projects/automated_workflow_executions/_automated_workflow_execution.html.erb b/app/views/projects/automated_workflow_executions/_automated_workflow_execution.html.erb
@@ -28,6 +28,13 @@
   <td class="px-6 py-4 whitespace-nowrap">
     <%= local_time_ago(automated_workflow_execution["updated_at"]) %>
   </td>
+  <td class="px-6 py-4 whitespace-nowrap">
+    <% if automated_workflow_execution["disabled"] %>
+      <%= viral_pill(text: t(:".disabled"), color: "red") %>
+    <% else %>
+      <%= viral_pill(text: t(:".enabled"), color: "green") %>
+    <% end %>
+  </td>
   <td
     class="
       px-6 py-4 space-x-2 whitespace-nowrap sticky right-0 bg-white dark:bg-slate-800
@@ -48,17 +55,20 @@
       class:
         "font-medium text-blue-600 underline dark:text-blue-500 hover:no-underline cursor-pointer",
     ) %>
-    <%= link_to t(:"projects.automated_workflow_executions.actions.edit_button"),
-    edit_namespace_project_automated_workflow_execution_path(
-      @project.parent,
-      @project,
-      automated_workflow_execution,
-    ),
-    data: {
-      turbo_stream: true,
-    },
-    class:
-      "font-medium text-blue-600 underline dark:text-blue-500 hover:no-underline cursor-pointer" %>
-
+    <% unless automated_workflow_execution.disabled %>
+      <%= link_to(
+        t(:"projects.automated_workflow_executions.actions.edit_button"),
+        edit_namespace_project_automated_workflow_execution_path(
+          @project.parent,
+          @project,
+          automated_workflow_execution,
+        ),
+        data: {
+          turbo_stream: true,
+        },
+        class:
+          "font-medium text-blue-600 underline dark:text-blue-500 hover:no-underline cursor-pointer",
+      ) %>
+    <% end %>
   </td>
 </tr>
diff --git a/app/views/projects/automated_workflow_executions/_table.html.erb b/app/views/projects/automated_workflow_executions/_table.html.erb
@@ -2,70 +2,63 @@
   <table
     id="automated_workflow_executions"
     class="
-      w-full
-      text-sm
-      text-left
-      rtl:text-right
-      text-slate-500
-      dark:text-slate-400
-      dark:divide-slate-600
-      whitespace-nowrap
-      "
+      w-full text-sm text-left rtl:text-right text-slate-500 dark:text-slate-400
+      dark:divide-slate-600 whitespace-nowrap
+    "
   >
     <thead
       class="
-          text-slate-700
-          uppercase
-          bg-slate-50
-          dark:bg-slate-700
-          dark:text-slate-400
-          whitespace-nowrap
-        "
+        text-slate-700 uppercase bg-slate-50 dark:bg-slate-700 dark:text-slate-400
+        whitespace-nowrap
+      "
     >
-    <tr>
-      <th scope="col" class="px-6 py-3 whitespace-nowrap text-left sticky left-0
-          bg-slate-50
-          dark:bg-slate-700">
-        <%= t(:".headers.id") %>
-      </th>
-      <th scope="col" class="px-6 py-3 whitespace-nowrap text-left">
-        <%= t(:".headers.name") %>
-      </th>
-      <th scope="col" class="px-6 py-3 whitespace-nowrap text-left">
-        <%= t(:".headers.workflow_name") %>
-      </th>
-      <th scope="col" class="px-6 py-3 whitespace-nowrap text-left">
-        <%= t(:".headers.workflow_version") %>
-      </th>
-      <th scope="col" class="px-6 py-3 whitespace-nowrap text-left">
-        <%= t(:".headers.created_at") %>
-      </th>
-      <th scope="col" class="px-6 py-3 whitespace-nowrap text-left">
-        <%= t(:".headers.updated_at") %>
-      </th>
-      <th scope="col" class="px-6 py-3 whitespace-nowrap text-left sticky right-0">
-        <%= t(:".headers.actions") %>
-      </th>
-    </tr>
+      <tr>
+        <th
+          scope="col"
+          class="
+            px-6 py-3 whitespace-nowrap text-left sticky left-0 bg-slate-50
+            dark:bg-slate-700
+          "
+        >
+          <%= t(:".headers.id") %>
+        </th>
+        <th scope="col" class="px-6 py-3 whitespace-nowrap text-left">
+          <%= t(:".headers.name") %>
+        </th>
+        <th scope="col" class="px-6 py-3 whitespace-nowrap text-left">
+          <%= t(:".headers.workflow_name") %>
+        </th>
+        <th scope="col" class="px-6 py-3 whitespace-nowrap text-left">
+          <%= t(:".headers.workflow_version") %>
+        </th>
+        <th scope="col" class="px-6 py-3 whitespace-nowrap text-left">
+          <%= t(:".headers.created_at") %>
+        </th>
+        <th scope="col" class="px-6 py-3 whitespace-nowrap text-left">
+          <%= t(:".headers.updated_at") %>
+        </th>
+        <th scope="col" class="px-6 py-3 whitespace-nowrap text-left">
+          <%= t(:".headers.status") %>
+        </th>
+        <th scope="col" class="px-6 py-3 whitespace-nowrap text-left sticky right-0">
+          <%= t(:".headers.actions") %>
+        </th>
+      </tr>
     </thead>
     <tbody
       class="
-          bg-white
-          divide-y
-          divide-slate-200
-          dark:bg-slate-800
-          dark:divide-slate-700
-        "
+        bg-white divide-y divide-slate-200 dark:bg-slate-800 dark:divide-slate-700
+      "
     >
-    <%= render partial: "automated_workflow_execution",
-               collection: @automated_workflow_executions %>
+      <%= render partial: "automated_workflow_execution",
+      collection: @automated_workflow_executions %>
     </tbody>
   </table>
   <div class="empty_state_message">
     <%= viral_empty(
-          title: t(:".empty.title"),
-          description: t(:".empty.description"),
-          icon_name: :document_text
-        ) %>
+      title: t(:".empty.title"),
+      description: t(:".empty.description"),
+      icon_name: :document_text,
+    ) %>
   </div>
 </div>
diff --git a/app/views/projects/automated_workflow_executions/edit.turbo_stream.erb b/app/views/projects/automated_workflow_executions/edit.turbo_stream.erb
@@ -0,0 +1,13 @@
+<% if @automated_workflow_execution.disabled %>
+  <%= turbo_stream.append "flashes" do %>
+    <%= viral_flash(type:, data: message) %>
+  <% end %>
+<% else %>
+  <%= turbo_stream.update(
+    "automated_workflow_execution_modal",
+    partial: "edit_dialog",
+    locals: {
+      open: true,
+    },
+  ) %>
+<% end %>
diff --git a/config/initializers/pipelines.rb b/config/initializers/pipelines.rb
@@ -5,3 +5,17 @@
 Rails.application.config.to_prepare do
   Irida::Pipelines.instance = Irida::Pipelines.new if Irida::Pipelines.instance.nil?
 end
+
+Rails.application.config.after_initialize do
+  if defined?(Rails::Server) ||
+     (Rails.env.test? && ActiveRecord::Base.connection.table_exists?('automated_workflow_executions'))
+
+    AutomatedWorkflowExecution.find_each do |automated_workflow_exectuion|
+      pipeline = Irida::Pipelines.instance.find_pipeline_by(automated_workflow_exectuion.metadata['workflow_name'],
+                                                            automated_workflow_exectuion.metadata['workflow_version'],
+                                                            'automatable')
+      automated_workflow_exectuion.disabled = pipeline ? !pipeline.executable : true
+      automated_workflow_exectuion.save
+    end
+  end
+end
diff --git a/config/locales/en.yml b/config/locales/en.yml
@@ -1019,12 +1019,17 @@ en:
         delete_button: Delete
         delete_confirm: Are you sure that you want to delete this automated pipeline?
         edit_button: Edit
+      automated_workflow_execution:
+        disabled: DISABLED
+        enabled: ENABLED
       create:
         error: Could not create an automated pipeline for %{workflow_name}
         success: Automated pipeline for %{workflow_name} was successfully created
       destroy:
         error: Could not delete automated pipeline for %{workflow_name}
         success: Automated pipeline for %{workflow_name} was successfully deleted
+      edit:
+        error: Cannot edit automated pipeline %{workflow_name}
       edit_dialog:
         title: 'Editing Automated Pipeline: %{workflow_name}'
       index:
@@ -1044,6 +1049,7 @@ en:
           created_at: Created
           id: ID
           name: Name
+          status: Status
           updated_at: Updated
           workflow_name: Workflow Name
           workflow_version: Workflow Version

diff --git a/config/locales/fr.yml b/config/locales/fr.yml
@@ -1019,12 +1019,17 @@ fr:
         delete_button: Delete
         delete_confirm: Are you sure that you want to delete this automated pipeline?
         edit_button: Edit
+      automated_workflow_execution:
+        disabled: DISABLED
+        enabled: ENABLED
       create:
         error: Could not create an automated pipeline for %{workflow_name}
         success: Automated pipeline for %{workflow_name} was successfully created
       destroy:
         error: Could not delete automated pipeline for %{workflow_name}
         success: Automated pipeline for %{workflow_name} was successfully deleted
+      edit:
+        error: Cannot edit automated pipeline %{workflow_name}
       edit_dialog:
         title: 'Editing Automated Pipeline: %{workflow_name}'
       index:
@@ -1044,6 +1049,7 @@ fr:
           created_at: Created
           id: ID
           name: Name
+          status: Status
           updated_at: Updated
           workflow_name: Workflow Name
           workflow_version: Workflow Version

diff --git a/db/migrate/20241017164233_add_disabled_to_automated_workflow_executions.rb b/db/migrate/20241017164233_add_disabled_to_automated_workflow_executions.rb
@@ -0,0 +1,8 @@
+# frozen_string_literal: true
+
+# Migration to add a new disabled column to the automated workflow executions table
+class AddDisabledToAutomatedWorkflowExecutions < ActiveRecord::Migration[7.2]
+  def change
+    add_column :automated_workflow_executions, :disabled, :boolean, default: false, null: false
+  end
+end
diff --git a/db/schema.rb b/db/schema.rb
diff --git a/test/config/pipelines_test.rb b/test/config/pipelines_test.rb
@@ -0,0 +1,39 @@
+# frozen_string_literal: true
+
+require 'test_helper'
+
+class PipelinesTest < ActiveSupport::TestCase
+  test 'disable automated workflow executions after pipeline registration' do
+    assert_not Irida::Pipelines.instance.available_pipelines.empty?
+    pipeline = Irida::Pipelines.instance.available_pipelines['phac-nml/iridanextexample_1.0.0']
+    assert_not_nil pipeline
+    assert_not pipeline.executable
+
+    automated_workflow_execution = AutomatedWorkflowExecution.find_by(
+      "metadata ->> 'workflow_name' = ? and metadata ->> 'workflow_version' = ?", pipeline.name, pipeline.version
+    )
+    assert_not_nil automated_workflow_execution
+    assert_not automated_workflow_execution.disabled
+
+    load Rails.root.join('config/initializers/pipelines.rb')
+
+    assert automated_workflow_execution.reload.disabled
+  end
+
+  test 'disable automated workflow executions after pipeline registration when the pipeline has been removed' do
+    pipeline_name =  'phac-nml/iridanextexample'
+    pipeline_version = '1.0.4'
+    assert_not Irida::Pipelines.instance.available_pipelines.empty?
+    assert_nil Irida::Pipelines.instance.available_pipelines["#{pipeline_name}_#{pipeline_version}"]
+
+    automated_workflow_execution = AutomatedWorkflowExecution.find_by(
+      "metadata ->> 'workflow_name' = ? and metadata ->> 'workflow_version' = ?", pipeline_name, pipeline_version
+    )
+    assert_not_nil automated_workflow_execution
+    assert_not automated_workflow_execution.disabled
+
+    load Rails.root.join('config/initializers/pipelines.rb')
+
+    assert automated_workflow_execution.reload.disabled
+  end
+end