Workflow Executions: Share results

app/components/nextflow_component.html.erb

@@ -118,6 +118,23 @@
                        t(:"components.nextflow.email_notification"),
                        class: "mr-2 text-sm font-medium text-slate-900 dark:text-white" %>
       </div>
+      <%# do not render checkbox for an automated workflow execution %>
+      <% if @namespace_type && [email protected]? %>
+        <div class="flex items-center h-5 mb-4">
+          <%= workflow.check_box :shared_with_namespace,
+                             {
+                               checked:
+                                 instance.present? && instance["shared_with_namespace"],
+                               class:
+                                 "w-4 h-4 mr-2.5 text-primary-600 bg-slate-100 border-slate-300 rounded focus:ring-primary-500 dark:focus:ring-primary-600 dark:ring-offset-slate-800 focus:ring-2 dark:bg-slate-700 dark:border-slate-600",
+                             } %>
+          <%= workflow.label :shared_with_namespace,
+                         t(
+                           :"components.nextflow.shared_with.#{@namespace_type.downcase}",
+                         ),
+                         class: "mr-2 text-sm font-medium text-slate-900 dark:text-white" %>
+        </div>
+      <% end %>
     <% end %>
 
     <button

app/components/nextflow_component.rb

@@ -7,16 +7,22 @@ class NextflowComponent < Component
   attr_reader :schema, :url, :workflow, :metadata_fields, :samples, :namespace_id, :instance
 
   # rubocop:disable Metrics/ParameterLists
-  def initialize(url:, samples:, workflow:, fields:, namespace_id:,
-                 allowed_to_update_samples: true, instance: nil)
+  def initialize(url:, samples:, workflow:, fields:, namespace_id:, allowed_to_update_samples: true, instance: nil)
     @samples = samples
     @namespace_id = namespace_id
     @url = url
     @workflow = workflow
     @metadata_fields = fields
     @allowed_to_update_samples = allowed_to_update_samples
     @instance = instance
+    @namespace_type = namespace_type(namespace_id)
   end
-
   # rubocop:enable Metrics/ParameterLists
+
+  def namespace_type(namespace_id)
+    namespace = Namespace.find_by(id: namespace_id)
+    return unless namespace
+
+    namespace.type
+  end
 end

app/components/workflow_executions/table_component.html.erb

@@ -145,31 +145,33 @@
                 tag: 'td',
                 classes: class_names('px-3 py-3 sticky right-0 bg-white dark:bg-slate-800 z-10 space-x-2')
               ) do %>
-                <% if workflow_execution.cancellable? && @row_actions.key?(:cancel) %>
-                  <%= link_to(
-                    t(:"workflow_executions.index.actions.cancel_button"),
-                    cancel_path(workflow_execution),
-                    data: {
-                      turbo_stream: true,
-                      turbo_method: :put,
-                      turbo_confirm: t(:"workflow_executions.index.actions.cancel_confirm"),
-                    },
-                    class:
-                      "font-medium text-blue-600 underline dark:text-blue-500 hover:no-underline cursor-pointer",
-                  ) %>
-                <% end %>
-                <% if workflow_execution.deletable? && @row_actions.key?(:destroy) %>
-                  <%= link_to(
-                    t(:"workflow_executions.index.actions.delete_button"),
-                    individual_path(workflow_execution),
-                    data: {
-                      turbo_stream: true,
-                      turbo_method: :delete,
-                      turbo_confirm: t(:"workflow_executions.index.actions.delete_confirm"),
-                    },
-                    class:
-                      "font-medium text-blue-600 underline dark:text-blue-500 hover:no-underline cursor-pointer",
-                  ) %>
+                <% if !workflow_execution.shared_with_namespace || @namespace.nil? %>
+                  <% if workflow_execution.cancellable? && @row_actions.key?(:cancel) %>
+                    <%= link_to(
+                      t(:"workflow_executions.index.actions.cancel_button"),
+                      cancel_path(workflow_execution),
+                      data: {
+                        turbo_stream: true,
+                        turbo_method: :put,
+                        turbo_confirm: t(:"workflow_executions.index.actions.cancel_confirm"),
+                      },
+                      class:
+                        "font-medium text-blue-600 underline dark:text-blue-500 hover:no-underline cursor-pointer",
+                    ) %>
+                  <% end %>
+                  <% if workflow_execution.deletable? && @row_actions.key?(:destroy) %>
+                    <%= link_to(
+                      t(:"workflow_executions.index.actions.delete_button"),
+                      individual_path(workflow_execution),
+                      data: {
+                        turbo_stream: true,
+                        turbo_method: :delete,
+                        turbo_confirm: t(:"workflow_executions.index.actions.delete_confirm"),
+                      },
+                      class:
+                        "font-medium text-blue-600 underline dark:text-blue-500 hover:no-underline cursor-pointer",
+                    ) %>
+                  <% end %>
                 <% end %>
               <% end %>
             <% end %>

app/components/workflow_executions/table_component.rb

@@ -78,7 +78,7 @@ def cancel_path(workflow_execution)
     end
 
     def individual_path(workflow_execution)
-      if @namespace
+      if @namespace && @namespace.type == 'Project'
         namespace_project_workflow_execution_path(
           @namespace.parent,
           @namespace.project,

app/controllers/data_exports_controller.rb

@@ -178,11 +178,10 @@ def redirect_to_project
 
   def redirect_to_workflow_execution
     workflow_execution = WorkflowExecution.find_by(id: params['identifier'])
-    submitter = workflow_execution.submitter
-    if submitter.user_type == 'human'
+    if workflow_execution.submitter == current_user
       redirect_to workflow_execution_path(workflow_execution)
     else
-      namespace = Namespace.find_by(puid: submitter.first_name)
+      namespace = workflow_execution.namespace
       redirect_to namespace_project_workflow_execution_path(namespace.parent, namespace.project, workflow_execution)
     end
   end

app/controllers/projects/workflow_executions_controller.rb

@@ -16,15 +16,22 @@ def namespace
     end
 
     def workflow_execution
-      @workflow_execution = WorkflowExecution.find_by!(id: params[:id], submitter: @project.namespace.automation_bot)
+      @workflow_execution = WorkflowExecution.find_by(
+        id: params[:id],
+        submitter: @project.namespace.automation_bot,
+        shared_with_namespace: false
+      ) || WorkflowExecution.find_by(id: params[:id], namespace:, shared_with_namespace: true)
+
+      raise ActiveRecord::RecordNotFound if @workflow_execution.nil?
     end
 
     def workflow_execution_update_params
       params.require(:workflow_execution).permit(:name)
     end
 
     def load_workflows
-      authorized_scope(WorkflowExecution, type: :relation, as: :automated, scope_options: { project: @project })
+      authorized_scope(WorkflowExecution, type: :relation, as: :automated_and_shared,
+                                          scope_options: { project: @project })
     end
 
     def current_page

app/controllers/workflow_executions/submissions_controller.rb

@@ -16,8 +16,9 @@ def pipeline_selection
     end
 
     def create
+      @namespace = Namespace.find_by(id: @namespace_id)
       fields_for_namespace(
-        namespace: Namespace.find_by(id: @namespace_id),
+        namespace: @namespace,
         show_fields: true
       )
       render status: :ok

app/controllers/workflow_executions_controller.rb

@@ -40,6 +40,7 @@ def workflow_execution_params_attributes
       :namespace_id,
       :update_samples,
       :email_notification,
+      :shared_with_namespace,
       { metadata: {},
         workflow_params: {},
         samples_workflow_executions_attributes: samples_workflow_execution_params_attributes }

app/policies/workflow_execution_policy.rb

@@ -21,16 +21,13 @@ def project_automation_bot?(user)
     User.user_types[user.user_type] == User.user_types[:project_automation_bot]
   end
 
-  def destroy? # rubocop:disable Metrics/AbcSize, Metrics/CyclomaticComplexity
-    unless project_automation_bot?(user)
-      return true if record.submitter.id == user.id
-      return true if Member::AccessLevel.manageable.include?(effective_access_level)
-    end
+  def destroy? # rubocop:disable Metrics/AbcSize
+    return true if record.submitter.id == user.id
 
+    # submitted by automation bot and user has managable access
     if (record.namespace.type == Namespaces::ProjectNamespace.sti_name) &&
        (record.submitter.id == record.namespace.automation_bot.id) &&
-       (record.namespace.automation_bot.id == user.id) &&
-       Member::AccessLevel.manageable.include?(effective_access_level(record.namespace.automation_bot))
+       Member::AccessLevel.manageable.include?(effective_access_level)
       return true
     end
 
@@ -40,18 +37,18 @@ def destroy? # rubocop:disable Metrics/AbcSize, Metrics/CyclomaticComplexity
   end
 
   def read? # rubocop:disable Metrics/AbcSize, Metrics/CyclomaticComplexity
-    unless project_automation_bot?(user)
-      return true if record.submitter.id == user.id
-      return true if effective_access_level(user) > Member::AccessLevel::NO_ACCESS
-    end
+    return true if record.submitter.id == user.id
 
+    # submitted by automation bot and user has access
     if (record.namespace.type == Namespaces::ProjectNamespace.sti_name) &&
-       (record.submitter.id == record.namespace.automation_bot.id) &&
-       (record.namespace.automation_bot.id == user.id) &&
-       (effective_access_level(record.namespace.automation_bot) > Member::AccessLevel::NO_ACCESS)
+       record.namespace.automation_bot && (record.submitter.id == record.namespace.automation_bot.id) &&
+       (effective_access_level > Member::AccessLevel::NO_ACCESS)
       return true
     end
 
+    # shared by submitter to namespace
+    return true if record.shared_with_namespace && (effective_access_level > Member::AccessLevel::NO_ACCESS)
+
     details[:id] = record.id
     false
   end
@@ -64,16 +61,13 @@ def create?
     false
   end
 
-  def cancel? # rubocop:disable Metrics/AbcSize, Metrics/CyclomaticComplexity
-    unless project_automation_bot?(user)
-      return true if record.submitter.id == user.id
-      return true if Member::AccessLevel.manageable.include?(effective_access_level)
-    end
+  def cancel? # rubocop:disable Metrics/AbcSize
+    return true if record.submitter.id == user.id
 
+    # submitted by automation bot and user has managable access
     if (record.namespace.type == Namespaces::ProjectNamespace.sti_name) &&
-       (record.submitter.id == record.namespace.automation_bot.id) &&
-       (record.namespace.automation_bot.id == user.id) &&
-       Member::AccessLevel.manageable.include?(effective_access_level(record.namespace.automation_bot))
+       record.namespace.automation_bot && (record.submitter.id == record.namespace.automation_bot.id) &&
+       Member::AccessLevel.manageable.include?(effective_access_level)
       return true
     end
 
@@ -82,17 +76,29 @@ def cancel? # rubocop:disable Metrics/AbcSize, Metrics/CyclomaticComplexity
     false
   end
 
-  def edit?
+  def edit? # rubocop:disable Metrics/AbcSize
     return true if record.submitter.id == user.id
-    return true if effective_access_level >= Member::AccessLevel::ANALYST
+
+    # submitted by automation bot and user is analyst or higher
+    if (record.namespace.type == Namespaces::ProjectNamespace.sti_name) &&
+       record.namespace.automation_bot && (record.submitter.id == record.namespace.automation_bot.id) &&
+       (effective_access_level >= Member::AccessLevel::ANALYST)
+      return true
+    end
 
     details[:id] = record.id
     false
   end
 
-  def update?
+  def update? # rubocop:disable Metrics/AbcSize
     return true if record.submitter.id == user.id
-    return true if effective_access_level >= Member::AccessLevel::ANALYST
+
+    # submitted by automation bot and user is analyst or higher
+    if (record.namespace.type == Namespaces::ProjectNamespace.sti_name) &&
+       record.namespace.automation_bot && (record.submitter.id == record.namespace.automation_bot.id) &&
+       (effective_access_level >= Member::AccessLevel::ANALYST)
+      return true
+    end
 
     details[:id] = record.id
     false
@@ -109,4 +115,11 @@ def update?
 
     relation.where(submitter_id: user.id)
   end
+
+  scope_for :relation, :automated_and_shared do |relation, options|
+    project = options[:project]
+
+    relation.where(submitter: project.namespace.automation_bot)
+            .or(relation.where(namespace_id: project.namespace.id, shared_with_namespace: true))
+  end
 end

app/services/data_exports/create_service.rb

@@ -71,7 +71,7 @@ def authorized_export_samples(namespace, sample_ids)
     def authorized_export_project_workflows
       project_namespace = Namespace.find(params['export_parameters']['namespace_id'])
       authorize! project_namespace, to: :export_data?
-      authorized_scope(WorkflowExecution, type: :relation, as: :automated,
+      authorized_scope(WorkflowExecution, type: :relation, as: :automated_and_shared,
                                           scope_options: { project: project_namespace.project })
         .where(id: params['export_parameters']['ids'])
     end

config/locales/en.yml

@@ -422,6 +422,9 @@ en:
     nextflow:
       email_notification: Receive an email notification when your analysis has completed?
       required: Required
+      shared_with:
+        group: Share results with Group members?
+        project: Share results with Project members?
       update_samples: Update samples with analysis results
     pagination:
       next: Next
@@ -1617,7 +1620,7 @@ en:
         search:
           placeholder: Filter by ID or name
         select_all_button: Select All
-        subtitle: These are the workflow executions that have been automatically launched for this project
+        subtitle: These are the workflow executions that have been automatically launched for this project, along with workflow executions that have been shared by any of its members.
         title: Workflow Executions
       show:
         cancel_button: Cancel

config/locales/fr.yml

@@ -422,6 +422,9 @@ fr:
     nextflow:
       email_notification: Receive an email notification when your analysis has completed?
       required: Required
+      shared_with:
+        group: Share results with Group members?
+        project: Share results with Project members?
       update_samples: Update samples with analysis results
     pagination:
       next: Next
@@ -1617,7 +1620,7 @@ fr:
         search:
           placeholder: Filter by ID or name
         select_all_button: Select All
-        subtitle: These are the workflow executions that have been automatically launched for this project
+        subtitle: These are the workflow executions that have been automatically launched for this project, along with workflow executions that have been shared by any of its members.
         title: Workflow Executions
       show:
         cancel_button: Cancel

db/migrate/20250108200329_add_shared_with_namespace_to_workflow_executions.rb

@@ -0,0 +1,8 @@
+# frozen_string_literal: true
+
+# Migration to add a new shared_with_namespace column to the workflow executions table
+class AddSharedWithNamespaceToWorkflowExecutions < ActiveRecord::Migration[7.2]
+  def change
+    add_column :workflow_executions, :shared_with_namespace, :boolean, default: false, null: false
+  end
+end

test/components/nextflow_component_test.rb

@@ -22,13 +22,15 @@ class NextflowComponentTest < ViewComponentTestCase
       workflow:,
       samples: [sample43, sample44],
       url: 'https://nf-co.re/testpipeline',
-      namespace_id: 'SDSDDFDSFDS',
+      namespace_id: projects(:project1).namespace,
       fields: %w[metadata_1 metadata_2 metadata_3]
     )
 
     assert_selector 'form' do
       assert_selector 'h1', text: 'phac-nml/iridanextexample', count: 1
       assert_selector 'input[type=text][name="workflow_execution[name]"]'
+      assert_selector 'input[type=checkbox][name="workflow_execution[shared_with_namespace]"]'
+      assert_text 'Share results with Project members?'
     end
   end
 
@@ -155,15 +157,17 @@ class NextflowComponentTest < ViewComponentTestCase
                                      url: 'https://github.com/phac-nml/mikrokondo',
                                      name: 'phac-nml/mikrokondo',
                                      description: 'Mikrokondo pipeline'
-                                   }, '0.1.2',
+                                   },
+                                   { 'name' => '0.1.2',
+                                     'automatable' => true },
                                    Rails.root.join('test/fixtures/files/nextflow/mikrokondo/nextflow_schema.json'),
                                    Rails.root.join('test/fixtures/files/nextflow/samplesheet_schema.json'))
 
     render_inline NextflowComponent.new(
       workflow:,
       samples: [],
       url: 'https://nf-co.re/testpipeline',
-      namespace_id: 'SDSDDFDSFDS',
+      namespace_id: projects(:project1).namespace,
       fields: %w[metadata_1 metadata_2 metadata_3],
       instance:
     )
@@ -179,6 +183,7 @@ class NextflowComponentTest < ViewComponentTestCase
       assert_selector 'input[type="radio"][name="workflow_execution[workflow_params][skip_depth_sampling]"][value="false"][checked="checked"]',
                       count: 1
       assert_no_selector 'input[type="radio"][name="workflow_execution[workflow_params][skip_depth_sampling]"][value="true"][checked="checked"]'
+      assert_no_selector 'input[type=checkbox][name="workflow_execution[shared_with_namespace]"]'
     end
     # rubocop:enable Layout/LineLength
   end