From eea92bd9a4b7fa5e4942e508926b73f95a2c639d Mon Sep 17 00:00:00 2001
From: Meghan Chua <17057809+malchua@users.noreply.github.com>
Date: Wed, 8 Jan 2025 14:20:53 -0600
Subject: [PATCH 01/57] Add migration to add shared_with_namespace column to
 workflow executions

---
 ...29_add_shared_with_namespace_to_workflow_executions.rb | 8 ++++++++
 db/schema.rb                                              | 1 +
 2 files changed, 9 insertions(+)
 create mode 100644 db/migrate/20250108200329_add_shared_with_namespace_to_workflow_executions.rb

diff --git a/db/migrate/20250108200329_add_shared_with_namespace_to_workflow_executions.rb b/db/migrate/20250108200329_add_shared_with_namespace_to_workflow_executions.rb
new file mode 100644
index 0000000000..5fa9ad4190
--- /dev/null
+++ b/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
diff --git a/db/schema.rb b/db/schema.rb
index ca8c7f3b1e..95eb413b05 100644
--- a/db/schema.rb
+++ b/db/schema.rb
@@ -335,6 +335,7 @@
     t.uuid "namespace_id"
     t.boolean "cleaned", default: false, null: false
     t.jsonb "log_data"
+    t.boolean "shared_with_namespace", default: false, null: false
     t.index ["created_at"], name: "index_workflow_executions_on_created_at"
     t.index ["namespace_id"], name: "index_workflow_executions_on_namespace_id"
     t.index ["state"], name: "index_workflow_executions_on_state"

From ee9c1c030bf51364b3e4f02ed94ff17c42383a6d Mon Sep 17 00:00:00 2001
From: Meghan Chua <17057809+malchua@users.noreply.github.com>
Date: Thu, 9 Jan 2025 15:22:19 -0600
Subject: [PATCH 02/57] Add checkbox to workflow execution creation form

---
 app/components/nextflow_component.html.erb    | 24 +++++++++++++++++++
 .../workflow_executions_controller.rb         |  3 ++-
 config/locales/en.yml                         |  1 +
 config/locales/fr.yml                         |  1 +
 4 files changed, 28 insertions(+), 1 deletion(-)

diff --git a/app/components/nextflow_component.html.erb b/app/components/nextflow_component.html.erb
index 83c0327193..2c0cf69059 100644
--- a/app/components/nextflow_component.html.erb
+++ b/app/components/nextflow_component.html.erb
@@ -118,6 +118,30 @@
                        t(:"components.nextflow.email_notification"),
                        class: "mr-2 text-sm font-medium text-slate-900 dark:text-white" %>
       </div>
+      <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"),
+                       class: "mr-2 text-sm font-medium text-slate-900 dark:text-white" %>
+      </div>
     <% end %>
 
     <button
diff --git a/app/controllers/workflow_executions_controller.rb b/app/controllers/workflow_executions_controller.rb
index 01c231ea9a..587446a0bf 100644
--- a/app/controllers/workflow_executions_controller.rb
+++ b/app/controllers/workflow_executions_controller.rb
@@ -34,12 +34,13 @@ def workflow_execution_update_params
     params.require(:workflow_execution).permit(:name)
   end
 
-  def workflow_execution_params_attributes
+  def workflow_execution_params_attributes # rubocop:disable Metrics/MethodLength
     [
       :name,
       :namespace_id,
       :update_samples,
       :email_notification,
+      :shared_with_namespace,
       { metadata: {},
         workflow_params: {},
         samples_workflow_executions_attributes: samples_workflow_execution_params_attributes }
diff --git a/config/locales/en.yml b/config/locales/en.yml
index 3e9ed86011..840f0bf82c 100644
--- a/config/locales/en.yml
+++ b/config/locales/en.yml
@@ -422,6 +422,7 @@ en:
     nextflow:
       email_notification: Receive an email notification when your analysis has completed?
       required: Required
+      shared_with_namespace: Share results with Project/Group?
       update_samples: Update samples with analysis results
     pagination:
       next: Next
diff --git a/config/locales/fr.yml b/config/locales/fr.yml
index aaff3e4f85..67e5c8a871 100644
--- a/config/locales/fr.yml
+++ b/config/locales/fr.yml
@@ -422,6 +422,7 @@ fr:
     nextflow:
       email_notification: Receive an email notification when your analysis has completed?
       required: Required
+      shared_with_namespace: Share results with Project/Group?
       update_samples: Update samples with analysis results
     pagination:
       next: Next

From b33854910b4cebdc90371819f3603c3c4c0d2a0b Mon Sep 17 00:00:00 2001
From: Meghan Chua <17057809+malchua@users.noreply.github.com>
Date: Thu, 9 Jan 2025 15:24:25 -0600
Subject: [PATCH 03/57] Update workflow execution creation tests

---
 test/controllers/workflow_executions_controller_test.rb | 2 ++
 test/system/workflow_executions/submissions_test.rb     | 7 +++++++
 2 files changed, 9 insertions(+)

diff --git a/test/controllers/workflow_executions_controller_test.rb b/test/controllers/workflow_executions_controller_test.rb
index 4c00eb9eee..a61e8a3b9b 100644
--- a/test/controllers/workflow_executions_controller_test.rb
+++ b/test/controllers/workflow_executions_controller_test.rb
@@ -25,6 +25,7 @@ class WorkflowExecutionsControllerTest < ActionDispatch::IntegrationTest
                workflow_engine_parameters: { '-r': 'dev' },
                workflow_url: 'https://github.com/phac-nml/iridanextexample',
                email_notification: true,
+               shared_with_namespace: true,
                namespace_id: projects(:project1).namespace.id,
                samples_workflow_executions_attributes: [
                  {
@@ -49,6 +50,7 @@ class WorkflowExecutionsControllerTest < ActionDispatch::IntegrationTest
     assert_equal 1, created_workflow_execution.samples_workflow_executions.count
     assert_equal @sample1, created_workflow_execution.samples_workflow_executions.first.sample
     assert_equal true, created_workflow_execution.email_notification
+    assert_equal true, created_workflow_execution.shared_with_namespace
   end
 
   test 'should cancel a new workflow with valid params' do
diff --git a/test/system/workflow_executions/submissions_test.rb b/test/system/workflow_executions/submissions_test.rb
index 3a5bd9ee92..cb4932293d 100644
--- a/test/system/workflow_executions/submissions_test.rb
+++ b/test/system/workflow_executions/submissions_test.rb
@@ -69,6 +69,7 @@ class SubmissionsTest < ApplicationSystemTestCase
 
         assert_text I18n.t(:'components.nextflow.update_samples')
         assert_text I18n.t(:'components.nextflow.email_notification')
+        assert_text I18n.t(:'components.nextflow.shared_with_namespace')
       end
     end
 
@@ -103,6 +104,7 @@ class SubmissionsTest < ApplicationSystemTestCase
 
         assert_text I18n.t(:'components.nextflow.update_samples')
         assert_text I18n.t(:'components.nextflow.email_notification')
+        assert_text I18n.t(:'components.nextflow.shared_with_namespace')
       end
     end
 
@@ -137,6 +139,7 @@ class SubmissionsTest < ApplicationSystemTestCase
 
         assert_no_text I18n.t(:'components.nextflow.update_samples')
         assert_text I18n.t(:'components.nextflow.email_notification')
+        assert_text I18n.t(:'components.nextflow.shared_with_namespace')
       end
     end
 
@@ -174,6 +177,7 @@ class SubmissionsTest < ApplicationSystemTestCase
 
         assert_no_text I18n.t(:'components.nextflow.update_samples')
         assert_text I18n.t(:'components.nextflow.email_notification')
+        assert_text I18n.t(:'components.nextflow.shared_with_namespace')
       end
     end
 
@@ -216,6 +220,7 @@ class SubmissionsTest < ApplicationSystemTestCase
 
         assert_text I18n.t(:'components.nextflow.update_samples')
         assert_text I18n.t(:'components.nextflow.email_notification')
+        assert_text I18n.t(:'components.nextflow.shared_with_namespace')
       end
     end
 
@@ -250,6 +255,7 @@ class SubmissionsTest < ApplicationSystemTestCase
 
         assert_text I18n.t(:'components.nextflow.update_samples')
         assert_text I18n.t(:'components.nextflow.email_notification')
+        assert_text I18n.t(:'components.nextflow.shared_with_namespace')
       end
     end
 
@@ -284,6 +290,7 @@ class SubmissionsTest < ApplicationSystemTestCase
 
         assert_no_text I18n.t(:'components.nextflow.update_samples')
         assert_text I18n.t(:'components.nextflow.email_notification')
+        assert_text I18n.t(:'components.nextflow.shared_with_namespace')
       end
     end
 

From e022bdbf6e0c841adda1215f7f604e261765039e Mon Sep 17 00:00:00 2001
From: Meghan Chua <17057809+malchua@users.noreply.github.com>
Date: Fri, 10 Jan 2025 14:24:13 -0600
Subject: [PATCH 04/57] Define new scope for returning shared workflow
 executions

---
 app/policies/workflow_execution_policy.rb       |  7 +++++++
 test/fixtures/workflow_executions.yml           | 11 +++++++++++
 test/policies/workflow_execution_policy_test.rb |  9 +++++++++
 3 files changed, 27 insertions(+)

diff --git a/app/policies/workflow_execution_policy.rb b/app/policies/workflow_execution_policy.rb
index 60914957e0..33b297f8e9 100644
--- a/app/policies/workflow_execution_policy.rb
+++ b/app/policies/workflow_execution_policy.rb
@@ -109,4 +109,11 @@ 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
diff --git a/test/fixtures/workflow_executions.yml b/test/fixtures/workflow_executions.yml
index 8b517043c5..383d7f6faa 100644
--- a/test/fixtures/workflow_executions.yml
+++ b/test/fixtures/workflow_executions.yml
@@ -863,3 +863,14 @@ workflow_execution_valid_on_group:
   run_id: "my_group_run_id_1"
   submitter_id: <%= ActiveRecord::FixtureSet.identify(:james_doe, :uuid) %>
   namespace_id: <%= ActiveRecord::FixtureSet.identify(:group_one, :uuid) %>
+
+workflow_execution_shared:
+  <<: *DEFAULTS
+  metadata: { "workflow_name": "wn1", "workflow_version": "wv1" }
+  workflow_params: { "key_a": "value_a" }
+  workflow_engine_parameters: { "-r": "dev" }
+  workflow_url: "my_workflow_url"
+  run_id: "my_run_id_1"
+  submitter_id: <%= ActiveRecord::FixtureSet.identify(:john_doe, :uuid) %>
+  namespace_id: <%= ActiveRecord::FixtureSet.identify(:project1_namespace, :uuid) %>
+  shared_with_namespace: true
diff --git a/test/policies/workflow_execution_policy_test.rb b/test/policies/workflow_execution_policy_test.rb
index f96f3250ba..d27008a160 100644
--- a/test/policies/workflow_execution_policy_test.rb
+++ b/test/policies/workflow_execution_policy_test.rb
@@ -131,4 +131,13 @@ def setup
 
     assert_equal 19, scoped_user_workflow_executions.count
   end
+
+  test 'automated and shared scope' do
+    project = projects(:project1)
+
+    workflow_executions = @policy.apply_scope(WorkflowExecution, type: :relation, name: :automated_and_shared,
+                                                                 scope_options: { project: })
+
+    assert_equal 11, workflow_executions.count
+  end
 end

From fd899d2f1d2a5599704189a7d93488c28f934de6 Mon Sep 17 00:00:00 2001
From: Meghan Chua <17057809+malchua@users.noreply.github.com>
Date: Fri, 10 Jan 2025 15:34:17 -0600
Subject: [PATCH 05/57] Add shared workflow executions to list of WEs for a
 project

---
 app/components/workflow_executions/table_component.html.erb | 2 +-
 app/controllers/projects/workflow_executions_controller.rb  | 3 ++-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/app/components/workflow_executions/table_component.html.erb b/app/components/workflow_executions/table_component.html.erb
index 02a8d4e9f9..091850df00 100644
--- a/app/components/workflow_executions/table_component.html.erb
+++ b/app/components/workflow_executions/table_component.html.erb
@@ -140,7 +140,7 @@
                 <% end %>
               <% end %>
             <% end %>
-            <% if @renders_row_actions %>
+            <% if @renders_row_actions && !workflow_execution.shared_with_namespace %>
               <%= render_cell(
                 tag: 'td',
                 classes: class_names('px-3 py-3 sticky right-0 bg-white dark:bg-slate-800 z-10 space-x-2')
diff --git a/app/controllers/projects/workflow_executions_controller.rb b/app/controllers/projects/workflow_executions_controller.rb
index b6d255ace9..c2e7eb37e8 100644
--- a/app/controllers/projects/workflow_executions_controller.rb
+++ b/app/controllers/projects/workflow_executions_controller.rb
@@ -24,7 +24,8 @@ def workflow_execution_update_params
     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

From 2c1b9ccbbd787c719aca55d6d65ba7b25161e164 Mon Sep 17 00:00:00 2001
From: Meghan Chua <17057809+malchua@users.noreply.github.com>
Date: Mon, 13 Jan 2025 12:08:47 -0600
Subject: [PATCH 06/57] Create new policy for getting shared workflow
 executions

---
 app/policies/workflow_execution_policy.rb     |  6 +++++
 test/fixtures/workflow_executions.yml         | 26 +++++++++++++++++--
 .../workflow_execution_policy_test.rb         | 12 +++++++--
 3 files changed, 40 insertions(+), 4 deletions(-)

diff --git a/app/policies/workflow_execution_policy.rb b/app/policies/workflow_execution_policy.rb
index 33b297f8e9..39e3c86d6e 100644
--- a/app/policies/workflow_execution_policy.rb
+++ b/app/policies/workflow_execution_policy.rb
@@ -116,4 +116,10 @@ def update?
     relation.where(submitter: project.namespace.automation_bot)
             .or(relation.where(namespace_id: project.namespace.id, shared_with_namespace: true))
   end
+
+  scope_for :relation, :user_and_shared do |relation, options|
+    user = options[:user]
+
+    relation.where(submitter_id: user.id).or(relation.where(shared_with_namespace: true))
+  end
 end
diff --git a/test/fixtures/workflow_executions.yml b/test/fixtures/workflow_executions.yml
index 383d7f6faa..7e82aa32fc 100644
--- a/test/fixtures/workflow_executions.yml
+++ b/test/fixtures/workflow_executions.yml
@@ -864,13 +864,35 @@ workflow_execution_valid_on_group:
   submitter_id: <%= ActiveRecord::FixtureSet.identify(:james_doe, :uuid) %>
   namespace_id: <%= ActiveRecord::FixtureSet.identify(:group_one, :uuid) %>
 
-workflow_execution_shared:
+workflow_execution_shared1:
   <<: *DEFAULTS
   metadata: { "workflow_name": "wn1", "workflow_version": "wv1" }
   workflow_params: { "key_a": "value_a" }
   workflow_engine_parameters: { "-r": "dev" }
   workflow_url: "my_workflow_url"
-  run_id: "my_run_id_1"
+  run_id: "my_run_id_shared_1"
   submitter_id: <%= ActiveRecord::FixtureSet.identify(:john_doe, :uuid) %>
   namespace_id: <%= ActiveRecord::FixtureSet.identify(:project1_namespace, :uuid) %>
   shared_with_namespace: true
+
+workflow_execution_shared2:
+  <<: *DEFAULTS
+  metadata: { "workflow_name": "wn1", "workflow_version": "wv1" }
+  workflow_params: { "key_a": "value_a" }
+  workflow_engine_parameters: { "-r": "dev" }
+  workflow_url: "my_workflow_url"
+  run_id: "my_run_id_shared_2"
+  submitter_id: <%= ActiveRecord::FixtureSet.identify(:james_doe, :uuid) %>
+  namespace_id: <%= ActiveRecord::FixtureSet.identify(:project1_namespace, :uuid) %>
+  shared_with_namespace: true
+
+workflow_execution_shared3:
+  <<: *DEFAULTS
+  metadata: { "workflow_name": "wn1", "workflow_version": "wv1" }
+  workflow_params: { "key_a": "value_a" }
+  workflow_engine_parameters: { "-r": "dev" }
+  workflow_url: "my_workflow_url"
+  run_id: "my_run_id_shared_3"
+  submitter_id: <%= ActiveRecord::FixtureSet.identify(:james_doe, :uuid) %>
+  namespace_id: <%= ActiveRecord::FixtureSet.identify(:project2_namespace, :uuid) %>
+  shared_with_namespace: true
diff --git a/test/policies/workflow_execution_policy_test.rb b/test/policies/workflow_execution_policy_test.rb
index d27008a160..ce7984d89a 100644
--- a/test/policies/workflow_execution_policy_test.rb
+++ b/test/policies/workflow_execution_policy_test.rb
@@ -129,7 +129,7 @@ def setup
     scoped_user_workflow_executions = @policy.apply_scope(WorkflowExecution, type: :relation, name: :user,
                                                                              scope_options: { user: @user })
 
-    assert_equal 19, scoped_user_workflow_executions.count
+    assert_equal 20, scoped_user_workflow_executions.count
   end
 
   test 'automated and shared scope' do
@@ -138,6 +138,14 @@ def setup
     workflow_executions = @policy.apply_scope(WorkflowExecution, type: :relation, name: :automated_and_shared,
                                                                  scope_options: { project: })
 
-    assert_equal 11, workflow_executions.count
+    assert_equal 12, workflow_executions.count
+  end
+
+  test 'user and shared scope' do
+    workflow_executions = @policy.apply_scope(WorkflowExecution, type: :relation, name: :user_and_shared,
+                                                                 scope_options: { user: @user })
+
+    assert_equal 22, workflow_executions.count
+    assert workflow_executions.exists?(run_id: 'my_run_id_shared_2')
   end
 end

From 34ee741a398b9eadd54d3bf424c222c227f9972d Mon Sep 17 00:00:00 2001
From: Meghan Chua <17057809+malchua@users.noreply.github.com>
Date: Mon, 13 Jan 2025 12:30:38 -0600
Subject: [PATCH 07/57] Update load_workflows to add workflows shared to the
 Project

---
 app/controllers/workflow_executions_controller.rb | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

diff --git a/app/controllers/workflow_executions_controller.rb b/app/controllers/workflow_executions_controller.rb
index 587446a0bf..81a7985200 100644
--- a/app/controllers/workflow_executions_controller.rb
+++ b/app/controllers/workflow_executions_controller.rb
@@ -23,7 +23,17 @@ def workflow_execution
   end
 
   def load_workflows
-    authorized_scope(WorkflowExecution, type: :relation, as: :user, scope_options: { user: current_user })
+    workflow_executions = authorized_scope(WorkflowExecution, type: :relation, as: :user_and_shared,
+                                                              scope_options: { user: current_user })
+
+    shared_workflow_executions = []
+    workflow_executions.where(shared_with_namespace: true).find_each do |workflow_execution|
+      shared_workflow_executions.append(workflow_execution) if authorize! workflow_execution.namespace,
+                                                                          to: :view_workflow_executions?
+    end
+
+    workflow_executions.where(shared_with_namespace: false)
+                       .or(workflow_executions.where(id: shared_workflow_executions.map(&:id)))
   end
 
   def workflow_execution_params

From d8f274c8afbfe0dc186d59899ee444242d2994ee Mon Sep 17 00:00:00 2001
From: Meghan Chua <17057809+malchua@users.noreply.github.com>
Date: Tue, 14 Jan 2025 13:36:09 -0600
Subject: [PATCH 08/57] Remove scope for getting user and shared workflows

---
 app/controllers/workflow_executions_controller.rb | 12 +-----------
 app/policies/workflow_execution_policy.rb         |  6 ------
 test/policies/workflow_execution_policy_test.rb   |  8 --------
 3 files changed, 1 insertion(+), 25 deletions(-)

diff --git a/app/controllers/workflow_executions_controller.rb b/app/controllers/workflow_executions_controller.rb
index 81a7985200..587446a0bf 100644
--- a/app/controllers/workflow_executions_controller.rb
+++ b/app/controllers/workflow_executions_controller.rb
@@ -23,17 +23,7 @@ def workflow_execution
   end
 
   def load_workflows
-    workflow_executions = authorized_scope(WorkflowExecution, type: :relation, as: :user_and_shared,
-                                                              scope_options: { user: current_user })
-
-    shared_workflow_executions = []
-    workflow_executions.where(shared_with_namespace: true).find_each do |workflow_execution|
-      shared_workflow_executions.append(workflow_execution) if authorize! workflow_execution.namespace,
-                                                                          to: :view_workflow_executions?
-    end
-
-    workflow_executions.where(shared_with_namespace: false)
-                       .or(workflow_executions.where(id: shared_workflow_executions.map(&:id)))
+    authorized_scope(WorkflowExecution, type: :relation, as: :user, scope_options: { user: current_user })
   end
 
   def workflow_execution_params
diff --git a/app/policies/workflow_execution_policy.rb b/app/policies/workflow_execution_policy.rb
index 39e3c86d6e..33b297f8e9 100644
--- a/app/policies/workflow_execution_policy.rb
+++ b/app/policies/workflow_execution_policy.rb
@@ -116,10 +116,4 @@ def update?
     relation.where(submitter: project.namespace.automation_bot)
             .or(relation.where(namespace_id: project.namespace.id, shared_with_namespace: true))
   end
-
-  scope_for :relation, :user_and_shared do |relation, options|
-    user = options[:user]
-
-    relation.where(submitter_id: user.id).or(relation.where(shared_with_namespace: true))
-  end
 end
diff --git a/test/policies/workflow_execution_policy_test.rb b/test/policies/workflow_execution_policy_test.rb
index ce7984d89a..ab7e607d0d 100644
--- a/test/policies/workflow_execution_policy_test.rb
+++ b/test/policies/workflow_execution_policy_test.rb
@@ -140,12 +140,4 @@ def setup
 
     assert_equal 12, workflow_executions.count
   end
-
-  test 'user and shared scope' do
-    workflow_executions = @policy.apply_scope(WorkflowExecution, type: :relation, name: :user_and_shared,
-                                                                 scope_options: { user: @user })
-
-    assert_equal 22, workflow_executions.count
-    assert workflow_executions.exists?(run_id: 'my_run_id_shared_2')
-  end
 end

From 88f90ae1c9287c394f62f794c4c5eb8d1bc4f0ab Mon Sep 17 00:00:00 2001
From: Meghan Chua <17057809+malchua@users.noreply.github.com>
Date: Tue, 14 Jan 2025 13:39:49 -0600
Subject: [PATCH 09/57] Update system tests since we added new fixtures

---
 .../projects/workflow_executions_test.rb      | 34 ++++++++++---------
 test/system/workflow_executions_test.rb       | 14 ++++----
 2 files changed, 26 insertions(+), 22 deletions(-)

diff --git a/test/system/projects/workflow_executions_test.rb b/test/system/projects/workflow_executions_test.rb
index 48d299c529..f34a19a987 100644
--- a/test/system/projects/workflow_executions_test.rb
+++ b/test/system/projects/workflow_executions_test.rb
@@ -27,13 +27,15 @@ class WorkflowExecutionsTest < ApplicationSystemTestCase
       assert_selector 'h1', text: I18n.t(:'projects.workflow_executions.index.title')
       assert_selector 'p', text: I18n.t(:'projects.workflow_executions.index.subtitle')
 
-      assert_selector '#workflow-executions-table table tbody tr', count: 10
+      assert_selector '#workflow-executions-table table tbody tr', count: 12
     end
 
     test 'should sort a list of workflow executions' do
       workflow_execution1 = workflow_executions(:automated_workflow_execution)
       workflow_execution3 = workflow_executions(:automated_example_canceling)
       workflow_execution4 = workflow_executions(:automated_workflow_execution_existing)
+      workflow_execution_shared1 = workflow_executions(:workflow_execution_shared1)
+      workflow_execution_shared2 = workflow_executions(:workflow_execution_shared2)
 
       visit namespace_project_workflow_executions_path(@namespace, @project)
 
@@ -44,19 +46,19 @@ class WorkflowExecutionsTest < ApplicationSystemTestCase
       assert_selector "#workflow-executions-table table thead th:nth-child(#{@run_id_col}) svg.icon-arrow_up"
 
       within('#workflow-executions-table table tbody') do
-        assert_selector 'tr', count: 10
+        assert_selector 'tr', count: 12
         assert_selector "tr:first-child td:nth-child(#{@run_id_col})", text: workflow_execution4.run_id
         assert_selector "tr:nth-child(#{@run_id_col}) td:nth-child(#{@run_id_col})", text: workflow_execution1.run_id
-        assert_selector "tr:last-child td:nth-child(#{@run_id_col})", text: @workflow_execution2.run_id
+        assert_selector "tr:last-child td:nth-child(#{@run_id_col})", text: workflow_execution_shared2.run_id
       end
 
       click_on 'Run ID'
       assert_selector "#workflow-executions-table table thead th:nth-child(#{@run_id_col}) svg.icon-arrow_down"
 
       within('#workflow-executions-table table tbody') do
-        assert_selector 'tr', count: 10
-        assert_selector "tr:first-child td:nth-child(#{@run_id_col})", text: @workflow_execution2.run_id
-        assert_selector "tr:nth-child(2) td:nth-child(#{@run_id_col})", text: workflow_execution3.run_id
+        assert_selector 'tr', count: 12
+        assert_selector "tr:first-child td:nth-child(#{@run_id_col})", text: workflow_execution_shared2.run_id
+        assert_selector "tr:nth-child(2) td:nth-child(#{@run_id_col})", text: workflow_execution_shared1.run_id
         assert_selector "tr:last-child td:nth-child(#{@run_id_col})", text: workflow_execution4.run_id
       end
 
@@ -64,24 +66,24 @@ class WorkflowExecutionsTest < ApplicationSystemTestCase
       assert_selector "#workflow-executions-table table thead th:nth-child(#{@workflow_name_col}) svg.icon-arrow_up"
 
       within('#workflow-executions-table table tbody') do
-        assert_selector 'tr', count: 10
+        assert_selector 'tr', count: 12
         assert_selector "tr:first-child td:nth-child(#{@workflow_name_col})",
                         text: @workflow_execution2.metadata['workflow_name']
         assert_selector "tr:nth-child(2) td:nth-child(#{@workflow_name_col})",
                         text: workflow_execution3.metadata['workflow_name']
         assert_selector "tr:last-child td:nth-child(#{@workflow_name_col})",
-                        text: workflow_execution4.metadata['workflow_name']
+                        text: workflow_execution_shared2.metadata['workflow_name']
       end
 
       click_on I18n.t(:'workflow_executions.table_component.workflow_name')
       assert_selector "#workflow-executions-table table thead th:nth-child(#{@workflow_name_col}) svg.icon-arrow_down"
 
       within('#workflow-executions-table table tbody') do
-        assert_selector 'tr', count: 10
+        assert_selector 'tr', count: 12
         assert_selector "tr:first-child td:nth-child(#{@workflow_name_col})",
-                        text: workflow_execution4.metadata['workflow_name']
+                        text: workflow_execution_shared1.metadata['workflow_name']
         assert_selector "tr:nth-child(2) td:nth-child(#{@workflow_name_col})",
-                        text: workflow_execution1.metadata['workflow_name']
+                        text: workflow_execution_shared2.metadata['workflow_name']
         assert_selector "tr:last-child td:nth-child(#{@workflow_name_col})",
                         text: @workflow_execution2.metadata['workflow_name']
       end
@@ -315,7 +317,7 @@ class WorkflowExecutionsTest < ApplicationSystemTestCase
       end
 
       within %(#workflow-executions-table table tbody) do
-        assert_selector 'tr', count: 9
+        assert_selector 'tr', count: 11
         assert_no_text @workflow_execution1.id
       end
     end
@@ -323,8 +325,8 @@ class WorkflowExecutionsTest < ApplicationSystemTestCase
     test 'can filter by ID and name on projects workflow execution index page' do
       visit namespace_project_workflow_executions_path(@namespace, @project)
 
-      assert_text 'Displaying 10 items'
-      assert_selector 'table tbody tr', count: 10
+      assert_text 'Displaying 12 items'
+      assert_selector 'table tbody tr', count: 12
 
       within('table tbody') do
         assert_text @workflow_execution1.id
@@ -351,8 +353,8 @@ class WorkflowExecutionsTest < ApplicationSystemTestCase
               with: ''
       find('input.t-search-component').native.send_keys(:return)
 
-      assert_text 'Displaying 10 items'
-      assert_selector 'table tbody tr', count: 10
+      assert_text 'Displaying 12 items'
+      assert_selector 'table tbody tr', count: 12
 
       fill_in placeholder: I18n.t(:'workflow_executions.index.search.placeholder'),
               with: @workflow_execution2.name
diff --git a/test/system/workflow_executions_test.rb b/test/system/workflow_executions_test.rb
index d37b7b79f6..e4ebccb584 100644
--- a/test/system/workflow_executions_test.rb
+++ b/test/system/workflow_executions_test.rb
@@ -3,7 +3,7 @@
 require 'application_system_test_case'
 
 class WorkflowExecutionsTest < ApplicationSystemTestCase
-  WORKFLOW_EXECUTION_COUNT = 19
+  WORKFLOW_EXECUTION_COUNT = 20
 
   setup do
     @user = users(:john_doe)
@@ -27,6 +27,7 @@ class WorkflowExecutionsTest < ApplicationSystemTestCase
 
     assert_selector 'h1', text: I18n.t(:'workflow_executions.index.title')
 
+    assert_text 'Displaying 20 items'
     assert_selector '#workflow-executions-table table tbody tr', count: WORKFLOW_EXECUTION_COUNT
   end
 
@@ -57,6 +58,7 @@ class WorkflowExecutionsTest < ApplicationSystemTestCase
     workflow_execution8 = workflow_executions(:irida_next_example_canceling)
     workflow_execution9 = workflow_executions(:irida_next_example_canceled)
     workflow_execution12 = workflow_executions(:irida_next_example_new)
+    workflow_execution_shared1 = workflow_executions(:workflow_execution_shared1)
 
     visit workflow_executions_path
 
@@ -78,7 +80,7 @@ class WorkflowExecutionsTest < ApplicationSystemTestCase
     within('#workflow-executions-table table tbody') do
       assert_selector 'tr', count: WORKFLOW_EXECUTION_COUNT
       assert_selector "tr:first-child td:nth-child(#{@run_id_col})", text: workflow_execution.run_id
-      assert_selector "tr:nth-child(3) td:nth-child(#{@run_id_col})", text: workflow_execution9.run_id
+      assert_selector "tr:nth-child(3) td:nth-child(#{@run_id_col})", text: workflow_execution_shared1.run_id
       assert_selector "tr:last-child td:nth-child(#{@run_id_col})", text: workflow_execution1.run_id
     end
 
@@ -374,8 +376,8 @@ class WorkflowExecutionsTest < ApplicationSystemTestCase
   test 'can filter by ID and name on workflow execution index page' do
     visit workflow_executions_path
 
-    assert_text 'Displaying 19 items'
-    assert_selector 'table tbody tr', count: 19
+    assert_text 'Displaying 20 items'
+    assert_selector 'table tbody tr', count: WORKFLOW_EXECUTION_COUNT
 
     within('table tbody') do
       assert_text @workflow_execution2.id
@@ -402,8 +404,8 @@ class WorkflowExecutionsTest < ApplicationSystemTestCase
             with: ''
     find('input.t-search-component').native.send_keys(:return)
 
-    assert_text 'Displaying 19 items'
-    assert_selector 'table tbody tr', count: 19
+    assert_text 'Displaying 20 items'
+    assert_selector 'table tbody tr', count: WORKFLOW_EXECUTION_COUNT
 
     fill_in placeholder: I18n.t(:'workflow_executions.index.search.placeholder'),
             with: @workflow_execution3.name

From 49fe0c4591b1ded18e1063fe1f9ffe81b8993e13 Mon Sep 17 00:00:00 2001
From: Meghan Chua <17057809+malchua@users.noreply.github.com>
Date: Fri, 17 Jan 2025 07:25:03 -0600
Subject: [PATCH 10/57] Add workflow execution section in Groups sidebar

---
 app/views/layouts/groups.html.erb | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/app/views/layouts/groups.html.erb b/app/views/layouts/groups.html.erb
index d5587b770e..3bd2114bff 100644
--- a/app/views/layouts/groups.html.erb
+++ b/app/views/layouts/groups.html.erb
@@ -38,6 +38,14 @@
             label: t(:"groups.sidebar.activity"),
             selected: @current_page == t(:"groups.sidebar.activity"),
           ) %>
+          <% if allowed_to?(:view_workflow_executions?, @group) && @pipelines_enabled %>
+            <%= render section.with_item(
+              url: group_workflow_executions_path(@group),
+              icon: "command_line",
+              label: t(:"groups.sidebar.workflow_executions"),
+              selected: @current_page == t(:"groups.sidebar.workflow_executions"),
+            ) %>
+          <% end %>
           <% if allowed_to?(:update?, @group) %>
             <%= render section.with_multi_level_menu(
               title: t(:"groups.sidebar.settings"),

From b99d04d405632c9c83e5a4e64825eac0834a7b5d Mon Sep 17 00:00:00 2001
From: Meghan Chua <17057809+malchua@users.noreply.github.com>
Date: Fri, 17 Jan 2025 07:27:44 -0600
Subject: [PATCH 11/57] Create new workflow execution controller for Groups

---
 .../groups/workflow_executions_controller.rb  | 60 +++++++++++++++++++
 1 file changed, 60 insertions(+)
 create mode 100644 app/controllers/groups/workflow_executions_controller.rb

diff --git a/app/controllers/groups/workflow_executions_controller.rb b/app/controllers/groups/workflow_executions_controller.rb
new file mode 100644
index 0000000000..88c88b8444
--- /dev/null
+++ b/app/controllers/groups/workflow_executions_controller.rb
@@ -0,0 +1,60 @@
+# frozen_string_literal: true
+
+module Groups
+  class WorkflowExecutionsController < Groups::ApplicationController
+    include BreadcrumbNavigation
+    include Metadata
+    include WorkflowExecutionActions
+
+    before_action :namespace
+
+    private
+
+    def namespace
+      @namespace = @group
+    end
+
+    def workflow_execution
+      @workflow_execution = WorkflowExecution.find_by!(id: params[:id])
+    end
+
+    def workflow_execution_update_params
+      params.require(:workflow_execution).permit(:name)
+    end
+
+    def load_workflows
+      authorized_scope(WorkflowExecution, type: :relation, as: :group_shared,
+                                          scope_options: { group: @group })
+    end
+
+    def current_page
+      @current_page = t(:'general.default_sidebar.workflows')
+    end
+
+    def context_crumbs
+      super
+      @context_crumbs +=
+        [{
+          name: I18n.t('projects.workflow_executions.index.title'),
+          path: namespace_project_workflow_executions_path
+        }]
+      return unless action_name == 'show' && !@workflow_execution.nil?
+
+      @context_crumbs +=
+        [{
+          name: @workflow_execution.id,
+          path: namespace_project_workflow_execution_path(@workflow_execution)
+        }]
+    end
+
+    protected
+
+    def layout_fixed
+      @fixed = false
+    end
+
+    def redirect_path
+      namespace_project_workflow_executions_path
+    end
+  end
+end

From 80a36f7f8a508793686cdbfabb7690d691014712 Mon Sep 17 00:00:00 2001
From: Meghan Chua <17057809+malchua@users.noreply.github.com>
Date: Fri, 17 Jan 2025 07:29:25 -0600
Subject: [PATCH 12/57] Add new workflow execution controller test file

---
 .../groups/workflow_executions_controller_test.rb          | 7 +++++++
 1 file changed, 7 insertions(+)
 create mode 100644 test/controllers/groups/workflow_executions_controller_test.rb

diff --git a/test/controllers/groups/workflow_executions_controller_test.rb b/test/controllers/groups/workflow_executions_controller_test.rb
new file mode 100644
index 0000000000..f3c2228053
--- /dev/null
+++ b/test/controllers/groups/workflow_executions_controller_test.rb
@@ -0,0 +1,7 @@
+require "test_helper"
+
+class Groups::WorkflowExecutionsControllerTest < ActionDispatch::IntegrationTest
+  # test "the truth" do
+  #   assert true
+  # end
+end

From 088c1c7cf99bd6c930437941d1a036df46dfff54 Mon Sep 17 00:00:00 2001
From: Meghan Chua <17057809+malchua@users.noreply.github.com>
Date: Fri, 17 Jan 2025 07:31:33 -0600
Subject: [PATCH 13/57] Create new policy for viewing workflow executions in
 Groups

---
 app/policies/group_policy.rb | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/app/policies/group_policy.rb b/app/policies/group_policy.rb
index 66e5f1fe1c..b8f10d6cb6 100644
--- a/app/policies/group_policy.rb
+++ b/app/policies/group_policy.rb
@@ -174,6 +174,13 @@ def submit_workflow?
     false
   end
 
+  def view_workflow_executions?
+    return true if effective_access_level >= Member::AccessLevel::ANALYST
+
+    details[:name] = record.name
+    false
+  end
+
   def export_data?
     return true if effective_access_level >= Member::AccessLevel::ANALYST
 

From 2ed0a918a462463bda4e6452e767183ce73936ff Mon Sep 17 00:00:00 2001
From: Meghan Chua <17057809+malchua@users.noreply.github.com>
Date: Fri, 17 Jan 2025 07:32:54 -0600
Subject: [PATCH 14/57] Add new scope for finding shared WEs in a Group

---
 app/policies/workflow_execution_policy.rb | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/app/policies/workflow_execution_policy.rb b/app/policies/workflow_execution_policy.rb
index 33b297f8e9..0343ef83b9 100644
--- a/app/policies/workflow_execution_policy.rb
+++ b/app/policies/workflow_execution_policy.rb
@@ -116,4 +116,14 @@ def update?
     relation.where(submitter: project.namespace.automation_bot)
             .or(relation.where(namespace_id: project.namespace.id, shared_with_namespace: true))
   end
+
+  scope_for :relation, :group_shared do |relation, options|
+    group = options[:group]
+
+    relation
+      .where(
+        namespace_id: Namespaces::ProjectNamespace.where(parent_id: group.self_and_descendants.select(:id)).select(:id),
+        shared_with_namespace: true
+      )
+  end
 end

From 6066105485dcd72aa2607225c929be82c02b1b30 Mon Sep 17 00:00:00 2001
From: Meghan Chua <17057809+malchua@users.noreply.github.com>
Date: Fri, 17 Jan 2025 07:34:00 -0600
Subject: [PATCH 15/57] Add an index page for group workflow executions

---
 .../groups/workflow_executions/index.html.erb | 57 +++++++++++++++++++
 1 file changed, 57 insertions(+)
 create mode 100644 app/views/groups/workflow_executions/index.html.erb

diff --git a/app/views/groups/workflow_executions/index.html.erb b/app/views/groups/workflow_executions/index.html.erb
new file mode 100644
index 0000000000..2b25d1290e
--- /dev/null
+++ b/app/views/groups/workflow_executions/index.html.erb
@@ -0,0 +1,57 @@
+<%= render Viral::PageHeaderComponent.new(
+  title: t(".title"),
+  subtitle: t(".subtitle"),
+) do |component| %>
+  <%= component.with_buttons do %>
+    <%= link_to t(".create_export_button"),
+    new_data_export_path(
+      export_type: "analysis",
+      analysis_type: "project",
+      namespace_id: @namespace.id,
+    ),
+    data: {
+      action: "turbo:morph-element->action-link#idempotentConnect",
+      turbo_stream: true,
+      controller: "action-link",
+      action_link_required_value: 1,
+    },
+    class: "button button--size-default button--state-default action-link" %>
+  <% end %>
+<% end %>
+<div class="flow-root">
+  <div class="flex mb-2">
+    <% if allowed_to?(:export_data?, @project.namespace) %>
+      <div class="inline-flex grow space-x-2">
+        <%= search_form_for(
+                @q,
+                url: select_namespace_project_workflow_executions_url(**request.query_parameters),
+                html: { id: "select-all-form" },
+                class: "filters align-middle"
+              ) do |f| %>
+          <input type="hidden" name="format" value="turbo_stream"/>
+          <input type="hidden" name="select" value="on"/>
+          <%= f.submit t(".select_all_button"),
+                   class: "button button--state-default button--size-default" %>
+        <% end %>
+        <%= search_form_for(
+                @q,
+                url: select_namespace_project_workflow_executions_url(**request.query_parameters),
+                html: { id: "deselect-all-form" },
+                class: "filters align-middle"
+              ) do |f| %>
+          <input type="hidden" name="format" value="turbo_stream"/>
+          <%= f.submit t(".deselect_all_button"),
+                   class: "button button--state-default button--size-default" %>
+        <% end %>
+      </div>
+    <% end %>
+    <div class="grow-0">
+      <%= render SearchComponent.new(
+        query: @q,
+        url: namespace_project_workflow_executions_path(**request.query_parameters),
+        search_attribute: :name_or_id_cont,
+        placeholder: t(".search.placeholder"),
+      ) %>
+    </div>
+  </div>
+</div>

From 5bf25fb5e7601fbc11b2b1b8d0d227f0f89456f0 Mon Sep 17 00:00:00 2001
From: Meghan Chua <17057809+malchua@users.noreply.github.com>
Date: Fri, 17 Jan 2025 07:34:46 -0600
Subject: [PATCH 16/57] Update translations

---
 config/locales/en.yml | 18 ++++++++++++++++++
 config/locales/fr.yml | 18 ++++++++++++++++++
 2 files changed, 36 insertions(+)

diff --git a/config/locales/en.yml b/config/locales/en.yml
index 840f0bf82c..9cb1252ac3 100644
--- a/config/locales/en.yml
+++ b/config/locales/en.yml
@@ -886,6 +886,7 @@ en:
       metadata_templates: Metadata Templates
       samples: Samples
       settings: Settings
+      workflow_executions: Workflow Executions
     subgroups:
       index:
         pagy:
@@ -901,6 +902,23 @@ en:
       success: Group transferred successfully
     update:
       success: Group %{group_name} was successfully updated
+    workflow_executions:
+      files:
+        table_header:
+          created_at: Created At
+          filename: Filename
+          format: Format
+          puid: ID
+          size: Size
+          type: Type
+      index:
+        create_export_button: Create Export
+        deselect_all_button: Deselect All
+        search:
+          placeholder: Filter by ID or name
+        select_all_button: Select All
+        subtitle: These are the workflow executions that have been shared within this group
+        title: Workflow Executions
   layouts:
     application:
       site_title: IRIDA Next
diff --git a/config/locales/fr.yml b/config/locales/fr.yml
index 67e5c8a871..fb555912c7 100644
--- a/config/locales/fr.yml
+++ b/config/locales/fr.yml
@@ -886,6 +886,7 @@ fr:
       metadata_templates: Metadata Templates
       samples: Samples
       settings: Settings
+      workflow_executions: Workflow Executions
     subgroups:
       index:
         pagy:
@@ -901,6 +902,23 @@ fr:
       success: Group transferred successfully
     update:
       success: Group %{group_name} was successfully updated
+    workflow_executions:
+      files:
+        table_header:
+          created_at: Created At
+          filename: Filename
+          format: Format
+          puid: ID
+          size: Size
+          type: Type
+      index:
+        create_export_button: Create Export
+        deselect_all_button: Deselect All
+        search:
+          placeholder: Filter by ID or name
+        select_all_button: Select All
+        subtitle: These are the workflow executions that have been shared within this group
+        title: Workflow Executions
   layouts:
     application:
       site_title: IRIDA Next

From 9748460b6401da05bed132ee5b316e22a4cc8024 Mon Sep 17 00:00:00 2001
From: Meghan Chua <17057809+malchua@users.noreply.github.com>
Date: Fri, 17 Jan 2025 07:35:22 -0600
Subject: [PATCH 17/57] Update group routes

---
 config/routes/group.rb | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/config/routes/group.rb b/config/routes/group.rb
index ac359d30bf..575d9a323a 100644
--- a/config/routes/group.rb
+++ b/config/routes/group.rb
@@ -27,6 +27,17 @@
       end
     end
 
+    if Irida::Pipelines.instance.available_pipelines.any?
+      resources :workflow_executions, only: %i[index destroy show edit update] do
+        member do
+          put :cancel
+        end
+        collection do
+          get :select
+        end
+      end
+    end
+
     resources :attachments, only: %i[create destroy index new] do
       get :new_destroy
     end

From 845d85e2db96fa9a22a84aa0c34b97a6d706646f Mon Sep 17 00:00:00 2001
From: Meghan Chua <17057809+malchua@users.noreply.github.com>
Date: Mon, 20 Jan 2025 07:55:28 -0600
Subject: [PATCH 18/57] Create test for new group_shared scope

---
 test/policies/workflow_execution_policy_test.rb | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/test/policies/workflow_execution_policy_test.rb b/test/policies/workflow_execution_policy_test.rb
index ab7e607d0d..413eddcfd3 100644
--- a/test/policies/workflow_execution_policy_test.rb
+++ b/test/policies/workflow_execution_policy_test.rb
@@ -140,4 +140,13 @@ def setup
 
     assert_equal 12, workflow_executions.count
   end
+
+  test 'group shared scope' do
+    group = groups(:group_one)
+
+    workflow_executions = @policy.apply_scope(WorkflowExecution, type: :relation, name: :group_shared,
+                                                                 scope_options: { group: })
+
+    assert_equal 3, workflow_executions.count
+  end
 end

From 628990b466754168621555377e44d515d7e7f57f Mon Sep 17 00:00:00 2001
From: Meghan Chua <17057809+malchua@users.noreply.github.com>
Date: Mon, 20 Jan 2025 07:57:28 -0600
Subject: [PATCH 19/57] Fix errors for calling groups workflow executions page

---
 .../groups/workflow_executions_controller.rb       | 14 +++++++++-----
 .../groups/workflow_executions/index.html.erb      |  8 ++++----
 2 files changed, 13 insertions(+), 9 deletions(-)

diff --git a/app/controllers/groups/workflow_executions_controller.rb b/app/controllers/groups/workflow_executions_controller.rb
index 88c88b8444..24743b2074 100644
--- a/app/controllers/groups/workflow_executions_controller.rb
+++ b/app/controllers/groups/workflow_executions_controller.rb
@@ -11,7 +11,11 @@ class WorkflowExecutionsController < Groups::ApplicationController
     private
 
     def namespace
-      @namespace = @group
+      @namespace = group
+    end
+
+    def group
+      @group ||= Group.find_by_full_path(request.params[:group_id] || request.params[:id]) # rubocop:disable Rails/DynamicFindBy
     end
 
     def workflow_execution
@@ -35,15 +39,15 @@ def context_crumbs
       super
       @context_crumbs +=
         [{
-          name: I18n.t('projects.workflow_executions.index.title'),
-          path: namespace_project_workflow_executions_path
+          name: I18n.t('groups.workflow_executions.index.title'),
+          path: group_workflow_executions_path
         }]
       return unless action_name == 'show' && !@workflow_execution.nil?
 
       @context_crumbs +=
         [{
           name: @workflow_execution.id,
-          path: namespace_project_workflow_execution_path(@workflow_execution)
+          path: group_workflow_executions_path(@workflow_execution)
         }]
     end
 
@@ -54,7 +58,7 @@ def layout_fixed
     end
 
     def redirect_path
-      namespace_project_workflow_executions_path
+      group_workflow_executions_path
     end
   end
 end
diff --git a/app/views/groups/workflow_executions/index.html.erb b/app/views/groups/workflow_executions/index.html.erb
index 2b25d1290e..952989b687 100644
--- a/app/views/groups/workflow_executions/index.html.erb
+++ b/app/views/groups/workflow_executions/index.html.erb
@@ -20,11 +20,11 @@
 <% end %>
 <div class="flow-root">
   <div class="flex mb-2">
-    <% if allowed_to?(:export_data?, @project.namespace) %>
+    <% if allowed_to?(:export_data?, @namespace) %>
       <div class="inline-flex grow space-x-2">
         <%= search_form_for(
                 @q,
-                url: select_namespace_project_workflow_executions_url(**request.query_parameters),
+                url: select_group_workflow_executions_url(**request.query_parameters),
                 html: { id: "select-all-form" },
                 class: "filters align-middle"
               ) do |f| %>
@@ -35,7 +35,7 @@
         <% end %>
         <%= search_form_for(
                 @q,
-                url: select_namespace_project_workflow_executions_url(**request.query_parameters),
+                url: select_group_workflow_executions_url(**request.query_parameters),
                 html: { id: "deselect-all-form" },
                 class: "filters align-middle"
               ) do |f| %>
@@ -48,7 +48,7 @@
     <div class="grow-0">
       <%= render SearchComponent.new(
         query: @q,
-        url: namespace_project_workflow_executions_path(**request.query_parameters),
+        url: group_workflow_executions_path(**request.query_parameters),
         search_attribute: :name_or_id_cont,
         placeholder: t(".search.placeholder"),
       ) %>

From 90416870fd29d4875fa6c242b400c3c74c703a32 Mon Sep 17 00:00:00 2001
From: Meghan Chua <17057809+malchua@users.noreply.github.com>
Date: Mon, 20 Jan 2025 07:59:16 -0600
Subject: [PATCH 20/57] Add test for calling new workflow execution page

---
 .../workflow_executions_controller_test.rb    | 22 +++++++++++++++----
 1 file changed, 18 insertions(+), 4 deletions(-)

diff --git a/test/controllers/groups/workflow_executions_controller_test.rb b/test/controllers/groups/workflow_executions_controller_test.rb
index f3c2228053..7b0d17748b 100644
--- a/test/controllers/groups/workflow_executions_controller_test.rb
+++ b/test/controllers/groups/workflow_executions_controller_test.rb
@@ -1,7 +1,21 @@
 require "test_helper"
 
-class Groups::WorkflowExecutionsControllerTest < ActionDispatch::IntegrationTest
-  # test "the truth" do
-  #   assert true
-  # end
+module Groups
+  class WorkflowExecutionsControllerTest < ActionDispatch::IntegrationTest
+    setup do
+      sign_in users(:john_doe)
+      @sample1 = samples(:sample1)
+      @attachment1 = attachments(:attachment1)
+      @workflow_execution = workflow_executions(:automated_example_completed)
+      @namespace = groups(:group_one)
+      @project = projects(:project1)
+      @group = groups(:group_one)
+    end
+
+    test 'should show a listing of workflow executions for the project' do
+      get group_workflow_executions_path(@group)
+
+      assert_response :success
+    end
+  end
 end

From 14cf8182ac70c0fc2fe145b833cda61e014c9693 Mon Sep 17 00:00:00 2001
From: Meghan Chua <17057809+malchua@users.noreply.github.com>
Date: Thu, 23 Jan 2025 12:13:12 -0600
Subject: [PATCH 21/57] Add workflow execution table toGroups

---
 .../groups/workflow_executions/_table.html.erb | 18 ++++++++++++++++++
 .../groups/workflow_executions/index.html.erb  |  8 ++++++++
 2 files changed, 26 insertions(+)
 create mode 100644 app/views/groups/workflow_executions/_table.html.erb

diff --git a/app/views/groups/workflow_executions/_table.html.erb b/app/views/groups/workflow_executions/_table.html.erb
new file mode 100644
index 0000000000..ab9bd15ede
--- /dev/null
+++ b/app/views/groups/workflow_executions/_table.html.erb
@@ -0,0 +1,18 @@
+<%= render WorkflowExecutions::TableComponent.new(
+  workflow_executions,
+  pagy,
+  q,
+  namespace: namespace,
+  search_params: @search_params,
+  abilities: {
+    select_workflow_executions: allowed_to?(:export_data?, namespace),
+  },
+  row_actions: {
+    cancel: allowed_to?(:update?, namespace),
+    destroy: allowed_to?(:update?, namespace),
+  },
+  empty: {
+    title: t(:".empty.title"),
+    description: t(:".empty.description"),
+  },
+) %>
diff --git a/app/views/groups/workflow_executions/index.html.erb b/app/views/groups/workflow_executions/index.html.erb
index 952989b687..49c58827dc 100644
--- a/app/views/groups/workflow_executions/index.html.erb
+++ b/app/views/groups/workflow_executions/index.html.erb
@@ -55,3 +55,11 @@
     </div>
   </div>
 </div>
+
+<%= render partial: "table",
+locals: {
+  workflow_executions: @workflow_executions,
+  pagy: @pagy,
+  q: @q,
+  namespace: @namespace,
+} %>

From 8958544f601972ead75c81d974d0ddc25cd45563 Mon Sep 17 00:00:00 2001
From: Meghan Chua <17057809+malchua@users.noreply.github.com>
Date: Thu, 23 Jan 2025 12:14:04 -0600
Subject: [PATCH 22/57] Update translations

---
 config/locales/en.yml | 4 ++++
 config/locales/fr.yml | 4 ++++
 2 files changed, 8 insertions(+)

diff --git a/config/locales/en.yml b/config/locales/en.yml
index 9cb1252ac3..58f469169d 100644
--- a/config/locales/en.yml
+++ b/config/locales/en.yml
@@ -919,6 +919,10 @@ en:
         select_all_button: Select All
         subtitle: These are the workflow executions that have been shared within this group
         title: Workflow Executions
+      table:
+        empty:
+          description: There are no automated pipelines associated with this project.
+          title: No automated pipelines.
   layouts:
     application:
       site_title: IRIDA Next
diff --git a/config/locales/fr.yml b/config/locales/fr.yml
index fb555912c7..69f2836a46 100644
--- a/config/locales/fr.yml
+++ b/config/locales/fr.yml
@@ -919,6 +919,10 @@ fr:
         select_all_button: Select All
         subtitle: These are the workflow executions that have been shared within this group
         title: Workflow Executions
+      table:
+        empty:
+          description: There are no automated pipelines associated with this project.
+          title: No automated pipelines.
   layouts:
     application:
       site_title: IRIDA Next

From c0fcca068cbee3f3abb7e989d0a3ad4d17144e60 Mon Sep 17 00:00:00 2001
From: Meghan Chua <17057809+malchua@users.noreply.github.com>
Date: Thu, 23 Jan 2025 12:16:45 -0600
Subject: [PATCH 23/57] Fix bug where namespace.project is called on a group

---
 app/components/workflow_executions/table_component.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/app/components/workflow_executions/table_component.rb b/app/components/workflow_executions/table_component.rb
index 0a2b9cee51..ff5fdce92c 100644
--- a/app/components/workflow_executions/table_component.rb
+++ b/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,

From accfd8c907cbcf0e723e6a4031ffabd597775826 Mon Sep 17 00:00:00 2001
From: Meghan Chua <17057809+malchua@users.noreply.github.com>
Date: Thu, 23 Jan 2025 12:48:26 -0600
Subject: [PATCH 24/57] Include shared workflow executions in the show route

---
 .../projects/workflow_executions_controller.rb            | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/app/controllers/projects/workflow_executions_controller.rb b/app/controllers/projects/workflow_executions_controller.rb
index c2e7eb37e8..8b5c5b7d15 100644
--- a/app/controllers/projects/workflow_executions_controller.rb
+++ b/app/controllers/projects/workflow_executions_controller.rb
@@ -16,7 +16,13 @@ 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

From 62cc40d0a4577c1a86b47a87382c6ea3a4cdde4b Mon Sep 17 00:00:00 2001
From: Meghan Chua <17057809+malchua@users.noreply.github.com>
Date: Thu, 23 Jan 2025 12:49:15 -0600
Subject: [PATCH 25/57] Update tests for project workflow execution controller

---
 .../workflow_executions_controller_test.rb    | 25 +++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/test/controllers/projects/workflow_executions_controller_test.rb b/test/controllers/projects/workflow_executions_controller_test.rb
index c191cd561b..27e556689f 100644
--- a/test/controllers/projects/workflow_executions_controller_test.rb
+++ b/test/controllers/projects/workflow_executions_controller_test.rb
@@ -43,6 +43,31 @@ class WorkflowExecutionsControllerTest < ActionDispatch::IntegrationTest
       assert_response :success
     end
 
+    test 'should show shared workflow execution' do
+      workflow_execution = workflow_executions(:workflow_execution_shared1)
+
+      get namespace_project_workflow_execution_path(@namespace, @project, workflow_execution)
+
+      assert_response :success
+    end
+
+    test 'should not show shared workflow execution for user with incorrect permissions' do
+      sign_in users(:micha_doe)
+      workflow_execution = workflow_executions(:workflow_execution_shared1)
+
+      get namespace_project_workflow_execution_path(@namespace, @project, workflow_execution)
+
+      assert_response :unauthorized
+    end
+
+    test 'should not show workflow execution that is not shared' do
+      workflow_execution = workflow_executions(:workflow_execution_valid)
+
+      get namespace_project_workflow_execution_path(@namespace, @project, workflow_execution)
+
+      assert_response :not_found
+    end
+
     test 'should not show workflow execution for user with incorrect permissions' do
       sign_in users(:micha_doe)
       workflow_execution = workflow_executions(:automated_workflow_execution)

From 5feb45e67d2c978784ff67642c2aab87a23bf57a Mon Sep 17 00:00:00 2001
From: Meghan Chua <17057809+malchua@users.noreply.github.com>
Date: Sun, 26 Jan 2025 22:32:41 -0600
Subject: [PATCH 26/57] Remove changes relating to group to move to new branch

---
 .../groups/workflow_executions_controller.rb  | 64 ------------------
 app/policies/group_policy.rb                  |  7 --
 app/policies/workflow_execution_policy.rb     | 10 ---
 .../workflow_executions/_table.html.erb       | 18 -----
 .../groups/workflow_executions/index.html.erb | 65 -------------------
 app/views/layouts/groups.html.erb             |  8 ---
 config/locales/en.yml                         | 22 -------
 config/locales/fr.yml                         | 22 -------
 config/routes/group.rb                        | 11 ----
 .../workflow_executions_controller_test.rb    | 21 ------
 .../workflow_execution_policy_test.rb         |  9 ---
 11 files changed, 257 deletions(-)
 delete mode 100644 app/controllers/groups/workflow_executions_controller.rb
 delete mode 100644 app/views/groups/workflow_executions/_table.html.erb
 delete mode 100644 app/views/groups/workflow_executions/index.html.erb
 delete mode 100644 test/controllers/groups/workflow_executions_controller_test.rb

diff --git a/app/controllers/groups/workflow_executions_controller.rb b/app/controllers/groups/workflow_executions_controller.rb
deleted file mode 100644
index 24743b2074..0000000000
--- a/app/controllers/groups/workflow_executions_controller.rb
+++ /dev/null
@@ -1,64 +0,0 @@
-# frozen_string_literal: true
-
-module Groups
-  class WorkflowExecutionsController < Groups::ApplicationController
-    include BreadcrumbNavigation
-    include Metadata
-    include WorkflowExecutionActions
-
-    before_action :namespace
-
-    private
-
-    def namespace
-      @namespace = group
-    end
-
-    def group
-      @group ||= Group.find_by_full_path(request.params[:group_id] || request.params[:id]) # rubocop:disable Rails/DynamicFindBy
-    end
-
-    def workflow_execution
-      @workflow_execution = WorkflowExecution.find_by!(id: params[:id])
-    end
-
-    def workflow_execution_update_params
-      params.require(:workflow_execution).permit(:name)
-    end
-
-    def load_workflows
-      authorized_scope(WorkflowExecution, type: :relation, as: :group_shared,
-                                          scope_options: { group: @group })
-    end
-
-    def current_page
-      @current_page = t(:'general.default_sidebar.workflows')
-    end
-
-    def context_crumbs
-      super
-      @context_crumbs +=
-        [{
-          name: I18n.t('groups.workflow_executions.index.title'),
-          path: group_workflow_executions_path
-        }]
-      return unless action_name == 'show' && !@workflow_execution.nil?
-
-      @context_crumbs +=
-        [{
-          name: @workflow_execution.id,
-          path: group_workflow_executions_path(@workflow_execution)
-        }]
-    end
-
-    protected
-
-    def layout_fixed
-      @fixed = false
-    end
-
-    def redirect_path
-      group_workflow_executions_path
-    end
-  end
-end
diff --git a/app/policies/group_policy.rb b/app/policies/group_policy.rb
index b8f10d6cb6..66e5f1fe1c 100644
--- a/app/policies/group_policy.rb
+++ b/app/policies/group_policy.rb
@@ -174,13 +174,6 @@ def submit_workflow?
     false
   end
 
-  def view_workflow_executions?
-    return true if effective_access_level >= Member::AccessLevel::ANALYST
-
-    details[:name] = record.name
-    false
-  end
-
   def export_data?
     return true if effective_access_level >= Member::AccessLevel::ANALYST
 
diff --git a/app/policies/workflow_execution_policy.rb b/app/policies/workflow_execution_policy.rb
index 0343ef83b9..33b297f8e9 100644
--- a/app/policies/workflow_execution_policy.rb
+++ b/app/policies/workflow_execution_policy.rb
@@ -116,14 +116,4 @@ def update?
     relation.where(submitter: project.namespace.automation_bot)
             .or(relation.where(namespace_id: project.namespace.id, shared_with_namespace: true))
   end
-
-  scope_for :relation, :group_shared do |relation, options|
-    group = options[:group]
-
-    relation
-      .where(
-        namespace_id: Namespaces::ProjectNamespace.where(parent_id: group.self_and_descendants.select(:id)).select(:id),
-        shared_with_namespace: true
-      )
-  end
 end
diff --git a/app/views/groups/workflow_executions/_table.html.erb b/app/views/groups/workflow_executions/_table.html.erb
deleted file mode 100644
index ab9bd15ede..0000000000
--- a/app/views/groups/workflow_executions/_table.html.erb
+++ /dev/null
@@ -1,18 +0,0 @@
-<%= render WorkflowExecutions::TableComponent.new(
-  workflow_executions,
-  pagy,
-  q,
-  namespace: namespace,
-  search_params: @search_params,
-  abilities: {
-    select_workflow_executions: allowed_to?(:export_data?, namespace),
-  },
-  row_actions: {
-    cancel: allowed_to?(:update?, namespace),
-    destroy: allowed_to?(:update?, namespace),
-  },
-  empty: {
-    title: t(:".empty.title"),
-    description: t(:".empty.description"),
-  },
-) %>
diff --git a/app/views/groups/workflow_executions/index.html.erb b/app/views/groups/workflow_executions/index.html.erb
deleted file mode 100644
index 49c58827dc..0000000000
--- a/app/views/groups/workflow_executions/index.html.erb
+++ /dev/null
@@ -1,65 +0,0 @@
-<%= render Viral::PageHeaderComponent.new(
-  title: t(".title"),
-  subtitle: t(".subtitle"),
-) do |component| %>
-  <%= component.with_buttons do %>
-    <%= link_to t(".create_export_button"),
-    new_data_export_path(
-      export_type: "analysis",
-      analysis_type: "project",
-      namespace_id: @namespace.id,
-    ),
-    data: {
-      action: "turbo:morph-element->action-link#idempotentConnect",
-      turbo_stream: true,
-      controller: "action-link",
-      action_link_required_value: 1,
-    },
-    class: "button button--size-default button--state-default action-link" %>
-  <% end %>
-<% end %>
-<div class="flow-root">
-  <div class="flex mb-2">
-    <% if allowed_to?(:export_data?, @namespace) %>
-      <div class="inline-flex grow space-x-2">
-        <%= search_form_for(
-                @q,
-                url: select_group_workflow_executions_url(**request.query_parameters),
-                html: { id: "select-all-form" },
-                class: "filters align-middle"
-              ) do |f| %>
-          <input type="hidden" name="format" value="turbo_stream"/>
-          <input type="hidden" name="select" value="on"/>
-          <%= f.submit t(".select_all_button"),
-                   class: "button button--state-default button--size-default" %>
-        <% end %>
-        <%= search_form_for(
-                @q,
-                url: select_group_workflow_executions_url(**request.query_parameters),
-                html: { id: "deselect-all-form" },
-                class: "filters align-middle"
-              ) do |f| %>
-          <input type="hidden" name="format" value="turbo_stream"/>
-          <%= f.submit t(".deselect_all_button"),
-                   class: "button button--state-default button--size-default" %>
-        <% end %>
-      </div>
-    <% end %>
-    <div class="grow-0">
-      <%= render SearchComponent.new(
-        query: @q,
-        url: group_workflow_executions_path(**request.query_parameters),
-        search_attribute: :name_or_id_cont,
-        placeholder: t(".search.placeholder"),
-      ) %>
-    </div>
-  </div>
-</div>
-
-<%= render partial: "table",
-locals: {
-  workflow_executions: @workflow_executions,
-  pagy: @pagy,
-  q: @q,
-  namespace: @namespace,
-} %>
diff --git a/app/views/layouts/groups.html.erb b/app/views/layouts/groups.html.erb
index 3bd2114bff..d5587b770e 100644
--- a/app/views/layouts/groups.html.erb
+++ b/app/views/layouts/groups.html.erb
@@ -38,14 +38,6 @@
             label: t(:"groups.sidebar.activity"),
             selected: @current_page == t(:"groups.sidebar.activity"),
           ) %>
-          <% if allowed_to?(:view_workflow_executions?, @group) && @pipelines_enabled %>
-            <%= render section.with_item(
-              url: group_workflow_executions_path(@group),
-              icon: "command_line",
-              label: t(:"groups.sidebar.workflow_executions"),
-              selected: @current_page == t(:"groups.sidebar.workflow_executions"),
-            ) %>
-          <% end %>
           <% if allowed_to?(:update?, @group) %>
             <%= render section.with_multi_level_menu(
               title: t(:"groups.sidebar.settings"),
diff --git a/config/locales/en.yml b/config/locales/en.yml
index 58f469169d..840f0bf82c 100644
--- a/config/locales/en.yml
+++ b/config/locales/en.yml
@@ -886,7 +886,6 @@ en:
       metadata_templates: Metadata Templates
       samples: Samples
       settings: Settings
-      workflow_executions: Workflow Executions
     subgroups:
       index:
         pagy:
@@ -902,27 +901,6 @@ en:
       success: Group transferred successfully
     update:
       success: Group %{group_name} was successfully updated
-    workflow_executions:
-      files:
-        table_header:
-          created_at: Created At
-          filename: Filename
-          format: Format
-          puid: ID
-          size: Size
-          type: Type
-      index:
-        create_export_button: Create Export
-        deselect_all_button: Deselect All
-        search:
-          placeholder: Filter by ID or name
-        select_all_button: Select All
-        subtitle: These are the workflow executions that have been shared within this group
-        title: Workflow Executions
-      table:
-        empty:
-          description: There are no automated pipelines associated with this project.
-          title: No automated pipelines.
   layouts:
     application:
       site_title: IRIDA Next
diff --git a/config/locales/fr.yml b/config/locales/fr.yml
index 69f2836a46..67e5c8a871 100644
--- a/config/locales/fr.yml
+++ b/config/locales/fr.yml
@@ -886,7 +886,6 @@ fr:
       metadata_templates: Metadata Templates
       samples: Samples
       settings: Settings
-      workflow_executions: Workflow Executions
     subgroups:
       index:
         pagy:
@@ -902,27 +901,6 @@ fr:
       success: Group transferred successfully
     update:
       success: Group %{group_name} was successfully updated
-    workflow_executions:
-      files:
-        table_header:
-          created_at: Created At
-          filename: Filename
-          format: Format
-          puid: ID
-          size: Size
-          type: Type
-      index:
-        create_export_button: Create Export
-        deselect_all_button: Deselect All
-        search:
-          placeholder: Filter by ID or name
-        select_all_button: Select All
-        subtitle: These are the workflow executions that have been shared within this group
-        title: Workflow Executions
-      table:
-        empty:
-          description: There are no automated pipelines associated with this project.
-          title: No automated pipelines.
   layouts:
     application:
       site_title: IRIDA Next
diff --git a/config/routes/group.rb b/config/routes/group.rb
index 575d9a323a..ac359d30bf 100644
--- a/config/routes/group.rb
+++ b/config/routes/group.rb
@@ -27,17 +27,6 @@
       end
     end
 
-    if Irida::Pipelines.instance.available_pipelines.any?
-      resources :workflow_executions, only: %i[index destroy show edit update] do
-        member do
-          put :cancel
-        end
-        collection do
-          get :select
-        end
-      end
-    end
-
     resources :attachments, only: %i[create destroy index new] do
       get :new_destroy
     end
diff --git a/test/controllers/groups/workflow_executions_controller_test.rb b/test/controllers/groups/workflow_executions_controller_test.rb
deleted file mode 100644
index 7b0d17748b..0000000000
--- a/test/controllers/groups/workflow_executions_controller_test.rb
+++ /dev/null
@@ -1,21 +0,0 @@
-require "test_helper"
-
-module Groups
-  class WorkflowExecutionsControllerTest < ActionDispatch::IntegrationTest
-    setup do
-      sign_in users(:john_doe)
-      @sample1 = samples(:sample1)
-      @attachment1 = attachments(:attachment1)
-      @workflow_execution = workflow_executions(:automated_example_completed)
-      @namespace = groups(:group_one)
-      @project = projects(:project1)
-      @group = groups(:group_one)
-    end
-
-    test 'should show a listing of workflow executions for the project' do
-      get group_workflow_executions_path(@group)
-
-      assert_response :success
-    end
-  end
-end
diff --git a/test/policies/workflow_execution_policy_test.rb b/test/policies/workflow_execution_policy_test.rb
index 413eddcfd3..ab7e607d0d 100644
--- a/test/policies/workflow_execution_policy_test.rb
+++ b/test/policies/workflow_execution_policy_test.rb
@@ -140,13 +140,4 @@ def setup
 
     assert_equal 12, workflow_executions.count
   end
-
-  test 'group shared scope' do
-    group = groups(:group_one)
-
-    workflow_executions = @policy.apply_scope(WorkflowExecution, type: :relation, name: :group_shared,
-                                                                 scope_options: { group: })
-
-    assert_equal 3, workflow_executions.count
-  end
 end

From b404526b46daedd1b8c064a304fe6926d103ccd8 Mon Sep 17 00:00:00 2001
From: Meghan Chua <17057809+malchua@users.noreply.github.com>
Date: Mon, 27 Jan 2025 00:10:44 -0600
Subject: [PATCH 27/57] Fix rubocop warning

---
 app/controllers/workflow_executions_controller.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/app/controllers/workflow_executions_controller.rb b/app/controllers/workflow_executions_controller.rb
index 587446a0bf..08fb938612 100644
--- a/app/controllers/workflow_executions_controller.rb
+++ b/app/controllers/workflow_executions_controller.rb
@@ -34,7 +34,7 @@ def workflow_execution_update_params
     params.require(:workflow_execution).permit(:name)
   end
 
-  def workflow_execution_params_attributes # rubocop:disable Metrics/MethodLength
+  def workflow_execution_params_attributes
     [
       :name,
       :namespace_id,

From 5433ab4808577915ab7bdb1c30efde14b8ff0261 Mon Sep 17 00:00:00 2001
From: Meghan Chua <17057809+malchua@users.noreply.github.com>
Date: Mon, 27 Jan 2025 00:12:22 -0600
Subject: [PATCH 28/57] Add namespace_type variable to translations

---
 config/locales/en.yml | 2 +-
 config/locales/fr.yml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/config/locales/en.yml b/config/locales/en.yml
index 840f0bf82c..09d25d8e41 100644
--- a/config/locales/en.yml
+++ b/config/locales/en.yml
@@ -422,7 +422,7 @@ en:
     nextflow:
       email_notification: Receive an email notification when your analysis has completed?
       required: Required
-      shared_with_namespace: Share results with Project/Group?
+      shared_with_namespace: Share results with %{namespace_type} members?
       update_samples: Update samples with analysis results
     pagination:
       next: Next
diff --git a/config/locales/fr.yml b/config/locales/fr.yml
index 67e5c8a871..c8a98edf8b 100644
--- a/config/locales/fr.yml
+++ b/config/locales/fr.yml
@@ -422,7 +422,7 @@ fr:
     nextflow:
       email_notification: Receive an email notification when your analysis has completed?
       required: Required
-      shared_with_namespace: Share results with Project/Group?
+      shared_with_namespace: Share results with %{namespace_type} members?
       update_samples: Update samples with analysis results
     pagination:
       next: Next

From b7ee981940f7fe3424227863a60c3f3404a094b7 Mon Sep 17 00:00:00 2001
From: Meghan Chua <17057809+malchua@users.noreply.github.com>
Date: Mon, 27 Jan 2025 00:15:43 -0600
Subject: [PATCH 29/57] Modify checkbox prompt to use proper namespace type

---
 app/components/nextflow_component.html.erb    | 29 ++++++++++---------
 app/components/nextflow_component.rb          |  5 ++--
 .../submissions_controller.rb                 |  3 +-
 .../_edit_dialog.html.erb                     |  1 +
 ...utomated_workflow_execution_modal.html.erb |  1 +
 .../submissions/create.turbo_stream.erb       |  1 +
 6 files changed, 24 insertions(+), 16 deletions(-)

diff --git a/app/components/nextflow_component.html.erb b/app/components/nextflow_component.html.erb
index 2c0cf69059..04fcad5734 100644
--- a/app/components/nextflow_component.html.erb
+++ b/app/components/nextflow_component.html.erb
@@ -125,21 +125,24 @@
                                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",
+                                                                                                                                                                        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"),
+                       t(
+                         :"components.nextflow.shared_with_namespace",
+                         namespace_type: @namespace_type,
+                       ),
                        class: "mr-2 text-sm font-medium text-slate-900 dark:text-white" %>
       </div>
     <% end %>
diff --git a/app/components/nextflow_component.rb b/app/components/nextflow_component.rb
index 631b348cc1..9075821ab4 100644
--- a/app/components/nextflow_component.rb
+++ b/app/components/nextflow_component.rb
@@ -7,8 +7,8 @@ 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,
+                 namespace_type: nil)
     @samples = samples
     @namespace_id = namespace_id
     @url = url
@@ -16,6 +16,7 @@ def initialize(url:, samples:, workflow:, fields:, namespace_id:,
     @metadata_fields = fields
     @allowed_to_update_samples = allowed_to_update_samples
     @instance = instance
+    @namespace_type = namespace_type.nil? ? 'Project' : namespace_type
   end
 
   # rubocop:enable Metrics/ParameterLists
diff --git a/app/controllers/workflow_executions/submissions_controller.rb b/app/controllers/workflow_executions/submissions_controller.rb
index 9978003c3a..a8c09c0369 100644
--- a/app/controllers/workflow_executions/submissions_controller.rb
+++ b/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
diff --git a/app/views/projects/automated_workflow_executions/_edit_dialog.html.erb b/app/views/projects/automated_workflow_executions/_edit_dialog.html.erb
index 44a1b5e0b1..744e722c9e 100644
--- a/app/views/projects/automated_workflow_executions/_edit_dialog.html.erb
+++ b/app/views/projects/automated_workflow_executions/_edit_dialog.html.erb
@@ -22,6 +22,7 @@
       namespace_id: @project.namespace.id,
       fields: nil,
       instance: @automated_workflow_execution,
+      namespace_type: @project.namespace.type,
     ) %>
   <% end %>
 <% end %>
diff --git a/app/views/projects/automated_workflow_executions/_new_automated_workflow_execution_modal.html.erb b/app/views/projects/automated_workflow_executions/_new_automated_workflow_execution_modal.html.erb
index 3c05a696d3..b28dce3c05 100644
--- a/app/views/projects/automated_workflow_executions/_new_automated_workflow_execution_modal.html.erb
+++ b/app/views/projects/automated_workflow_executions/_new_automated_workflow_execution_modal.html.erb
@@ -8,6 +8,7 @@
       allowed_to_update_samples: true,
       namespace_id: @project.namespace.id,
       fields: nil,
+      namespace_type: @project.namespace.type,
     ) %>
   <% end %>
 <% end %>
diff --git a/app/views/workflow_executions/submissions/create.turbo_stream.erb b/app/views/workflow_executions/submissions/create.turbo_stream.erb
index 45689ea4fb..46375d2dd2 100644
--- a/app/views/workflow_executions/submissions/create.turbo_stream.erb
+++ b/app/views/workflow_executions/submissions/create.turbo_stream.erb
@@ -10,6 +10,7 @@
         allowed_to_update_samples: @allowed_to_update_samples,
         namespace_id: @namespace_id,
         fields: @fields,
+        namespace_type: @namespace.nil? ? nil : @namespace.type,
       ) %>
     <% end %>
   <% end %>

From 7414dd8594ed8f5a83bbf0dd1bd423ed04b2b311 Mon Sep 17 00:00:00 2001
From: Meghan Chua <17057809+malchua@users.noreply.github.com>
Date: Mon, 27 Jan 2025 00:40:14 -0600
Subject: [PATCH 30/57] Remove action buttons from show page

---
 app/views/projects/workflow_executions/show.html.erb | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/app/views/projects/workflow_executions/show.html.erb b/app/views/projects/workflow_executions/show.html.erb
index 268c492d7f..49df86ac96 100644
--- a/app/views/projects/workflow_executions/show.html.erb
+++ b/app/views/projects/workflow_executions/show.html.erb
@@ -41,7 +41,7 @@
             "button button--size-default button--state-default pointer-events-none cursor-not-allowed bg-slate-100 text-slate-600 mr-2 dark:bg-slate-600 dark:text-slate-300" %>
         <% end %>
       <% end %>
-      <% if @workflow_execution.cancellable? && allowed_to?(:cancel?, @workflow_execution) %>
+      <% if @workflow_execution.cancellable? && allowed_to?(:cancel?, @workflow_execution) && !@workflow_execution.shared_with_namespace %>
         <%= link_to(
           t("projects.workflow_executions.show.cancel_button"),
           cancel_namespace_project_workflow_execution_path(
@@ -57,7 +57,7 @@
           class: "button button--state-default button--size-default mr-1",
         ) %>
       <% end %>
-      <% if allowed_to?(:update?, @workflow_execution) %>
+      <% if allowed_to?(:update?, @workflow_execution) && !@workflow_execution.shared_with_namespace %>
         <%= link_to(
           t("projects.workflow_executions.show.edit_button"),
           edit_namespace_project_workflow_execution_path(
@@ -71,7 +71,7 @@
           class: "button button--state-default button--size-default mr-1",
         ) %>
       <% end %>
-      <% if @workflow_execution.deletable? && allowed_to?(:destroy?, @workflow_execution) %>
+      <% if @workflow_execution.deletable? && allowed_to?(:destroy?, @workflow_execution) && !@workflow_execution.shared_with_namespace %>
         <%= link_to(
           t("projects.workflow_executions.show.remove_button"),
           namespace_project_workflow_execution_path(

From e3ae1fe8bda764f749812bbeea10a9625addd88d Mon Sep 17 00:00:00 2001
From: Meghan Chua <17057809+malchua@users.noreply.github.com>
Date: Mon, 27 Jan 2025 01:11:31 -0600
Subject: [PATCH 31/57] Fix workflow executions submissions tests

---
 .../system/workflow_executions/submissions_test.rb | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/test/system/workflow_executions/submissions_test.rb b/test/system/workflow_executions/submissions_test.rb
index cb4932293d..eef0947860 100644
--- a/test/system/workflow_executions/submissions_test.rb
+++ b/test/system/workflow_executions/submissions_test.rb
@@ -69,7 +69,7 @@ class SubmissionsTest < ApplicationSystemTestCase
 
         assert_text I18n.t(:'components.nextflow.update_samples')
         assert_text I18n.t(:'components.nextflow.email_notification')
-        assert_text I18n.t(:'components.nextflow.shared_with_namespace')
+        assert_text I18n.t(:'components.nextflow.shared_with_namespace', namespace_type: @project.namespace.type)
       end
     end
 
@@ -104,7 +104,7 @@ class SubmissionsTest < ApplicationSystemTestCase
 
         assert_text I18n.t(:'components.nextflow.update_samples')
         assert_text I18n.t(:'components.nextflow.email_notification')
-        assert_text I18n.t(:'components.nextflow.shared_with_namespace')
+        assert_text I18n.t(:'components.nextflow.shared_with_namespace', namespace_type: @project.namespace.type)
       end
     end
 
@@ -139,7 +139,7 @@ class SubmissionsTest < ApplicationSystemTestCase
 
         assert_no_text I18n.t(:'components.nextflow.update_samples')
         assert_text I18n.t(:'components.nextflow.email_notification')
-        assert_text I18n.t(:'components.nextflow.shared_with_namespace')
+        assert_text I18n.t(:'components.nextflow.shared_with_namespace', namespace_type: @project.namespace.type)
       end
     end
 
@@ -177,7 +177,7 @@ class SubmissionsTest < ApplicationSystemTestCase
 
         assert_no_text I18n.t(:'components.nextflow.update_samples')
         assert_text I18n.t(:'components.nextflow.email_notification')
-        assert_text I18n.t(:'components.nextflow.shared_with_namespace')
+        assert_text I18n.t(:'components.nextflow.shared_with_namespace', namespace_type: @project.namespace.type)
       end
     end
 
@@ -220,7 +220,7 @@ class SubmissionsTest < ApplicationSystemTestCase
 
         assert_text I18n.t(:'components.nextflow.update_samples')
         assert_text I18n.t(:'components.nextflow.email_notification')
-        assert_text I18n.t(:'components.nextflow.shared_with_namespace')
+        assert_text I18n.t(:'components.nextflow.shared_with_namespace', namespace_type: @namespace.type)
       end
     end
 
@@ -255,7 +255,7 @@ class SubmissionsTest < ApplicationSystemTestCase
 
         assert_text I18n.t(:'components.nextflow.update_samples')
         assert_text I18n.t(:'components.nextflow.email_notification')
-        assert_text I18n.t(:'components.nextflow.shared_with_namespace')
+        assert_text I18n.t(:'components.nextflow.shared_with_namespace', namespace_type: @namespace.type)
       end
     end
 
@@ -290,7 +290,7 @@ class SubmissionsTest < ApplicationSystemTestCase
 
         assert_no_text I18n.t(:'components.nextflow.update_samples')
         assert_text I18n.t(:'components.nextflow.email_notification')
-        assert_text I18n.t(:'components.nextflow.shared_with_namespace')
+        assert_text I18n.t(:'components.nextflow.shared_with_namespace', namespace_type: @namespace.type)
       end
     end
 

From 887893fd1a70732c2d852b962695c89f468d3d40 Mon Sep 17 00:00:00 2001
From: Meghan Chua <17057809+malchua@users.noreply.github.com>
Date: Tue, 28 Jan 2025 13:16:48 -0600
Subject: [PATCH 32/57] Fix format of class list

---
 app/components/nextflow_component.html.erb | 14 +-------------
 1 file changed, 1 insertion(+), 13 deletions(-)

diff --git a/app/components/nextflow_component.html.erb b/app/components/nextflow_component.html.erb
index 04fcad5734..707b97045e 100644
--- a/app/components/nextflow_component.html.erb
+++ b/app/components/nextflow_component.html.erb
@@ -124,19 +124,7 @@
                              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",
+                               "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(

From 182dfdf7ddda39d11768037151d0f1e9bc5249ca Mon Sep 17 00:00:00 2001
From: Meghan Chua <17057809+malchua@users.noreply.github.com>
Date: Tue, 28 Jan 2025 13:20:57 -0600
Subject: [PATCH 33/57] Allow user actions for shared workflows they submitted

---
 app/components/workflow_executions/table_component.html.erb | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/app/components/workflow_executions/table_component.html.erb b/app/components/workflow_executions/table_component.html.erb
index 091850df00..23df567cab 100644
--- a/app/components/workflow_executions/table_component.html.erb
+++ b/app/components/workflow_executions/table_component.html.erb
@@ -140,7 +140,9 @@
                 <% end %>
               <% end %>
             <% end %>
-            <% if @renders_row_actions && !workflow_execution.shared_with_namespace %>
+            <% if @renders_row_actions &&
+              (!workflow_execution.shared_with_namespace ||
+                (workflow_execution.shared_with_namespace && @namespace.nil?)) %>
               <%= render_cell(
                 tag: 'td',
                 classes: class_names('px-3 py-3 sticky right-0 bg-white dark:bg-slate-800 z-10 space-x-2')

From 2b34766cc70c7e4eb62415ab1e70078d08fcd87a Mon Sep 17 00:00:00 2001
From: Meghan Chua <17057809+malchua@users.noreply.github.com>
Date: Tue, 28 Jan 2025 13:26:46 -0600
Subject: [PATCH 34/57] Update description for workflow index page

---
 config/locales/en.yml | 2 +-
 config/locales/fr.yml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/config/locales/en.yml b/config/locales/en.yml
index 09d25d8e41..bbff0c3aa8 100644
--- a/config/locales/en.yml
+++ b/config/locales/en.yml
@@ -1618,7 +1618,7 @@ 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
diff --git a/config/locales/fr.yml b/config/locales/fr.yml
index c8a98edf8b..a8c75092ba 100644
--- a/config/locales/fr.yml
+++ b/config/locales/fr.yml
@@ -1618,7 +1618,7 @@ 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

From 6711441aabac5734bba3feb74eb2b0c2480a51ed Mon Sep 17 00:00:00 2001
From: Meghan Chua <17057809+malchua@users.noreply.github.com>
Date: Tue, 28 Jan 2025 13:32:03 -0600
Subject: [PATCH 35/57] Add UI tests to ensure shared workflows are displayed
 properly

---
 .../projects/workflow_executions_test.rb      | 45 +++++++++++++++++++
 test/system/workflow_executions_test.rb       | 38 ++++++++++++++++
 2 files changed, 83 insertions(+)

diff --git a/test/system/projects/workflow_executions_test.rb b/test/system/projects/workflow_executions_test.rb
index f34a19a987..9de91bbaea 100644
--- a/test/system/projects/workflow_executions_test.rb
+++ b/test/system/projects/workflow_executions_test.rb
@@ -89,6 +89,35 @@ class WorkflowExecutionsTest < ApplicationSystemTestCase
       end
     end
 
+    test 'should include workflows that have been shared to the project' do
+      workflow_execution1 = workflow_executions(:workflow_execution_shared1)
+      workflow_execution2 = workflow_executions(:workflow_execution_shared2)
+
+      visit namespace_project_workflow_executions_path(@namespace, @project)
+
+      assert_selector 'h1', text: I18n.t(:'projects.workflow_executions.index.title')
+
+      tr = find('a', text: workflow_execution1.id).ancestor('tr')
+      within tr do
+        assert_no_link 'Cancel'
+        assert_no_link 'Destroy'
+      end
+
+      tr = find('a', text: workflow_execution2.id).ancestor('tr')
+      within tr do
+        assert_no_link 'Cancel'
+        assert_no_link 'Destroy'
+      end
+    end
+
+    test 'should not include shared workflows that were not shared to that specific project' do
+      workflow_execution = workflow_executions(:workflow_execution_shared3)
+
+      visit namespace_project_workflow_executions_path(@namespace, @project)
+
+      assert_no_selector 'a', text: workflow_execution.id
+    end
+
     test 'should be able to cancel a workflow' do
       workflow_execution = workflow_executions(:automated_example_prepared)
 
@@ -408,5 +437,21 @@ class WorkflowExecutionsTest < ApplicationSystemTestCase
       assert_selector 'dd', text: new_we_name
       ### VERIFY END ###
     end
+
+    test 'can view a shared workflow execution that was shared by a different user' do
+      workflow_execution = workflow_executions(:workflow_execution_shared2)
+
+      visit namespace_project_workflow_execution_path(@namespace, @project, workflow_execution)
+
+      assert_text workflow_execution.id
+      assert_text I18n.t(:"workflow_executions.state.#{workflow_execution.state}")
+      assert_text workflow_execution.metadata['workflow_name']
+      assert_text workflow_execution.metadata['workflow_version']
+
+      assert_link I18n.t(:'workflow_executions.show.create_export_button')
+      assert_no_link I18n.t(:'workflow_executions.show.cancel_button')
+      assert_no_link I18n.t(:'workflow_executions.show.edit_button')
+      assert_no_link I18n.t(:'workflow_executions.show.remove_button')
+    end
   end
 end
diff --git a/test/system/workflow_executions_test.rb b/test/system/workflow_executions_test.rb
index e4ebccb584..e5243a2dba 100644
--- a/test/system/workflow_executions_test.rb
+++ b/test/system/workflow_executions_test.rb
@@ -111,6 +111,28 @@ class WorkflowExecutionsTest < ApplicationSystemTestCase
     end
   end
 
+  test 'should include a shared workflow in the list of workflow executions when the submitter is the current user' do
+    workflow_execution = workflow_executions(:workflow_execution_shared1)
+
+    visit workflow_executions_path
+
+    assert_selector 'h1', text: I18n.t(:'workflow_executions.index.title')
+
+    tr = find('a', text: workflow_execution.id).ancestor('tr')
+
+    within tr do
+      assert_link 'Cancel'
+    end
+  end
+
+  test 'should not include a shared workflow in the workflow executions when the submitter is not the current user' do
+    workflow_execution = workflow_executions(:workflow_execution_shared2)
+
+    visit workflow_executions_path
+
+    assert_no_selector 'a', text: workflow_execution.id
+  end
+
   test 'should be able to cancel a workflow' do
     workflow_execution = workflow_executions(:irida_next_example_prepared)
 
@@ -457,4 +479,20 @@ class WorkflowExecutionsTest < ApplicationSystemTestCase
     assert_selector 'dd', text: new_we_name
     ### VERIFY END ###
   end
+
+  test 'can view a shared workflow execution that the current user submitted' do
+    workflow_execution = workflow_executions(:workflow_execution_shared1)
+
+    visit workflow_execution_path(workflow_execution)
+
+    assert_text workflow_execution.id
+    assert_text I18n.t(:"workflow_executions.state.#{workflow_execution.state}")
+    assert_text workflow_execution.metadata['workflow_name']
+    assert_text workflow_execution.metadata['workflow_version']
+
+    assert_link I18n.t(:'workflow_executions.show.create_export_button')
+    assert_link I18n.t(:'workflow_executions.show.cancel_button')
+    assert_link I18n.t(:'workflow_executions.show.edit_button')
+    assert_no_link I18n.t(:'workflow_executions.show.remove_button')
+  end
 end

From 913d6eed5a0087db59a1a6dd98a9bc688e24aee3 Mon Sep 17 00:00:00 2001
From: Meghan Chua <17057809+malchua@users.noreply.github.com>
Date: Tue, 28 Jan 2025 14:05:37 -0600
Subject: [PATCH 36/57] Simplify rendering row action logic

---
 app/components/workflow_executions/table_component.html.erb | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/app/components/workflow_executions/table_component.html.erb b/app/components/workflow_executions/table_component.html.erb
index 23df567cab..a3aa07191a 100644
--- a/app/components/workflow_executions/table_component.html.erb
+++ b/app/components/workflow_executions/table_component.html.erb
@@ -140,9 +140,7 @@
                 <% end %>
               <% end %>
             <% end %>
-            <% if @renders_row_actions &&
-              (!workflow_execution.shared_with_namespace ||
-                (workflow_execution.shared_with_namespace && @namespace.nil?)) %>
+            <% if @renders_row_actions && (!workflow_execution.shared_with_namespace || @namespace.nil?) %>
               <%= render_cell(
                 tag: 'td',
                 classes: class_names('px-3 py-3 sticky right-0 bg-white dark:bg-slate-800 z-10 space-x-2')

From 196ca85f037dc4d1535fd7d47b45e0594b1ceeb3 Mon Sep 17 00:00:00 2001
From: Meghan Chua <17057809+malchua@users.noreply.github.com>
Date: Wed, 29 Jan 2025 14:11:06 -0600
Subject: [PATCH 37/57] Hide prompt when creating automated workflow executions

---
 app/components/nextflow_component.html.erb | 28 ++++++++++++----------
 1 file changed, 15 insertions(+), 13 deletions(-)

diff --git a/app/components/nextflow_component.html.erb b/app/components/nextflow_component.html.erb
index 707b97045e..92c312c9c6 100644
--- a/app/components/nextflow_component.html.erb
+++ b/app/components/nextflow_component.html.erb
@@ -119,19 +119,21 @@
                        class: "mr-2 text-sm font-medium text-slate-900 dark:text-white" %>
       </div>
       <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",
-                         namespace_type: @namespace_type,
-                       ),
-                       class: "mr-2 text-sm font-medium text-slate-900 dark:text-white" %>
+        <% if !@workflow.automatable %>
+          <%= 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",
+                           namespace_type: @namespace_type,
+                         ),
+                         class: "mr-2 text-sm font-medium text-slate-900 dark:text-white" %>
+        <% end %>
       </div>
     <% end %>
 

From 78fb565fbdca7c3b82401e47ce00643bf75a7ce5 Mon Sep 17 00:00:00 2001
From: Meghan Chua <17057809+malchua@users.noreply.github.com>
Date: Wed, 29 Jan 2025 14:14:59 -0600
Subject: [PATCH 38/57] Use namespace_id to get namespace_type

---
 app/components/nextflow_component.rb                | 13 +++++++++----
 .../_edit_dialog.html.erb                           |  1 -
 ..._new_automated_workflow_execution_modal.html.erb |  1 -
 .../submissions/create.turbo_stream.erb             |  1 -
 4 files changed, 9 insertions(+), 7 deletions(-)

diff --git a/app/components/nextflow_component.rb b/app/components/nextflow_component.rb
index 9075821ab4..58f9a5272a 100644
--- a/app/components/nextflow_component.rb
+++ b/app/components/nextflow_component.rb
@@ -7,8 +7,7 @@ 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,
-                 namespace_type: nil)
+  def initialize(url:, samples:, workflow:, fields:, namespace_id:, allowed_to_update_samples: true, instance: nil)
     @samples = samples
     @namespace_id = namespace_id
     @url = url
@@ -16,8 +15,14 @@ def initialize(url:, samples:, workflow:, fields:, namespace_id:, allowed_to_upd
     @metadata_fields = fields
     @allowed_to_update_samples = allowed_to_update_samples
     @instance = instance
-    @namespace_type = namespace_type.nil? ? 'Project' : namespace_type
+    @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
diff --git a/app/views/projects/automated_workflow_executions/_edit_dialog.html.erb b/app/views/projects/automated_workflow_executions/_edit_dialog.html.erb
index 744e722c9e..44a1b5e0b1 100644
--- a/app/views/projects/automated_workflow_executions/_edit_dialog.html.erb
+++ b/app/views/projects/automated_workflow_executions/_edit_dialog.html.erb
@@ -22,7 +22,6 @@
       namespace_id: @project.namespace.id,
       fields: nil,
       instance: @automated_workflow_execution,
-      namespace_type: @project.namespace.type,
     ) %>
   <% end %>
 <% end %>
diff --git a/app/views/projects/automated_workflow_executions/_new_automated_workflow_execution_modal.html.erb b/app/views/projects/automated_workflow_executions/_new_automated_workflow_execution_modal.html.erb
index b28dce3c05..3c05a696d3 100644
--- a/app/views/projects/automated_workflow_executions/_new_automated_workflow_execution_modal.html.erb
+++ b/app/views/projects/automated_workflow_executions/_new_automated_workflow_execution_modal.html.erb
@@ -8,7 +8,6 @@
       allowed_to_update_samples: true,
       namespace_id: @project.namespace.id,
       fields: nil,
-      namespace_type: @project.namespace.type,
     ) %>
   <% end %>
 <% end %>
diff --git a/app/views/workflow_executions/submissions/create.turbo_stream.erb b/app/views/workflow_executions/submissions/create.turbo_stream.erb
index 46375d2dd2..45689ea4fb 100644
--- a/app/views/workflow_executions/submissions/create.turbo_stream.erb
+++ b/app/views/workflow_executions/submissions/create.turbo_stream.erb
@@ -10,7 +10,6 @@
         allowed_to_update_samples: @allowed_to_update_samples,
         namespace_id: @namespace_id,
         fields: @fields,
-        namespace_type: @namespace.nil? ? nil : @namespace.type,
       ) %>
     <% end %>
   <% end %>

From 900b97866f516366cb94084b2bddc0ad87f98fa6 Mon Sep 17 00:00:00 2001
From: Meghan Chua <17057809+malchua@users.noreply.github.com>
Date: Wed, 29 Jan 2025 14:16:30 -0600
Subject: [PATCH 39/57] Update nextflow_component_test.rb

---
 test/components/nextflow_component_test.rb | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/test/components/nextflow_component_test.rb b/test/components/nextflow_component_test.rb
index 25041b2538..7569da391f 100644
--- a/test/components/nextflow_component_test.rb
+++ b/test/components/nextflow_component_test.rb
@@ -29,6 +29,8 @@ class NextflowComponentTest < ViewComponentTestCase
     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
 
@@ -155,7 +157,9 @@ 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'))
 
@@ -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

From daeea28366d5f2d7bda6b283d207765172dfa56b Mon Sep 17 00:00:00 2001
From: Meghan Chua <17057809+malchua@users.noreply.github.com>
Date: Wed, 29 Jan 2025 14:22:13 -0600
Subject: [PATCH 40/57] Use nested translations for shared_with_namespace

---
 app/components/nextflow_component.html.erb | 5 ++---
 config/locales/en.yml                      | 4 +++-
 config/locales/fr.yml                      | 4 +++-
 3 files changed, 8 insertions(+), 5 deletions(-)

diff --git a/app/components/nextflow_component.html.erb b/app/components/nextflow_component.html.erb
index 92c312c9c6..4fd3a2e4a7 100644
--- a/app/components/nextflow_component.html.erb
+++ b/app/components/nextflow_component.html.erb
@@ -119,7 +119,7 @@
                        class: "mr-2 text-sm font-medium text-slate-900 dark:text-white" %>
       </div>
       <div class="flex items-center h-5 mb-4">
-        <% if !@workflow.automatable %>
+        <% if !@workflow.automatable && @namespace_type %>
           <%= workflow.check_box :shared_with_namespace,
                              {
                                checked:
@@ -129,8 +129,7 @@
                              } %>
           <%= workflow.label :shared_with_namespace,
                          t(
-                           :"components.nextflow.shared_with_namespace",
-                           namespace_type: @namespace_type,
+                           :"components.nextflow.shared_with.#{@namespace_type.downcase}",
                          ),
                          class: "mr-2 text-sm font-medium text-slate-900 dark:text-white" %>
         <% end %>
diff --git a/config/locales/en.yml b/config/locales/en.yml
index bbff0c3aa8..f4e1cb2323 100644
--- a/config/locales/en.yml
+++ b/config/locales/en.yml
@@ -422,7 +422,9 @@ en:
     nextflow:
       email_notification: Receive an email notification when your analysis has completed?
       required: Required
-      shared_with_namespace: Share results with %{namespace_type} members?
+      shared_with:
+        project: Share results with Project members?
+        group: Share results with Group members?
       update_samples: Update samples with analysis results
     pagination:
       next: Next
diff --git a/config/locales/fr.yml b/config/locales/fr.yml
index a8c75092ba..d3145a82bb 100644
--- a/config/locales/fr.yml
+++ b/config/locales/fr.yml
@@ -422,7 +422,9 @@ fr:
     nextflow:
       email_notification: Receive an email notification when your analysis has completed?
       required: Required
-      shared_with_namespace: Share results with %{namespace_type} members?
+      shared_with:
+        project: Share results with Project members?
+        group: Share results with Group members?
       update_samples: Update samples with analysis results
     pagination:
       next: Next

From bbab543eebc70ff230ca841f8874f5f24efdaac1 Mon Sep 17 00:00:00 2001
From: Meghan Chua <17057809+malchua@users.noreply.github.com>
Date: Wed, 29 Jan 2025 14:24:29 -0600
Subject: [PATCH 41/57] Update component test with proper namespace ids

---
 test/components/nextflow_component_test.rb | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/test/components/nextflow_component_test.rb b/test/components/nextflow_component_test.rb
index 7569da391f..e7bdb79402 100644
--- a/test/components/nextflow_component_test.rb
+++ b/test/components/nextflow_component_test.rb
@@ -22,7 +22,7 @@ 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]
     )
 
@@ -167,7 +167,7 @@ class NextflowComponentTest < ViewComponentTestCase
       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:
     )

From edf0ccf12f43a3d6c5a99b5b679246d904593823 Mon Sep 17 00:00:00 2001
From: Meghan Chua <17057809+malchua@users.noreply.github.com>
Date: Thu, 30 Jan 2025 10:39:25 -0600
Subject: [PATCH 42/57] Update submissions_test with new translations

---
 .../system/workflow_executions/submissions_test.rb | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/test/system/workflow_executions/submissions_test.rb b/test/system/workflow_executions/submissions_test.rb
index eef0947860..2e477a6e47 100644
--- a/test/system/workflow_executions/submissions_test.rb
+++ b/test/system/workflow_executions/submissions_test.rb
@@ -69,7 +69,7 @@ class SubmissionsTest < ApplicationSystemTestCase
 
         assert_text I18n.t(:'components.nextflow.update_samples')
         assert_text I18n.t(:'components.nextflow.email_notification')
-        assert_text I18n.t(:'components.nextflow.shared_with_namespace', namespace_type: @project.namespace.type)
+        assert_text I18n.t(:"components.nextflow.shared_with.#{@project.namespace.type.downcase}")
       end
     end
 
@@ -104,7 +104,7 @@ class SubmissionsTest < ApplicationSystemTestCase
 
         assert_text I18n.t(:'components.nextflow.update_samples')
         assert_text I18n.t(:'components.nextflow.email_notification')
-        assert_text I18n.t(:'components.nextflow.shared_with_namespace', namespace_type: @project.namespace.type)
+        assert_text I18n.t(:"components.nextflow.shared_with.#{@project.namespace.type.downcase}")
       end
     end
 
@@ -139,7 +139,7 @@ class SubmissionsTest < ApplicationSystemTestCase
 
         assert_no_text I18n.t(:'components.nextflow.update_samples')
         assert_text I18n.t(:'components.nextflow.email_notification')
-        assert_text I18n.t(:'components.nextflow.shared_with_namespace', namespace_type: @project.namespace.type)
+        assert_text I18n.t(:"components.nextflow.shared_with.#{@project.namespace.type.downcase}")
       end
     end
 
@@ -177,7 +177,7 @@ class SubmissionsTest < ApplicationSystemTestCase
 
         assert_no_text I18n.t(:'components.nextflow.update_samples')
         assert_text I18n.t(:'components.nextflow.email_notification')
-        assert_text I18n.t(:'components.nextflow.shared_with_namespace', namespace_type: @project.namespace.type)
+        assert_text I18n.t(:"components.nextflow.shared_with.#{@project.namespace.type.downcase}")
       end
     end
 
@@ -220,7 +220,7 @@ class SubmissionsTest < ApplicationSystemTestCase
 
         assert_text I18n.t(:'components.nextflow.update_samples')
         assert_text I18n.t(:'components.nextflow.email_notification')
-        assert_text I18n.t(:'components.nextflow.shared_with_namespace', namespace_type: @namespace.type)
+        assert_text I18n.t(:"components.nextflow.shared_with.#{@namespace.type.downcase}")
       end
     end
 
@@ -255,7 +255,7 @@ class SubmissionsTest < ApplicationSystemTestCase
 
         assert_text I18n.t(:'components.nextflow.update_samples')
         assert_text I18n.t(:'components.nextflow.email_notification')
-        assert_text I18n.t(:'components.nextflow.shared_with_namespace', namespace_type: @namespace.type)
+        assert_text I18n.t(:"components.nextflow.shared_with.#{@namespace.type.downcase}")
       end
     end
 
@@ -290,7 +290,7 @@ class SubmissionsTest < ApplicationSystemTestCase
 
         assert_no_text I18n.t(:'components.nextflow.update_samples')
         assert_text I18n.t(:'components.nextflow.email_notification')
-        assert_text I18n.t(:'components.nextflow.shared_with_namespace', namespace_type: @namespace.type)
+        assert_text I18n.t(:"components.nextflow.shared_with.#{@namespace.type.downcase}")
       end
     end
 

From 38b912479e8772fde6dd2933802f4d4250d0dbd6 Mon Sep 17 00:00:00 2001
From: Meghan Chua <17057809+malchua@users.noreply.github.com>
Date: Thu, 30 Jan 2025 11:27:45 -0600
Subject: [PATCH 43/57] Normalize translations

---
 config/locales/en.yml | 2 +-
 config/locales/fr.yml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/config/locales/en.yml b/config/locales/en.yml
index f4e1cb2323..d2656ac032 100644
--- a/config/locales/en.yml
+++ b/config/locales/en.yml
@@ -423,8 +423,8 @@ en:
       email_notification: Receive an email notification when your analysis has completed?
       required: Required
       shared_with:
-        project: Share results with Project members?
         group: Share results with Group members?
+        project: Share results with Project members?
       update_samples: Update samples with analysis results
     pagination:
       next: Next
diff --git a/config/locales/fr.yml b/config/locales/fr.yml
index d3145a82bb..387ebd3133 100644
--- a/config/locales/fr.yml
+++ b/config/locales/fr.yml
@@ -423,8 +423,8 @@ fr:
       email_notification: Receive an email notification when your analysis has completed?
       required: Required
       shared_with:
-        project: Share results with Project members?
         group: Share results with Group members?
+        project: Share results with Project members?
       update_samples: Update samples with analysis results
     pagination:
       next: Next

From ac4a30d11c861899906f6a7395ebe3ee5cc9a003 Mon Sep 17 00:00:00 2001
From: Meghan Chua <17057809+malchua@users.noreply.github.com>
Date: Thu, 30 Jan 2025 17:18:57 -0600
Subject: [PATCH 44/57] Modify nextflow component to not show empty div

---
 app/components/nextflow_component.html.erb | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/app/components/nextflow_component.html.erb b/app/components/nextflow_component.html.erb
index 4fd3a2e4a7..e0d58c4433 100644
--- a/app/components/nextflow_component.html.erb
+++ b/app/components/nextflow_component.html.erb
@@ -118,8 +118,8 @@
                        t(:"components.nextflow.email_notification"),
                        class: "mr-2 text-sm font-medium text-slate-900 dark:text-white" %>
       </div>
-      <div class="flex items-center h-5 mb-4">
-        <% if !@workflow.automatable && @namespace_type %>
+      <% if !@workflow.automatable && @namespace_type %>
+        <div class="flex items-center h-5 mb-4">
           <%= workflow.check_box :shared_with_namespace,
                              {
                                checked:
@@ -132,8 +132,8 @@
                            :"components.nextflow.shared_with.#{@namespace_type.downcase}",
                          ),
                          class: "mr-2 text-sm font-medium text-slate-900 dark:text-white" %>
-        <% end %>
-      </div>
+        </div>
+      <% end %>
     <% end %>
 
     <button

From e5d854dfd89e9fd088d69dc8269c621cf82a7186 Mon Sep 17 00:00:00 2001
From: Meghan Chua <17057809+malchua@users.noreply.github.com>
Date: Thu, 30 Jan 2025 17:21:31 -0600
Subject: [PATCH 45/57] Update workflow execution tests to be less flakey

---
 .../projects/workflow_executions_test.rb      | 19 ++++++++++---------
 test/system/workflow_executions_test.rb       | 10 +++++-----
 2 files changed, 15 insertions(+), 14 deletions(-)

diff --git a/test/system/projects/workflow_executions_test.rb b/test/system/projects/workflow_executions_test.rb
index 9de91bbaea..474e80da35 100644
--- a/test/system/projects/workflow_executions_test.rb
+++ b/test/system/projects/workflow_executions_test.rb
@@ -97,16 +97,16 @@ class WorkflowExecutionsTest < ApplicationSystemTestCase
 
       assert_selector 'h1', text: I18n.t(:'projects.workflow_executions.index.title')
 
-      tr = find('a', text: workflow_execution1.id).ancestor('tr')
-      within tr do
-        assert_no_link 'Cancel'
-        assert_no_link 'Destroy'
+      assert_selector "tr[id='#{workflow_execution1.id}']"
+      within("tr[id='#{workflow_execution1.id}'] td:last-child") do
+        assert_no_link I18n.t(:'workflow_executions.index.actions.cancel_button')
+        assert_no_link I18n.t(:'workflow_executions.index.actions.delete_button')
       end
 
-      tr = find('a', text: workflow_execution2.id).ancestor('tr')
-      within tr do
-        assert_no_link 'Cancel'
-        assert_no_link 'Destroy'
+      assert_selector "tr[id='#{workflow_execution2.id}']"
+      within("tr[id='#{workflow_execution2.id}'] td:last-child") do
+        assert_no_link I18n.t(:'workflow_executions.index.actions.cancel_button')
+        assert_no_link I18n.t(:'workflow_executions.index.actions.delete_button')
       end
     end
 
@@ -115,7 +115,8 @@ class WorkflowExecutionsTest < ApplicationSystemTestCase
 
       visit namespace_project_workflow_executions_path(@namespace, @project)
 
-      assert_no_selector 'a', text: workflow_execution.id
+      assert_selector '#workflow-executions-table'
+      assert_no_selector "tr[id='#{workflow_execution.id}']"
     end
 
     test 'should be able to cancel a workflow' do
diff --git a/test/system/workflow_executions_test.rb b/test/system/workflow_executions_test.rb
index e5243a2dba..e4a033d6db 100644
--- a/test/system/workflow_executions_test.rb
+++ b/test/system/workflow_executions_test.rb
@@ -118,10 +118,9 @@ class WorkflowExecutionsTest < ApplicationSystemTestCase
 
     assert_selector 'h1', text: I18n.t(:'workflow_executions.index.title')
 
-    tr = find('a', text: workflow_execution.id).ancestor('tr')
-
-    within tr do
-      assert_link 'Cancel'
+    assert_selector "tr[id='#{workflow_execution.id}']"
+    within("tr[id='#{workflow_execution.id}'] td:last-child") do
+      assert_link I18n.t(:'workflow_executions.index.actions.cancel_button')
     end
   end
 
@@ -130,7 +129,8 @@ class WorkflowExecutionsTest < ApplicationSystemTestCase
 
     visit workflow_executions_path
 
-    assert_no_selector 'a', text: workflow_execution.id
+    assert_selector '#workflow-executions-table'
+    assert_no_selector "tr[id='#{workflow_execution.id}']"
   end
 
   test 'should be able to cancel a workflow' do

From a7a117b116e9d01881e09b9e2f4f42d4696afd65 Mon Sep 17 00:00:00 2001
From: Meghan Chua <17057809+malchua@users.noreply.github.com>
Date: Thu, 30 Jan 2025 17:23:45 -0600
Subject: [PATCH 46/57] Update table to render Actions cell consistently

---
 .../workflow_executions/table_component.html.erb       | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/app/components/workflow_executions/table_component.html.erb b/app/components/workflow_executions/table_component.html.erb
index a3aa07191a..41ddeb8ed7 100644
--- a/app/components/workflow_executions/table_component.html.erb
+++ b/app/components/workflow_executions/table_component.html.erb
@@ -140,11 +140,11 @@
                 <% end %>
               <% end %>
             <% end %>
-            <% if @renders_row_actions && (!workflow_execution.shared_with_namespace || @namespace.nil?) %>
-              <%= render_cell(
-                tag: 'td',
-                classes: class_names('px-3 py-3 sticky right-0 bg-white dark:bg-slate-800 z-10 space-x-2')
-              ) do %>
+            <%= render_cell(
+              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 @renders_row_actions && (!workflow_execution.shared_with_namespace || @namespace.nil?) %>
                 <% if workflow_execution.cancellable? && @row_actions.key?(:cancel) %>
                   <%= link_to(
                     t(:"workflow_executions.index.actions.cancel_button"),

From c0a4281512b3de78f9f36b061d06b2b3e1bb8d16 Mon Sep 17 00:00:00 2001
From: Meghan Chua <17057809+malchua@users.noreply.github.com>
Date: Thu, 30 Jan 2025 17:25:51 -0600
Subject: [PATCH 47/57] Fix bug with exporting shared workflow executions

---
 app/services/data_exports/create_service.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/app/services/data_exports/create_service.rb b/app/services/data_exports/create_service.rb
index b2559eb880..21049243f0 100644
--- a/app/services/data_exports/create_service.rb
+++ b/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

From 4e003be8e88886746483574260230315ce3cd22e Mon Sep 17 00:00:00 2001
From: Meghan Chua <17057809+malchua@users.noreply.github.com>
Date: Fri, 31 Jan 2025 12:43:13 -0600
Subject: [PATCH 48/57] Fix table component actions cell logic

---
 .../table_component.html.erb                  | 62 ++++++++++---------
 1 file changed, 32 insertions(+), 30 deletions(-)

diff --git a/app/components/workflow_executions/table_component.html.erb b/app/components/workflow_executions/table_component.html.erb
index 41ddeb8ed7..cf973a0011 100644
--- a/app/components/workflow_executions/table_component.html.erb
+++ b/app/components/workflow_executions/table_component.html.erb
@@ -140,36 +140,38 @@
                 <% end %>
               <% end %>
             <% end %>
-            <%= render_cell(
-              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 @renders_row_actions && (!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",
-                  ) %>
+            <% if @renders_row_actions %>
+              <%= render_cell(
+                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.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 %>

From 2b2f7e740fda4fdb789930ed86e172cafc245ab4 Mon Sep 17 00:00:00 2001
From: Meghan Chua <17057809+malchua@users.noreply.github.com>
Date: Tue, 4 Feb 2025 19:00:33 -0600
Subject: [PATCH 49/57] Update workflow execution policies and tests

---
 app/policies/workflow_execution_policy.rb     |  56 ++++----
 .../workflow_execution_policy_test.rb         | 121 ++++++++++++++++--
 2 files changed, 141 insertions(+), 36 deletions(-)

diff --git a/app/policies/workflow_execution_policy.rb b/app/policies/workflow_execution_policy.rb
index 33b297f8e9..7cd716796d 100644
--- a/app/policies/workflow_execution_policy.rb
+++ b/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
 
@@ -39,19 +36,19 @@ def destroy? # rubocop:disable Metrics/AbcSize, Metrics/CyclomaticComplexity
     false
   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
+  def read? # rubocop:disable Metrics/AbcSize
+    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)
+       (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))
+       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.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.submitter.id == record.namespace.automation_bot.id) &&
+       (effective_access_level >= Member::AccessLevel::ANALYST)
+      return true
+    end
 
     details[:id] = record.id
     false
diff --git a/test/policies/workflow_execution_policy_test.rb b/test/policies/workflow_execution_policy_test.rb
index ab7e607d0d..3e2af16036 100644
--- a/test/policies/workflow_execution_policy_test.rb
+++ b/test/policies/workflow_execution_policy_test.rb
@@ -14,22 +14,34 @@ def setup
   test '#read?' do
     assert @policy.apply(:read?)
 
+    # shared workflow execution
+    # user is project member
     user = users(:ryan_doe)
-    policy = WorkflowExecutionPolicy.new(@workflow_execution, user:)
+    workflow_execution = workflow_executions(:workflow_execution_shared2)
+    policy = WorkflowExecutionPolicy.new(workflow_execution, user:)
 
     assert policy.apply(:read?)
 
-    user = users(:project1_automation_bot)
+    # user is not project member
     user_incorrect_permissions = users(:micha_doe)
+    policy = WorkflowExecutionPolicy.new(workflow_execution, user: user_incorrect_permissions)
+
+    assert_not policy.apply(:read?)
+
+    # automated workflow execution
+    # user is project automation bot
+    user = users(:project1_automation_bot)
     workflow_execution = workflow_executions(:automated_workflow_execution)
     policy = WorkflowExecutionPolicy.new(workflow_execution, user:)
 
     assert policy.apply(:read?)
 
+    # user is project creator
     policy = WorkflowExecutionPolicy.new(workflow_execution, user: @user)
 
     assert policy.apply(:read?)
 
+    # user with incorrect permissions
     policy = WorkflowExecutionPolicy.new(workflow_execution, user: user_incorrect_permissions)
 
     assert_not policy.apply(:read?)
@@ -48,15 +60,36 @@ def setup
   test 'update?' do
     assert @policy.apply(:update?)
 
-    user = users(:james_doe)
+    # automated workflow execution
+    # user is ANALYST
     workflow_execution = workflow_executions(:automated_workflow_execution)
-    policy = WorkflowExecutionPolicy.new(workflow_execution, user: user)
+    user = users(:james_doe)
+    policy = WorkflowExecutionPolicy.new(workflow_execution, user:)
 
     assert policy.apply(:update?)
 
+    # user is GUEST
     user = users(:ryan_doe)
-    workflow_execution = workflow_executions(:automated_workflow_execution)
-    policy = WorkflowExecutionPolicy.new(workflow_execution, user: user)
+    policy = WorkflowExecutionPolicy.new(workflow_execution, user:)
+
+    assert_not policy.apply(:update?)
+
+    # shared workflow execution
+    # user is submitter
+    workflow_execution = workflow_executions(:workflow_execution_shared2)
+    user = users(:james_doe)
+    policy = WorkflowExecutionPolicy.new(workflow_execution, user:)
+
+    assert policy.apply(:update?)
+
+    # user is member of project
+    policy = WorkflowExecutionPolicy.new(workflow_execution, user: @user)
+
+    assert_not policy.apply(:update?)
+
+    # user is not member of project
+    user = users(:micha_doe)
+    policy = WorkflowExecutionPolicy.new(workflow_execution, user:)
 
     assert_not policy.apply(:update?)
   end
@@ -64,15 +97,36 @@ def setup
   test 'edit?' do
     assert @policy.apply(:edit?)
 
+    # automated workflow execution
+    # user is ANALYST
     user = users(:james_doe)
     workflow_execution = workflow_executions(:automated_workflow_execution)
-    policy = WorkflowExecutionPolicy.new(workflow_execution, user: user)
+    policy = WorkflowExecutionPolicy.new(workflow_execution, user:)
 
     assert policy.apply(:edit?)
 
+    # user is GUEST
     user = users(:ryan_doe)
-    workflow_execution = workflow_executions(:automated_workflow_execution)
-    policy = WorkflowExecutionPolicy.new(workflow_execution, user: user)
+    policy = WorkflowExecutionPolicy.new(workflow_execution, user:)
+
+    assert_not policy.apply(:edit?)
+
+    # shared workflow execution
+    # user is submitter
+    workflow_execution = workflow_executions(:workflow_execution_shared2)
+    user = users(:james_doe)
+    policy = WorkflowExecutionPolicy.new(workflow_execution, user:)
+
+    assert policy.apply(:edit?)
+
+    # user is member of project
+    policy = WorkflowExecutionPolicy.new(workflow_execution, user: @user)
+
+    assert_not policy.apply(:edit?)
+
+    # user is not member of project
+    user = users(:micha_doe)
+    policy = WorkflowExecutionPolicy.new(workflow_execution, user:)
 
     assert_not policy.apply(:edit?)
   end
@@ -80,26 +134,50 @@ def setup
   test '#cancel?' do
     assert @policy.apply(:cancel?)
 
+    # automated workflow execution
+    # user is project automation bot
     user = users(:project1_automation_bot)
     workflow_execution = workflow_executions(:automated_workflow_execution)
     policy = WorkflowExecutionPolicy.new(workflow_execution, user:)
 
     assert policy.apply(:cancel?)
 
-    automated_workflow_execution = workflow_executions(:automated_workflow_execution)
-    policy = WorkflowExecutionPolicy.new(automated_workflow_execution, user: @user)
+    # user is project OWNER
+    policy = WorkflowExecutionPolicy.new(workflow_execution, user: @user)
 
     assert policy.apply(:cancel?)
 
+    # user with incorrect permissions
     user_incorrect_permissions = users(:ryan_doe)
     policy = WorkflowExecutionPolicy.new(workflow_execution, user: user_incorrect_permissions)
 
     assert_not policy.apply(:cancel?)
+
+    # shared workflow execution
+    # user is submitter
+    workflow_execution = workflow_executions(:workflow_execution_shared2)
+    user = users(:james_doe)
+    policy = WorkflowExecutionPolicy.new(workflow_execution, user:)
+
+    assert policy.apply(:cancel?)
+
+    # user is member of project
+    policy = WorkflowExecutionPolicy.new(workflow_execution, user: @user)
+
+    assert_not policy.apply(:cancel?)
+
+    # user is not member of project
+    user = users(:micha_doe)
+    policy = WorkflowExecutionPolicy.new(workflow_execution, user:)
+
+    assert_not policy.apply(:cancel?)
   end
 
   test '#destroy?' do
     assert @policy.apply(:destroy?)
 
+    # automated workflow execution
+    # user is project automation bot
     user = users(:project1_automation_bot)
     user_incorrect_permissions = users(:ryan_doe)
     workflow_execution = workflow_executions(:automated_workflow_execution)
@@ -107,13 +185,34 @@ def setup
 
     assert policy.apply(:destroy?)
 
+    # user is project OWNER
     policy = WorkflowExecutionPolicy.new(workflow_execution, user: @user)
 
     assert policy.apply(:destroy?)
 
+    # user with incorrect permissions
     policy = WorkflowExecutionPolicy.new(workflow_execution, user: user_incorrect_permissions)
 
     assert_not policy.apply(:destroy?)
+
+    # shared workflow execution
+    # user is submitter
+    workflow_execution = workflow_executions(:workflow_execution_shared2)
+    user = users(:james_doe)
+    policy = WorkflowExecutionPolicy.new(workflow_execution, user:)
+
+    assert policy.apply(:cancel?)
+
+    # user is member of project
+    policy = WorkflowExecutionPolicy.new(workflow_execution, user: @user)
+
+    assert_not policy.apply(:cancel?)
+
+    # user is not member of project
+    user = users(:micha_doe)
+    policy = WorkflowExecutionPolicy.new(workflow_execution, user:)
+
+    assert_not policy.apply(:cancel?)
   end
 
   test 'automated scope' do

From 4993ed81586201c142c37e59e112a407b3681da6 Mon Sep 17 00:00:00 2001
From: Meghan Chua <17057809+malchua@users.noreply.github.com>
Date: Tue, 4 Feb 2025 19:02:06 -0600
Subject: [PATCH 50/57] Remove unnecessary shared_with_namespace check

---
 app/views/projects/workflow_executions/show.html.erb | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/app/views/projects/workflow_executions/show.html.erb b/app/views/projects/workflow_executions/show.html.erb
index 49df86ac96..268c492d7f 100644
--- a/app/views/projects/workflow_executions/show.html.erb
+++ b/app/views/projects/workflow_executions/show.html.erb
@@ -41,7 +41,7 @@
             "button button--size-default button--state-default pointer-events-none cursor-not-allowed bg-slate-100 text-slate-600 mr-2 dark:bg-slate-600 dark:text-slate-300" %>
         <% end %>
       <% end %>
-      <% if @workflow_execution.cancellable? && allowed_to?(:cancel?, @workflow_execution) && !@workflow_execution.shared_with_namespace %>
+      <% if @workflow_execution.cancellable? && allowed_to?(:cancel?, @workflow_execution) %>
         <%= link_to(
           t("projects.workflow_executions.show.cancel_button"),
           cancel_namespace_project_workflow_execution_path(
@@ -57,7 +57,7 @@
           class: "button button--state-default button--size-default mr-1",
         ) %>
       <% end %>
-      <% if allowed_to?(:update?, @workflow_execution) && !@workflow_execution.shared_with_namespace %>
+      <% if allowed_to?(:update?, @workflow_execution) %>
         <%= link_to(
           t("projects.workflow_executions.show.edit_button"),
           edit_namespace_project_workflow_execution_path(
@@ -71,7 +71,7 @@
           class: "button button--state-default button--size-default mr-1",
         ) %>
       <% end %>
-      <% if @workflow_execution.deletable? && allowed_to?(:destroy?, @workflow_execution) && !@workflow_execution.shared_with_namespace %>
+      <% if @workflow_execution.deletable? && allowed_to?(:destroy?, @workflow_execution) %>
         <%= link_to(
           t("projects.workflow_executions.show.remove_button"),
           namespace_project_workflow_execution_path(

From c00066321519478a282258bd45c0125aac00d034 Mon Sep 17 00:00:00 2001
From: Meghan Chua <17057809+malchua@users.noreply.github.com>
Date: Tue, 4 Feb 2025 19:19:20 -0600
Subject: [PATCH 51/57] Include checkbox when using an automatable pipeline

---
 app/components/nextflow_component.html.erb | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/app/components/nextflow_component.html.erb b/app/components/nextflow_component.html.erb
index e0d58c4433..a6c76357b9 100644
--- a/app/components/nextflow_component.html.erb
+++ b/app/components/nextflow_component.html.erb
@@ -118,7 +118,8 @@
                        t(:"components.nextflow.email_notification"),
                        class: "mr-2 text-sm font-medium text-slate-900 dark:text-white" %>
       </div>
-      <% if !@workflow.automatable && @namespace_type %>
+      <%# do not render checkbox for an automated workflow execution %>
+      <% if @namespace_type && !@samples.empty? %>
         <div class="flex items-center h-5 mb-4">
           <%= workflow.check_box :shared_with_namespace,
                              {

From c0a2cedda11cb648f9d11f33cab2b03ccafeea28 Mon Sep 17 00:00:00 2001
From: Meghan Chua <17057809+malchua@users.noreply.github.com>
Date: Thu, 6 Feb 2025 15:50:46 -0600
Subject: [PATCH 52/57] Add new fixture files for export tests

---
 .../files/INXT_SAM_AAAAAAAABW.assembly.fa.gz     | Bin 0 -> 89 bytes
 test/fixtures/files/data_export_11.zip           | Bin 0 -> 2283 bytes
 test/fixtures/files/data_export_12.zip           | Bin 0 -> 2283 bytes
 3 files changed, 0 insertions(+), 0 deletions(-)
 create mode 100644 test/fixtures/files/INXT_SAM_AAAAAAAABW.assembly.fa.gz
 create mode 100644 test/fixtures/files/data_export_11.zip
 create mode 100644 test/fixtures/files/data_export_12.zip

diff --git a/test/fixtures/files/INXT_SAM_AAAAAAAABW.assembly.fa.gz b/test/fixtures/files/INXT_SAM_AAAAAAAABW.assembly.fa.gz
new file mode 100644
index 0000000000000000000000000000000000000000..c7ba1e149faa29bb6cecfcee7c4473beaf466a73
GIT binary patch
literal 89
zcmb2|=3oE==FOkKbaQm_mwo9i@A<;Z$6H`h#&tzkPt*63ua2JIS>IDDpA?mp@fVhq
ql$Dk9GhT9Fo4}gVbVGr!gZ)v{&jiK|91$8V+zf}MHBTe}O#}dq=pUs3

literal 0
HcmV?d00001

diff --git a/test/fixtures/files/data_export_11.zip b/test/fixtures/files/data_export_11.zip
new file mode 100644
index 0000000000000000000000000000000000000000..416f2c874461104200838b3d3d9386e355f14f45
GIT binary patch
literal 2283
zcmWIWW@Zs#;9y{2;9X)L1*G7>n1PeQAT8B0$;dEK*U~)ELf6E=%u?4f*&<2T#K_zv
z)iO23JlWh*zqm9vH?gQvucV?xFTE->gq49Y%6M+Nd^gBcAYeW_>3rU81D^KxbzN^5
zQ#_}ooZMR($;UWLX?2v2wd58T^?QHv%P!rl{k5{4k=bZLJ5w}gla1hyx(D0$-mg3L
z-mJa-tm6H*`R1!@Z4-jacWj!zt+lXI>GzJf{55|CTyO6_?40;Hc4GbAo5ySQ?CSP)
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diff --git a/test/fixtures/files/data_export_12.zip b/test/fixtures/files/data_export_12.zip
new file mode 100644
index 0000000000000000000000000000000000000000..416f2c874461104200838b3d3d9386e355f14f45
GIT binary patch
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From eb0656a07f5a28689ce2fed1c5f9721c909e74a5 Mon Sep 17 00:00:00 2001
From: Meghan Chua <17057809+malchua@users.noreply.github.com>
Date: Thu, 6 Feb 2025 15:54:14 -0600
Subject: [PATCH 53/57] Create fixtures for export testing

---
 test/fixtures/active_storage/attachments.yml  | 15 ++++++
 test/fixtures/active_storage/blobs.yml        |  6 +++
 test/fixtures/attachments.yml                 |  5 ++
 test/fixtures/data_exports.yml                | 23 ++++++++++
 test/fixtures/samples_workflow_executions.yml |  9 ++++
 test/fixtures/workflow_executions.yml         | 46 +++++++++++++++++++
 6 files changed, 104 insertions(+)

diff --git a/test/fixtures/active_storage/attachments.yml b/test/fixtures/active_storage/attachments.yml
index 3f4eb46613..4b846d4600 100644
--- a/test/fixtures/active_storage/attachments.yml
+++ b/test/fixtures/active_storage/attachments.yml
@@ -143,6 +143,11 @@ samples_workflow_execution_completed_output:
   record: samples_workflow_execution_completed_output_attachment (Attachment)
   blob: samples_workflow_execution_completed_output_blob
 
+samples_shared_workflow_execution_completed_output:
+  name: file
+  record: samples_shared_workflow_execution_completed_output_attachment (Attachment)
+  blob: samples_shared_workflow_execution_completed_output_blob
+
 data_export_7_test_export:
   name: file
   record: data_export_seven (DataExport)
@@ -158,6 +163,16 @@ data_export_9_test_export:
   record: data_export_nine (DataExport)
   blob: data_export_9_test_export_blob
 
+data_export_11_test_export:
+  name: file
+  record: data_export_eleven (DataExport)
+  blob: data_export_11_test_export_blob
+
+data_export_12_test_export:
+  name: file
+  record: data_export_twelve (DataExport)
+  blob: data_export_12_test_export_blob
+
 attachmentEndToEndFWD_file_test_file_fastq:
   name: file
   record: attachmentEndToEndFWD (Attachment)
diff --git a/test/fixtures/active_storage/blobs.yml b/test/fixtures/active_storage/blobs.yml
index ee0a1d90aa..7f5aaa7987 100644
--- a/test/fixtures/active_storage/blobs.yml
+++ b/test/fixtures/active_storage/blobs.yml
@@ -85,12 +85,18 @@ workflow_execution_completed_output_blob: <%= ActiveStorage::FixtureSet.blob fil
 
 samples_workflow_execution_completed_output_blob: <%= ActiveStorage::FixtureSet.blob filename: "INXT_SAM_AAAAAAAABV.assembly.fa.gz", service_name: "test" %>
 
+samples_shared_workflow_execution_completed_output_blob: <%= ActiveStorage::FixtureSet.blob filename: "INXT_SAM_AAAAAAAABW.assembly.fa.gz", service_name: "test" %>
+
 data_export_7_test_export_blob: <%= ActiveStorage::FixtureSet.blob filename: "data_export_7.zip", service_name: "test" %>
 
 data_export_8_test_export_blob: <%= ActiveStorage::FixtureSet.blob filename: "data_export_8.csv", service_name: "test" %>
 
 data_export_9_test_export_blob: <%= ActiveStorage::FixtureSet.blob filename: "data_export_9.xlsx", service_name: "test" %>
 
+data_export_11_test_export_blob: <%= ActiveStorage::FixtureSet.blob filename: "data_export_11.zip", service_name: "test" %>
+
+data_export_12_test_export_blob: <%= ActiveStorage::FixtureSet.blob filename: "data_export_12.zip", service_name: "test" %>
+
 attachmentEndToEndFWD_file_test_file_fastq_blob: <%= ActiveStorage::FixtureSet.blob filename: "test_file_end_to_end_F.fastq", service_name: "test" %>
 attachmentEndToEndREV_file_test_file_fastq_blob: <%= ActiveStorage::FixtureSet.blob filename: "test_file_end_to_end_R.fastq", service_name: "test" %>
 
diff --git a/test/fixtures/attachments.yml b/test/fixtures/attachments.yml
index 4180d6a9bb..81f15f58b8 100644
--- a/test/fixtures/attachments.yml
+++ b/test/fixtures/attachments.yml
@@ -232,6 +232,11 @@ samples_workflow_execution_completed_output_attachment:
   attachable: sample46_irida_next_example_completed_with_output (SamplesWorkflowExecution)
   puid: INXT_ATT_AAAAAAAAAU
 
+samples_shared_workflow_execution_completed_output_attachment:
+  metadata: {"type": "assembly", "format": "fasta", "compression": "gzip"}
+  attachable: sample47_workflow_execution_completed_shared2 (SamplesWorkflowExecution)
+  puid: INXT_ATT_AAAAAAAAAV
+
 attachmentEndToEndFWD:
   metadata:
     {
diff --git a/test/fixtures/data_exports.yml b/test/fixtures/data_exports.yml
index 9086523876..ce5d73557a 100644
--- a/test/fixtures/data_exports.yml
+++ b/test/fixtures/data_exports.yml
@@ -139,3 +139,26 @@ data_export_ten:
   expires_at: <%= 5.days.from_now %>
   manifest: '{"type":"Samples Export","date": "2024-01-01","children":[{"name":"INXT_PRJ_AAAAAAAAAB","type":"folder","irida-next-type":"project","irida-next-name":"Project 2","children":[{"name":"INXT_SAM_AAAAAAAAAV","type":"folder","irida-next-type":"sample","irida-next-name":"Project 2 Sample 22","children":[{"name":"INXT_ATT_ABAAAAAAAI","type":"folder","irida-next-type":"attachment","children":[{"name":"test_file_14.txt","type":"file","metadata":{"format":"text"}}]},{"name":"INXT_ATT_ABAAAAAAAH","type":"folder","irida-next-type":"attachment","children":[{"name":"test_file_5.fasta","type":"file","metadata":{"format":"fasta","type":"assembly"}}]}]}]}]}'
 
+data_export_eleven:
+  name: Data Export 11
+  export_type: analysis
+  status: ready
+  export_parameters: {ids: [<%= ActiveRecord::FixtureSet.identify(:workflow_execution_completed_shared2, :uuid) %>], analysis_type: 'user'}
+  email_notification: true
+  created_at: <%= 1.week.ago %>
+  updated_at: <%= 1.day.ago %>
+  user_id: <%= ActiveRecord::FixtureSet.identify(:micha_doe, :uuid) %>
+  expires_at: <%= 5.days.from_now %>
+  manifest: '{"type":"Analysis Export","date":"2024-01-01","children":[{"name":"<%= ActiveRecord::FixtureSet.identify(:workflow_execution_completed_shared2, :uuid) %>", "type":"folder","irida-next-type":"workflow_execution","irida-next-name":"<%= ActiveRecord::FixtureSet.identify(:workflow_execution_completed_shared2, :uuid) %>","children":[{"name":"summary.txt.gz","type":"file"},{"name":"INXT_SAM_AAAAAAAABW","type":"folder","irida-next-type":"sample","irida-next-name":"Sample 47","children":[{"name":"INXT_SAM_AAAAAAAABW.assembly.fa.gz","type":"file"}]}]}]}'
+
+data_export_twelve:
+  name: Data Export 12
+  export_type: analysis
+  status: ready
+  export_parameters: {ids: [<%= ActiveRecord::FixtureSet.identify(:workflow_execution_completed_shared2, :uuid) %>], analysis_type: 'user'}
+  email_notification: true
+  created_at: <%= 1.week.ago %>
+  updated_at: <%= 1.day.ago %>
+  user_id: <%= ActiveRecord::FixtureSet.identify(:james_doe, :uuid) %>
+  expires_at: <%= 5.days.from_now %>
+  manifest: '{"type":"Analysis Export","date":"2024-01-01","children":[{"name":"<%= ActiveRecord::FixtureSet.identify(:workflow_execution_completed_shared2, :uuid) %>", "type":"folder","irida-next-type":"workflow_execution","irida-next-name":"<%= ActiveRecord::FixtureSet.identify(:workflow_execution_completed_shared2, :uuid) %>","children":[{"name":"summary.txt.gz","type":"file"},{"name":"INXT_SAM_AAAAAAAABW","type":"folder","irida-next-type":"sample","irida-next-name":"Sample 47","children":[{"name":"INXT_SAM_AAAAAAAABW.assembly.fa.gz","type":"file"}]}]}]}'
diff --git a/test/fixtures/samples_workflow_executions.yml b/test/fixtures/samples_workflow_executions.yml
index fa0059b5eb..f6204da207 100644
--- a/test/fixtures/samples_workflow_executions.yml
+++ b/test/fixtures/samples_workflow_executions.yml
@@ -184,6 +184,15 @@ sample46_irida_next_example_completed_with_output:
     "fastq_2": ""
   }
 
+sample47_workflow_execution_completed_shared2:
+  sample_id: <%= ActiveRecord::FixtureSet.identify(:sample47, :uuid) %>
+  workflow_execution_id: <%= ActiveRecord::FixtureSet.identify(:workflow_execution_completed_shared2, :uuid) %>
+  samplesheet_params: {
+    "sample": <%= "Sample_#{ActiveRecord::FixtureSet.identify(:sample47, :uuid)}" %>,
+    "fastq_1": <%= "gid://irida/Attachment/#{ActiveRecord::FixtureSet.identify(:samples_shared_workflow_execution_completed_output, :uuid)}" %>,
+    "fastq_2": ""
+  }
+
 sample1_automated_example_submitted:
   sample_id: <%= ActiveRecord::FixtureSet.identify(:sample1, :uuid) %>
   workflow_execution_id: <%= ActiveRecord::FixtureSet.identify(:automated_example_submitted, :uuid) %>
diff --git a/test/fixtures/workflow_executions.yml b/test/fixtures/workflow_executions.yml
index 7e82aa32fc..58b18e2bb7 100644
--- a/test/fixtures/workflow_executions.yml
+++ b/test/fixtures/workflow_executions.yml
@@ -896,3 +896,49 @@ workflow_execution_shared3:
   submitter_id: <%= ActiveRecord::FixtureSet.identify(:james_doe, :uuid) %>
   namespace_id: <%= ActiveRecord::FixtureSet.identify(:project2_namespace, :uuid) %>
   shared_with_namespace: true
+
+workflow_execution_completed_shared1:
+  <<: *DEFAULTS
+  metadata:
+    {
+      "workflow_name": "phac-nml/iridanextexample",
+      "workflow_version": "1.0.2",
+    }
+  workflow_params:
+    {
+      "input": "/blah/samplesheet.csv",
+      "outdir": "/blah/output",
+    }
+  workflow_engine_parameters: { "-r": "dev" }
+  workflow_url: "https://github.com/phac-nml/irida_next_shared_example_completed_with_output"
+  run_id: "my_run_id_shared_1"
+  submitter_id: <%= ActiveRecord::FixtureSet.identify(:james_doe, :uuid) %>
+  namespace_id: <%= ActiveRecord::FixtureSet.identify(:project22_namespace, :uuid) %>
+  name: "irida_next_user_shared_example_completed_with_output"
+  state: "completed"
+  blob_run_directory: "not a run dir"
+  cleaned: false
+  shared_with_namespace: true
+
+workflow_execution_completed_shared2:
+  <<: *DEFAULTS
+  metadata:
+    {
+      "workflow_name": "phac-nml/iridanextexample",
+      "workflow_version": "1.0.2",
+    }
+  workflow_params:
+    {
+      "input": "/blah/samplesheet.csv",
+      "outdir": "/blah/output",
+    }
+  workflow_engine_parameters: { "-r": "dev" }
+  workflow_url: "https://github.com/phac-nml/irida_next_shared_example_completed_with_output"
+  run_id: "my_run_id_shared_2"
+  submitter_id: <%= ActiveRecord::FixtureSet.identify(:micha_doe, :uuid) %>
+  namespace_id: <%= ActiveRecord::FixtureSet.identify(:project22_namespace, :uuid) %>
+  name: "irida_next_member_shared_example_completed_with_output"
+  state: "completed"
+  blob_run_directory: "not a run dir"
+  cleaned: false
+  shared_with_namespace: true

From 667162d9a3e3d2f340c6d74022c86d55d740f644 Mon Sep 17 00:00:00 2001
From: Meghan Chua <17057809+malchua@users.noreply.github.com>
Date: Thu, 6 Feb 2025 15:56:33 -0600
Subject: [PATCH 54/57] Fix policy bug when user is not submitter or bot

---
 app/policies/workflow_execution_policy.rb | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/app/policies/workflow_execution_policy.rb b/app/policies/workflow_execution_policy.rb
index 7cd716796d..2c2257f77e 100644
--- a/app/policies/workflow_execution_policy.rb
+++ b/app/policies/workflow_execution_policy.rb
@@ -36,12 +36,12 @@ def destroy? # rubocop:disable Metrics/AbcSize
     false
   end
 
-  def read? # rubocop:disable Metrics/AbcSize
+  def read? # rubocop:disable Metrics/AbcSize, Metrics/CyclomaticComplexity
     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 && (record.submitter.id == record.namespace.automation_bot.id) &&
        (effective_access_level > Member::AccessLevel::NO_ACCESS)
       return true
     end
@@ -66,7 +66,7 @@ def cancel? # rubocop:disable Metrics/AbcSize
 
     # 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 && (record.submitter.id == record.namespace.automation_bot.id) &&
        Member::AccessLevel.manageable.include?(effective_access_level)
       return true
     end
@@ -81,7 +81,7 @@ def edit? # rubocop:disable Metrics/AbcSize
 
     # submitted by automation bot and user is analyst or higher
     if (record.namespace.type == Namespaces::ProjectNamespace.sti_name) &&
-       (record.submitter.id == record.namespace.automation_bot.id) &&
+       record.namespace.automation_bot && (record.submitter.id == record.namespace.automation_bot.id) &&
        (effective_access_level >= Member::AccessLevel::ANALYST)
       return true
     end
@@ -95,7 +95,7 @@ def update? # rubocop:disable Metrics/AbcSize
 
     # submitted by automation bot and user is analyst or higher
     if (record.namespace.type == Namespaces::ProjectNamespace.sti_name) &&
-       (record.submitter.id == record.namespace.automation_bot.id) &&
+       record.namespace.automation_bot && (record.submitter.id == record.namespace.automation_bot.id) &&
        (effective_access_level >= Member::AccessLevel::ANALYST)
       return true
     end

From ecfcfd6b7752184d087e29e83bf0f3434d734cc2 Mon Sep 17 00:00:00 2001
From: Meghan Chua <17057809+malchua@users.noreply.github.com>
Date: Thu, 6 Feb 2025 15:58:39 -0600
Subject: [PATCH 55/57] Add shared workflow tests to data_exports_test

---
 test/system/data_exports_test.rb | 280 +++++++++++++++++++++++++++++++
 1 file changed, 280 insertions(+)

diff --git a/test/system/data_exports_test.rb b/test/system/data_exports_test.rb
index 8bc4d4e122..4d0c46cb69 100644
--- a/test/system/data_exports_test.rb
+++ b/test/system/data_exports_test.rb
@@ -15,7 +15,9 @@ def setup # rubocop:disable Metrics/AbcSize, Metrics/MethodLength
     @data_export9 = data_exports(:data_export_nine)
     @data_export10 = data_exports(:data_export_ten)
     @group1 = groups(:group_one)
+    @group5 = groups(:group_five)
     @project1 = projects(:project1)
+    @project22 = projects(:project22)
     @sample1 = samples(:sample1)
     @sample2 = samples(:sample2)
     @sample30 = samples(:sample30)
@@ -24,6 +26,8 @@ def setup # rubocop:disable Metrics/AbcSize, Metrics/MethodLength
     @workflow_execution3 = workflow_executions(:irida_next_example_error)
     @workflow_execution4 = workflow_executions(:automated_workflow_execution)
     @workflow_execution5 = workflow_executions(:automated_example_error)
+    @shared_workflow_execution1 = workflow_executions(:workflow_execution_completed_shared1)
+    @shared_workflow_execution2 = workflow_executions(:workflow_execution_completed_shared2)
 
     Project.reset_counters(@project1.id, :samples_count)
 
@@ -529,6 +533,173 @@ def end
     assert_selector 'div:nth-child(2) dd', text: 'test data export'
   end
 
+  test 'create analysis export using users shared workflow execution from user workflow execution show page' do
+    login_as users(:james_doe)
+    visit workflow_execution_path(@shared_workflow_execution1)
+
+    click_link I18n.t('workflow_executions.show.create_export_button'), match: :first
+
+    within 'dialog[open].dialog--size-lg' do
+      assert_accessible
+      assert_text I18n.t('data_exports.new_analysis_export_dialog.title')
+      assert_text I18n.t('data_exports.new_single_analysis_export_dialog.single_selection')
+      assert_text I18n.t('data_exports.new.name_label')
+      assert_text I18n.t('data_exports.new.email_label')
+
+      assert_no_selector 'turbo-frame[id="list_selections"]'
+      assert_no_text @shared_workflow_execution1.id
+      assert_no_text I18n.t('data_exports.new_analysis_export_dialog.description.singular')
+      assert_no_text ActionController::Base.helpers.strip_tags(
+        I18n.t('data_exports.new.after_submission_description_html')
+      )
+
+      click_button I18n.t('data_exports.new_single_analysis_export_dialog.single_selection')
+      assert_text I18n.t('data_exports.new_analysis_export_dialog.description.singular')
+      assert_text ActionController::Base.helpers.strip_tags(
+        I18n.t('data_exports.new.after_submission_description_html')
+      )
+      assert_text @shared_workflow_execution1.id
+      assert_text @shared_workflow_execution1.run_id
+      assert_text @shared_workflow_execution1.metadata['workflow_name']
+      assert_text @shared_workflow_execution1.metadata['workflow_version']
+
+      find('input#data_export_name').fill_in with: 'test data export'
+      find("input[type='checkbox'][id='data_export_email_notification']").click
+      click_button I18n.t('data_exports.new.submit_button')
+    end
+
+    assert_selector 'dl', count: 1
+    assert_selector 'div:nth-child(2) dd', text: 'test data export'
+  end
+
+  test 'create analysis export using users shared workflow execution from project workflow execution show page' do
+    login_as users(:james_doe)
+    visit namespace_project_workflow_execution_path(@group5, @project22, @shared_workflow_execution1)
+
+    click_link I18n.t('workflow_executions.show.create_export_button'), match: :first
+
+    within 'dialog[open].dialog--size-lg' do
+      assert_accessible
+      assert_text I18n.t('data_exports.new_analysis_export_dialog.title')
+      assert_text I18n.t('data_exports.new_single_analysis_export_dialog.single_selection')
+      assert_text I18n.t('data_exports.new.name_label')
+      assert_text I18n.t('data_exports.new.email_label')
+
+      assert_no_selector 'turbo-frame[id="list_selections"]'
+      assert_no_text @shared_workflow_execution1.id
+      assert_no_text I18n.t('data_exports.new_analysis_export_dialog.description.singular')
+      assert_no_text ActionController::Base.helpers.strip_tags(
+        I18n.t('data_exports.new.after_submission_description_html')
+      )
+
+      click_button I18n.t('data_exports.new_single_analysis_export_dialog.single_selection')
+      assert_text I18n.t('data_exports.new_analysis_export_dialog.description.singular')
+      assert_text ActionController::Base.helpers.strip_tags(
+        I18n.t('data_exports.new.after_submission_description_html')
+      )
+      assert_text @shared_workflow_execution1.id
+      assert_text @shared_workflow_execution1.run_id
+      assert_text @shared_workflow_execution1.metadata['workflow_name']
+      assert_text @shared_workflow_execution1.metadata['workflow_version']
+
+      find('input#data_export_name').fill_in with: 'test data export'
+      find("input[type='checkbox'][id='data_export_email_notification']").click
+      click_button I18n.t('data_exports.new.submit_button')
+    end
+
+    assert_selector 'dl', count: 1
+    assert_selector 'div:nth-child(2) dd', text: 'test data export'
+  end
+
+  test 'create analysis export from project shared workflow execution from project workflow execution show page' do
+    login_as users(:james_doe)
+    visit namespace_project_workflow_execution_path(@group5, @project22, @shared_workflow_execution2)
+
+    click_link I18n.t('workflow_executions.show.create_export_button'), match: :first
+
+    within 'dialog[open].dialog--size-lg' do
+      assert_accessible
+      assert_text I18n.t('data_exports.new_analysis_export_dialog.title')
+      assert_text I18n.t('data_exports.new_single_analysis_export_dialog.single_selection')
+      assert_text I18n.t('data_exports.new.name_label')
+      assert_text I18n.t('data_exports.new.email_label')
+
+      assert_no_selector 'turbo-frame[id="list_selections"]'
+      assert_no_text @shared_workflow_execution2.id
+      assert_no_text I18n.t('data_exports.new_analysis_export_dialog.description.singular')
+      assert_no_text ActionController::Base.helpers.strip_tags(
+        I18n.t('data_exports.new.after_submission_description_html')
+      )
+
+      click_button I18n.t('data_exports.new_single_analysis_export_dialog.single_selection')
+      assert_text I18n.t('data_exports.new_analysis_export_dialog.description.singular')
+      assert_text ActionController::Base.helpers.strip_tags(
+        I18n.t('data_exports.new.after_submission_description_html')
+      )
+      assert_text @shared_workflow_execution2.id
+      assert_text @shared_workflow_execution2.run_id
+      assert_text @shared_workflow_execution2.metadata['workflow_name']
+      assert_text @shared_workflow_execution2.metadata['workflow_version']
+
+      find('input#data_export_name').fill_in with: 'test data export'
+      find("input[type='checkbox'][id='data_export_email_notification']").click
+      click_button I18n.t('data_exports.new.submit_button')
+    end
+
+    assert_selector 'dl', count: 1
+    assert_selector 'div:nth-child(2) dd', text: 'test data export'
+  end
+
+  test 'clicking links in preview tab for analysis data export from user shared workflow execution' do
+    login_as users(:micha_doe)
+    sample47 = samples(:sample47)
+    data_export11 = data_exports(:data_export_eleven)
+    visit data_export_path(data_export11, tab: 'preview')
+
+    click_link @shared_workflow_execution2.id
+
+    assert_current_path(workflow_execution_path(@shared_workflow_execution2))
+    assert_text @shared_workflow_execution2.id
+
+    within first('dl') do
+      assert_text @shared_workflow_execution2.run_id
+      assert_text @shared_workflow_execution2.metadata['workflow_name']
+      assert_text @shared_workflow_execution2.metadata['workflow_version']
+    end
+
+    visit data_export_path(data_export11, tab: 'preview')
+
+    click_link sample47.puid
+
+    assert_text sample47.name
+    assert_text sample47.puid
+  end
+
+  test 'clicking links in preview tab for analysis data export from project shared workflow execution' do
+    login_as users(:james_doe)
+    sample47 = samples(:sample47)
+    data_export11 = data_exports(:data_export_twelve)
+    visit data_export_path(data_export11, tab: 'preview')
+
+    click_link @shared_workflow_execution2.id
+
+    assert_current_path(namespace_project_workflow_execution_path(@group5, @project22, @shared_workflow_execution2))
+    assert_text @shared_workflow_execution2.id
+
+    within first('dl') do
+      assert_text @shared_workflow_execution2.run_id
+      assert_text @shared_workflow_execution2.metadata['workflow_name']
+      assert_text @shared_workflow_execution2.metadata['workflow_version']
+    end
+
+    visit data_export_path(data_export11, tab: 'preview')
+
+    click_link sample47.puid
+
+    assert_text sample47.name
+    assert_text sample47.puid
+  end
+
   test 'create export state between completed and non-completed workflow executions' do
     submitted_workflow_execution = workflow_executions(:irida_next_example_submitted)
     visit workflow_execution_path(submitted_workflow_execution)
@@ -989,6 +1160,115 @@ def end
     assert_selector 'div:nth-child(2) dd', text: 'test data export'
   end
 
+  test 'create analysis export with a workflow execution from user workflow executions index page' do
+    login_as users(:james_doe)
+    visit workflow_executions_path
+    assert_selector 'a.pointer-events-none.cursor-not-allowed.bg-slate-100.text-slate-600',
+                    text: I18n.t('workflow_executions.index.create_export_button')
+
+    within %(#workflow-executions-table) do
+      find("input[type='checkbox'][value='#{@shared_workflow_execution1.id}']").click
+    end
+
+    assert_no_selector 'a.pointer-events-none.cursor-not-allowed.bg-slate-100.text-slate-600',
+                       text: I18n.t('workflow_executions.index.create_export_button')
+    click_link I18n.t('workflow_executions.index.create_export_button')
+
+    within 'dialog[open].dialog--size-lg' do
+      assert_accessible
+      assert_text I18n.t('data_exports.new_analysis_export_dialog.title')
+      assert_text I18n.t('data_exports.new_analysis_export_dialog.selection_count.non_zero').gsub! 'COUNT_PLACEHOLDER',
+                                                                                                   '1'
+      assert_text I18n.t('data_exports.new.name_label')
+      assert_text I18n.t('data_exports.new.email_label')
+
+      assert_no_selector 'turbo-frame[id="list_selections"]'
+      assert_no_text @shared_workflow_execution1.id
+      assert_no_text I18n.t('data_exports.new_analysis_export_dialog.description.singular')
+      assert_no_text ActionController::Base.helpers.strip_tags(
+        I18n.t('data_exports.new.after_submission_description_html')
+      )
+      click_button I18n.t('data_exports.new_analysis_export_dialog.selection_count.non_zero').gsub! 'COUNT_PLACEHOLDER',
+                                                                                                    '1'
+      assert_text I18n.t('data_exports.new_analysis_export_dialog.description.singular')
+      assert_text ActionController::Base.helpers.strip_tags(
+        I18n.t('data_exports.new.after_submission_description_html')
+      )
+      assert_selector 'turbo-frame[id="list_selections"]'
+      within %(turbo-frame[id="list_selections"]) do
+        assert_text @shared_workflow_execution1.id
+        assert_text @shared_workflow_execution1.run_id
+        assert_text @shared_workflow_execution1.metadata['workflow_name']
+        assert_text @shared_workflow_execution1.metadata['workflow_version']
+      end
+
+      find('input#data_export_name').fill_in with: 'test data export'
+      find("input[type='checkbox'][id='data_export_email_notification']").click
+      click_button I18n.t('data_exports.new.submit_button')
+    end
+
+    assert_selector 'dl', count: 1
+    assert_selector 'div:nth-child(2) dd', text: 'test data export'
+    assert_selector 'div#data-export-tabs'
+  end
+
+  test 'create analysis export with multiple shared workflow executions from project workflow executions index page' do
+    login_as users(:james_doe)
+    visit namespace_project_workflow_executions_path(@group5, @project22)
+    assert_selector 'a.pointer-events-none.cursor-not-allowed.bg-slate-100.text-slate-600',
+                    text: I18n.t('projects.workflow_executions.index.create_export_button')
+
+    within %(#workflow-executions-table) do
+      find("input[type='checkbox'][value='#{@shared_workflow_execution1.id}']").click
+      find("input[type='checkbox'][value='#{@shared_workflow_execution2.id}']").click
+    end
+
+    assert_no_selector 'a.pointer-events-none.cursor-not-allowed.bg-slate-100.text-slate-600',
+                       text: I18n.t('projects.workflow_executions.index.create_export_button')
+    click_link I18n.t('projects.workflow_executions.index.create_export_button')
+
+    within 'dialog[open].dialog--size-lg' do
+      assert_accessible
+      assert_text I18n.t('data_exports.new_analysis_export_dialog.title')
+      assert_text I18n.t('data_exports.new_analysis_export_dialog.selection_count.non_zero').gsub! 'COUNT_PLACEHOLDER',
+                                                                                                   '2'
+      assert_text I18n.t('data_exports.new.name_label')
+      assert_text I18n.t('data_exports.new.email_label')
+
+      assert_no_selector 'turbo-frame[id="list_selections"]'
+      assert_no_text @shared_workflow_execution1.id
+      assert_no_text @shared_workflow_execution2.id
+      assert_no_text I18n.t('data_exports.new_analysis_export_dialog.description.plural').gsub! 'COUNT_PLACEHOLDER', '2'
+      assert_no_text ActionController::Base.helpers.strip_tags(
+        I18n.t('data_exports.new.after_submission_description_html')
+      )
+      click_button I18n.t('data_exports.new_analysis_export_dialog.selection_count.non_zero').gsub! 'COUNT_PLACEHOLDER',
+                                                                                                    '2'
+      assert_text  I18n.t('data_exports.new_analysis_export_dialog.description.plural').gsub! 'COUNT_PLACEHOLDER', '2'
+      assert_text ActionController::Base.helpers.strip_tags(
+        I18n.t('data_exports.new.after_submission_description_html')
+      )
+      assert_selector 'turbo-frame[id="list_selections"]'
+      within %(turbo-frame[id="list_selections"]) do
+        assert_text @shared_workflow_execution1.id
+        assert_text @shared_workflow_execution1.run_id
+        assert_text @shared_workflow_execution1.metadata['workflow_name']
+        assert_text @shared_workflow_execution1.metadata['workflow_version']
+        assert_text @shared_workflow_execution2.id
+        assert_text @shared_workflow_execution2.run_id
+        assert_text @shared_workflow_execution2.metadata['workflow_name']
+        assert_text @shared_workflow_execution2.metadata['workflow_version']
+      end
+
+      find('input#data_export_name').fill_in with: 'test data export'
+      find("input[type='checkbox'][id='data_export_email_notification']").click
+      click_button I18n.t('data_exports.new.submit_button')
+    end
+
+    assert_selector 'dl', count: 1
+    assert_selector 'div:nth-child(2) dd', text: 'test data export'
+  end
+
   test 'cannot create analysis export with non-completed workflow executions from user WE index page' do
     visit workflow_executions_path
     assert_selector 'a.pointer-events-none.cursor-not-allowed.bg-slate-100.text-slate-600',

From 7c93893609ca4aa55932cbf8d111ea450968b07e Mon Sep 17 00:00:00 2001
From: Meghan Chua <17057809+malchua@users.noreply.github.com>
Date: Thu, 6 Feb 2025 15:59:57 -0600
Subject: [PATCH 56/57] Fix bug where incorrect redirect path is used

---
 app/controllers/data_exports_controller.rb | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/app/controllers/data_exports_controller.rb b/app/controllers/data_exports_controller.rb
index 1e22ea86c5..924958154c 100644
--- a/app/controllers/data_exports_controller.rb
+++ b/app/controllers/data_exports_controller.rb
@@ -176,11 +176,16 @@ def redirect_to_project
     redirect_to namespace_project_path(project.parent, project)
   end
 
-  def redirect_to_workflow_execution
+  def redirect_to_workflow_execution # rubocop:disable Metrics/AbcSize
     workflow_execution = WorkflowExecution.find_by(id: params['identifier'])
     submitter = workflow_execution.submitter
     if submitter.user_type == 'human'
-      redirect_to workflow_execution_path(workflow_execution)
+      if workflow_execution.submitter == current_user
+        redirect_to workflow_execution_path(workflow_execution)
+      else
+        namespace = workflow_execution.namespace
+        redirect_to namespace_project_workflow_execution_path(namespace.parent, namespace.project, workflow_execution)
+      end
     else
       namespace = Namespace.find_by(puid: submitter.first_name)
       redirect_to namespace_project_workflow_execution_path(namespace.parent, namespace.project, workflow_execution)

From 73daa197ef3adbeef83c26bbb15a0f01cccab9f9 Mon Sep 17 00:00:00 2001
From: Meghan Chua <17057809+malchua@users.noreply.github.com>
Date: Fri, 7 Feb 2025 10:14:51 -0600
Subject: [PATCH 57/57] Simplify redirect_to_project method

---
 app/controllers/data_exports_controller.rb | 14 ++++----------
 1 file changed, 4 insertions(+), 10 deletions(-)

diff --git a/app/controllers/data_exports_controller.rb b/app/controllers/data_exports_controller.rb
index 924958154c..9c02151cb9 100644
--- a/app/controllers/data_exports_controller.rb
+++ b/app/controllers/data_exports_controller.rb
@@ -176,18 +176,12 @@ def redirect_to_project
     redirect_to namespace_project_path(project.parent, project)
   end
 
-  def redirect_to_workflow_execution # rubocop:disable Metrics/AbcSize
+  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 = workflow_execution.namespace
-        redirect_to namespace_project_workflow_execution_path(namespace.parent, namespace.project, workflow_execution)
-      end
+    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