Add missed notifications to steps and fix notification for protocol repository [SCI-7531]

app/controllers/my_modules_controller.rb

@@ -276,12 +276,14 @@ class MyModulesController < ApplicationController
 
   def update_protocol
     protocol = @my_module.protocol
+    old_description = protocol.description
 
     ActiveRecord::Base.transaction do
       protocol.update!(protocol_params)
       log_activity(:protocol_name_in_task_edited) if protocol.saved_change_to_name?
       log_activity(:protocol_description_in_task_edited) if protocol.saved_change_to_description?
       TinyMceAsset.update_images(protocol, params[:tiny_mce_images], current_user)
+      protocol_annotation_notification(old_description)
     end
 
     render json: protocol, serializer: ProtocolSerializer, user: current_user

app/controllers/projects_controller.rb

@@ -287,9 +287,6 @@ class ProjectsController < ApplicationController
   end
 
   def show
-    # This is the "info" view
-    current_team_switch(@project.team)
-
     view_state = @project.current_view_state(current_user)
     @current_sort = view_state.state.dig('experiments', experiments_view_mode(@project), 'sort') || 'atoz'
     @current_view_type = view_state.state.dig('experiments', 'view_type')
@@ -386,6 +383,7 @@ class ProjectsController < ApplicationController
   end
 
   def check_view_permissions
+    current_team_switch(@project.team) if current_team != @project.team
     render_403 unless can_read_project?(@project)
   end
 

app/controllers/protocols_controller.rb

@@ -16,6 +16,7 @@ class ProtocolsController < ApplicationController
   before_action :check_clone_permissions, only: [:clone]
   before_action :check_view_permissions, only: %i(
     show
+    edit
     protocol_status_bar
     updated_at_label
     preview
@@ -30,7 +31,6 @@ class ProtocolsController < ApplicationController
   # For update_from_parent and update_from_parent_modal we don't need to check
   # read permission for the parent protocol
   before_action :check_manage_permissions, only: %i(
-    edit
     update_keywords
     update_description
     update_name
@@ -161,13 +161,10 @@ class ProtocolsController < ApplicationController
   end
 
   def edit
-    # Switch to correct team
-    current_team_switch(@protocol.team)
+    render :show
   end
 
   def show
-    # Switch to correct team
-    current_team_switch(@protocol.team)
 
     respond_to do |format|
       format.json { render json: @protocol, serializer: ProtocolSerializer, user: current_user }
@@ -1102,6 +1099,7 @@ class ProtocolsController < ApplicationController
 
   def check_view_permissions
     @protocol = Protocol.find_by_id(params[:id])
+    current_team_switch(@protocol.team) if current_team != @protocol.team
     unless @protocol.present? &&
            (can_read_protocol_in_module?(@protocol) ||
            can_read_protocol_in_repository?(@protocol))
@@ -1245,7 +1243,7 @@ class ProtocolsController < ApplicationController
                user: current_user.full_name,
                protocol: @protocol.name),
       message: t('notifications.protocol_description_annotation_message_html',
-                 protocol: link_to(@protocol.name, edit_protocol_url(@protocol)))
+                 protocol: link_to(@protocol.name, protocol_url(@protocol)))
     )
   end
 end

app/controllers/step_elements/checklist_items_controller.rb

@@ -3,6 +3,7 @@
 module StepElements
   class ChecklistItemsController < ApplicationController
     include ApplicationHelper
+    include StepsActions
 
     before_action :load_vars
     before_action :load_checklist_item, only: %i(update toggle destroy)
@@ -21,6 +22,7 @@ module StepElements
             checklist_name: @checklist.name
           }
         )
+        checklist_item_annotation(@step, checklist_item)
       end
 
       render json: checklist_item, serializer: ChecklistItemSerializer, user: current_user
@@ -31,6 +33,7 @@ module StepElements
     end
 
     def update
+      old_text = @checklist_item.text
       @checklist_item.assign_attributes(
         checklist_item_params.merge(last_modified_by: current_user)
       )
@@ -41,6 +44,7 @@ module StepElements
           checklist_item: @checklist_item.text,
           checklist_name: @checklist.name
         )
+        checklist_item_annotation(@step, @checklist_item, old_text)
       end
 
       render json: @checklist_item, serializer: ChecklistItemSerializer, user: current_user
@@ -129,6 +133,8 @@ module StepElements
       @step = Step.find_by(id: params[:step_id])
       return render_404 unless @step
 
+      @protocol = @step.protocol
+
       @checklist = @step.checklists.find_by(id: params[:checklist_id])
       return render_404 unless @checklist
     end

app/controllers/step_elements/checklists_controller.rb

@@ -2,8 +2,9 @@
 
 module StepElements
   class ChecklistsController < BaseController
+    include ApplicationHelper
+    include StepsActions
     before_action :load_checklist, only: %i(update destroy duplicate)
-
     def create
       checklist = @step.checklists.build(
         name: t('protocols.steps.checklist.default_name', position: @step.checklists.length + 1)
@@ -11,6 +12,7 @@ module StepElements
       ActiveRecord::Base.transaction do
         create_in_step!(@step, checklist)
         log_step_activity(:checklist_added, { checklist_name: checklist.name })
+        checklist_name_annotation(@step, checklist)
       end
       render_step_orderable_element(checklist)
     rescue ActiveRecord::RecordInvalid
@@ -18,9 +20,11 @@ module StepElements
     end
 
     def update
+      old_name = @checklist.name
       ActiveRecord::Base.transaction do
         @checklist.update!(checklist_params)
         log_step_activity(:checklist_edited, { checklist_name: @checklist.name })
+        checklist_name_annotation(@step, @checklist, old_name)
       end
 
       render json: @checklist, serializer: ChecklistSerializer, user: current_user