Merge pull request #542 from ZmagoD/zd_SCI_825

Smart annotations and Notifications

app/assets/javascripts/samples/sample_datatable.js.erb

@@ -524,6 +524,7 @@ function onClickSave() {
 
     // First fetch all the data in input fields
     data = {
+        request_url: $('#samples').data('current-uri'),
         sample_id: $(selectedSample).attr("id"),
         sample: {},
         custom_fields: {}, // These fields are not currently bound to this sample

app/controllers/concerns/steps_actions.rb

@@ -0,0 +1,155 @@
+module StepsActions
+  extend ActiveSupport::Concern
+  # generates notification for smart annotations
+  def create_annotation_notifications(step)
+    # step description
+    step_description_annotation(step)
+    # checklists
+    step.checklists.each do |checklist|
+      checklist_name_annotation(step, checklist)
+      checklist.checklist_items.each do |checklist_item|
+        checklist_item_annotation(step, checklist_item)
+      end
+    end
+  end
+
+  def fetch_new_checklists_data
+    checklists = []
+    new_checklists = step_params[:checklists_attributes]
+
+    if new_checklists
+      new_checklists.each do |e|
+        list = PreviousChecklist.new(
+          e.second[:id].to_i,
+          e.second[:name]
+        )
+        if e.second[:checklist_items_attributes]
+          e.second[:checklist_items_attributes].each do |el|
+            list.add_checklist(
+              PreviousChecklistItem.new(el.second[:id].to_i, el.second[:text])
+            )
+          end
+        end
+        checklists << list
+      end
+    end
+    checklists
+  end
+
+  def fetch_old_checklists_data(step)
+    checklists = []
+    if step.checklists
+      step.checklists.each do |e|
+        list = PreviousChecklist.new(
+          e.id,
+          e.name
+        )
+        e.checklist_items.each do |el|
+          list.add_checklist(
+            PreviousChecklistItem.new(el.id, el.text)
+          )
+        end
+        checklists << list
+      end
+    end
+    checklists
+  end
+
+  # used for step update action it traverse through the input params and
+  # generates notifications
+  def update_annotation_notifications(step,
+                                      old_description,
+                                      new_checklists,
+                                      old_checklists)
+    step_description_annotation(step, old_description)
+    new_checklists.each do |e|
+      # generates smart annotaion if the checklist is new
+      add_new_checklist(step, e) if e.id.zero?
+      checklist_name_annotation(step, e) unless e.id
+      # else check if checklist is not deleted and generates
+      # new notifications
+      next unless old_checklists.map(&:id).include?(e.id)
+      old_checklist = old_checklists.select { |i| i.id == e.id }.first
+      checklist_name_annotation(step, e, old_checklist.name)
+      e.items.each do |ci|
+        old_list = old_checklists.select { |i| i.id == e.id }.first
+        old_item = old_list.items.select { |i| i.id == ci.id }.first if old_list
+
+        checklist_item_annotation(step, ci, old_item.text)
+      end
+    end
+  end
+
+  def add_new_checklist(step, checklist)
+    checklist_name_annotation(step, checklist)
+    checklist.items.each do |ci|
+      checklist_item_annotation(step, ci)
+    end
+  end
+
+  def checklist_item_annotation(step, checklist_item, old_text = nil)
+    smart_annotation_notification(
+      old_text: old_text,
+      new_text: checklist_item.text,
+      title: t('notifications.checklist_title',
+               user: current_user.full_name,
+               step: step.name),
+      message: annotation_message(step)
+    )
+  end
+
+  def checklist_name_annotation(step, checklist, old_text = nil)
+    smart_annotation_notification(
+      old_text: old_text,
+      new_text: checklist.name,
+      title: t('notifications.checklist_title',
+               user: current_user.full_name,
+               step: step.name),
+      message: annotation_message(step)
+    )
+  end
+
+  def step_description_annotation(step, old_text = nil)
+    smart_annotation_notification(
+      old_text: old_text,
+      new_text: step.description,
+      title: t('notifications.step_description_title',
+               user: current_user.full_name,
+               step: step.name),
+      message: annotation_message(step)
+    )
+  end
+
+  def annotation_message(step)
+    return t('notifications.step_annotation_message_html',
+             project: link_to(
+               step.my_module.experiment.project.name,
+               project_url(step.my_module.experiment.project)
+             ),
+             my_module: link_to(
+               step.my_module.name,
+               protocols_my_module_url(step.my_module)
+             ),
+             step: link_to(
+               step.name,
+               protocols_my_module_url(step.my_module)
+             )) if @protocol.in_module?
+
+    t('notifications.protocol_step_annotation_message_html',
+      protocol: link_to(
+        @protocol.name, edit_protocol_url(@protocol)
+      ))
+  end
+
+  # temporary data containers
+  PreviousChecklistItem = Struct.new(:id, :text)
+  PreviousChecklist = Struct.new(:id, :name, :items) do
+    def initialize(id, name, items = [])
+      super(id, name, items)
+    end
+
+    def add_checklist(item)
+      items << item
+    end
+  end
+end

app/controllers/experiments_controller.rb

@@ -3,6 +3,9 @@ class ExperimentsController < ApplicationController
   include PermissionHelper
   include TeamsHelper
   include InputSanitizeHelper
+  include ActionView::Helpers::TextHelper
+  include ApplicationHelper
+  include Rails.application.routes.url_helpers
 
   before_action :set_experiment,
                 except: [:new, :create]
@@ -43,6 +46,8 @@ class ExperimentsController < ApplicationController
     @experiment.last_modified_by = current_user
     @experiment.project = @project
     if @experiment.save
+
+      experiment_annotation_notification
       Activity.create(
         type_of: :create_experiment,
         project: @experiment.project,
@@ -87,9 +92,12 @@ class ExperimentsController < ApplicationController
   end
 
   def update
+    old_text = @experiment.description
     @experiment.update_attributes(experiment_params)
     @experiment.last_modified_by = current_user
     if @experiment.save
+
+      experiment_annotation_notification(old_text)
       Activity.create(
         type_of: :edit_experiment,
         project: @experiment.project,
@@ -346,4 +354,19 @@ class ExperimentsController < ApplicationController
   def choose_layout
     action_name.in?(%w(index archive)) ? 'main' : 'fluid'
   end
+
+  def experiment_annotation_notification(old_text = nil)
+    smart_annotation_notification(
+      old_text: old_text,
+      new_text: @experiment.description,
+      title: t('notifications.experiment_annotation_title',
+               experiment: @experiment.name,
+               user: current_user.full_name),
+      message: t('notifications.experiment_annotation_message_html',
+                 project: link_to(@experiment.project.name,
+                                  project_url(@experiment.project)),
+                 experiment: link_to(@experiment.name,
+                                     canvas_experiment_url(@experiment)))
+    )
+  end
 end

app/controllers/my_module_comments_controller.rb

@@ -2,6 +2,7 @@ class MyModuleCommentsController < ApplicationController
   include ActionView::Helpers::TextHelper
   include InputSanitizeHelper
   include ApplicationHelper
+  include Rails.application.routes.url_helpers
 
   before_action :load_vars
   before_action :check_view_permissions, only: :index
@@ -51,6 +52,8 @@ class MyModuleCommentsController < ApplicationController
 
     respond_to do |format|
       if @comment.save
+
+        my_module_comment_annotation_notification
         # Generate activity
         Activity.create(
           type_of: :add_comment_to_module,
@@ -102,10 +105,13 @@ class MyModuleCommentsController < ApplicationController
   end
 
   def update
+    old_text = @comment.message
     @comment.message = comment_params[:message]
     respond_to do |format|
       format.json do
         if @comment.save
+
+          my_module_comment_annotation_notification(old_text)
           # Generate activity
           Activity.create(
             type_of: :edit_module_comment,
@@ -190,4 +196,23 @@ class MyModuleCommentsController < ApplicationController
   def comment_params
     params.require(:comment).permit(:message)
   end
+
+  def my_module_comment_annotation_notification(old_text = nil)
+    smart_annotation_notification(
+      old_text: old_text,
+      new_text: @comment.message,
+      title: t('notifications.my_module_comment_annotation_title',
+               my_module: @my_module.name,
+               user: current_user.full_name),
+      message: t('notifications.my_module_annotation_message_html',
+                 project: link_to(@my_module.experiment.project.name,
+                                  project_url(@my_module
+                                              .experiment
+                                              .project)),
+                 my_module: link_to(@my_module.name,
+                                    protocols_my_module_url(
+                                      @my_module
+                                    )))
+    )
+  end
 end

app/controllers/project_comments_controller.rb

@@ -2,6 +2,7 @@ class ProjectCommentsController < ApplicationController
   include ActionView::Helpers::TextHelper
   include InputSanitizeHelper
   include ApplicationHelper
+  include Rails.application.routes.url_helpers
 
   before_action :load_vars
   before_action :check_view_permissions, only: :index
@@ -50,6 +51,7 @@ class ProjectCommentsController < ApplicationController
 
     respond_to do |format|
       if @comment.save
+        project_comment_annotation_notification
         # Generate activity
         Activity.create(
           type_of: :add_comment_to_project,
@@ -99,10 +101,13 @@ class ProjectCommentsController < ApplicationController
   end
 
   def update
+    old_text = @comment.message
     @comment.message = comment_params[:message]
     respond_to do |format|
       format.json do
         if @comment.save
+
+          project_comment_annotation_notification(old_text)
           # Generate activity
           Activity.create(
             type_of: :edit_project_comment,
@@ -185,4 +190,16 @@ class ProjectCommentsController < ApplicationController
   def comment_params
     params.require(:comment).permit(:message)
   end
+
+  def project_comment_annotation_notification(old_text = nil)
+    smart_annotation_notification(
+      old_text: old_text,
+      new_text: @comment.message,
+      title: t('notifications.project_comment_annotation_title',
+               project: @project.name,
+               user: current_user.full_name),
+      message: t('notifications.project_annotation_message_html',
+                 project: link_to(@project.name, project_url(@project)))
+    )
+  end
 end

app/controllers/result_comments_controller.rb

@@ -49,6 +49,7 @@ class ResultCommentsController < ApplicationController
     respond_to do |format|
       if @comment.save
 
+        result_comment_annotation_notification
         # Generate activity
         Activity.create(
           type_of: :add_comment_to_result,
@@ -100,10 +101,13 @@ class ResultCommentsController < ApplicationController
   end
 
   def update
+    old_text = @comment.message
     @comment.message = comment_params[:message]
     respond_to do |format|
       format.json do
         if @comment.save
+
+          result_comment_annotation_notification(old_text)
           # Generate activity
           Activity.create(
             type_of: :edit_result_comment,
@@ -192,4 +196,22 @@ class ResultCommentsController < ApplicationController
     params.require(:comment).permit(:message)
   end
 
+  def result_comment_annotation_notification(old_text = nil)
+    smart_annotation_notification(
+      old_text: (old_text if old_text),
+      new_text: @comment.message,
+      title: t('notifications.result_comment_annotation_title',
+               result: @result.name,
+               user: current_user.full_name),
+      message: t('notifications.result_annotation_message_html',
+                 project: link_to(@result.my_module.experiment.project.name,
+                                  project_url(@result.my_module
+                                                   .experiment
+                                                   .project)),
+                 my_module: link_to(@result.my_module.name,
+                                    protocols_my_module_url(
+                                      @result.my_module
+                                    )))
+    )
+  end
 end

app/controllers/result_texts_controller.rb

@@ -1,5 +1,8 @@
 class ResultTextsController < ApplicationController
   include ResultsHelper
+  include ActionView::Helpers::UrlHelper
+  include ApplicationHelper
+  include Rails.application.routes.url_helpers
 
   before_action :load_vars, only: [:edit, :update, :download]
   before_action :load_vars_nested, only: [:new, :create]
@@ -38,6 +41,8 @@ class ResultTextsController < ApplicationController
 
     respond_to do |format|
       if (@result.save and @result_text.save) then
+
+        result_annotation_notification
         # Generate activity
         Activity.create(
           type_of: :add_result,
@@ -88,6 +93,7 @@ class ResultTextsController < ApplicationController
   end
 
   def update
+    old_text = @result_text.text
     update_params = result_params
     @result.last_modified_by = current_user
     @result.assign_attributes(update_params)
@@ -129,6 +135,9 @@ class ResultTextsController < ApplicationController
         )
       end
     end
+
+    result_annotation_notification(old_text) if saved
+
     respond_to do |format|
       if saved
         format.html {
@@ -208,5 +217,22 @@ class ResultTextsController < ApplicationController
     )
   end
 
+  def result_annotation_notification(old_text = nil)
+    smart_annotation_notification(
+      old_text: (old_text if old_text),
+      new_text: @result_text.text,
+      title: t('notifications.result_annotation_title',
+               result: @result.name,
+               user: current_user.full_name),
+      message: t('notifications.result_annotation_message_html',
+                 project: link_to(@result.my_module.experiment.project.name,
+                                  project_url(@result.my_module
+                                                   .experiment
+                                                   .project)),
+                 my_module: link_to(@result.my_module.name,
+                                    protocols_my_module_url(
+                                      @result.my_module
+                                    )))
+    )
+  end
 end
-

app/controllers/samples_controller.rb

@@ -1,5 +1,7 @@
 class SamplesController < ApplicationController
   include InputSanitizeHelper
+  include ActionView::Helpers::TextHelper
+  include ApplicationHelper
 
   before_action :load_vars, only: [:edit, :update, :destroy, :show]
   before_action :load_vars_nested, only: [:new, :create]
@@ -82,6 +84,8 @@ class SamplesController < ApplicationController
               errors[:custom_fields] << {
                 "#{id}": scf.errors.messages
               }
+            else
+              sample_annotation_notification(sample, scf)
             end
           end
         end
@@ -198,6 +202,7 @@ class SamplesController < ApplicationController
             scf = SampleCustomField.where("custom_field_id = ? AND sample_id = ?", id, sample.id).take
 
             if scf
+              old_text = scf.value
               # Well, client was naughty, no XMAS for him this year, update
               # existing SCF instead of creating new one
               scf.value = val
@@ -207,6 +212,8 @@ class SamplesController < ApplicationController
                 errors[:custom_fields] << {
                   "#{id}": scf.errors.messages
                 }
+              else
+                sample_annotation_notification(sample, scf, old_text)
               end
             else
               # SCF doesn't exist, create it
@@ -220,6 +227,8 @@ class SamplesController < ApplicationController
                 errors[:custom_fields] << {
                   "#{id}": scf.errors.messages
                 }
+              else
+                sample_annotation_notification(sample, scf)
               end
             end
           end
@@ -235,6 +244,7 @@ class SamplesController < ApplicationController
               if val.empty?
                 scf_to_delete << scf
               else
+                old_text = scf.value
                 # SCF exists, update away
                 scf.value = val
 
@@ -242,6 +252,8 @@ class SamplesController < ApplicationController
                   errors[:sample_custom_fields] << {
                     "#{id}": scf.errors.messages
                   }
+                else
+                  sample_annotation_notification(sample, scf, old_text)
                 end
               end
             else
@@ -331,4 +343,19 @@ class SamplesController < ApplicationController
       :sample_group_id
     )
   end
+
+  def sample_annotation_notification(sample, scf, old_text = nil)
+    table_url = params.fetch(:request_url) { :request_url_must_be_present }
+    smart_annotation_notification(
+      old_text: (old_text if old_text),
+      new_text: scf.value,
+      title: t('notifications.sample_annotation_title',
+               user: current_user.full_name,
+               column: scf.custom_field.name,
+               sample: sample.name),
+      message: t('notifications.sample_annotation_message_html',
+                 sample: link_to(sample.name, table_url),
+                 column: link_to(scf.custom_field.name, table_url))
+    )
+  end
 end

app/controllers/step_comments_controller.rb

@@ -2,6 +2,7 @@ class StepCommentsController < ApplicationController
   include ActionView::Helpers::TextHelper
   include InputSanitizeHelper
   include ApplicationHelper
+  include Rails.application.routes.url_helpers
 
   before_action :load_vars
 
@@ -47,6 +48,8 @@ class StepCommentsController < ApplicationController
 
     respond_to do |format|
       if @comment.save
+
+        step_comment_annotation_notification
         # Generate activity (this can only occur in module,
         # but nonetheless check if my module is not nil)
         if @protocol.in_module?
@@ -101,10 +104,13 @@ class StepCommentsController < ApplicationController
   end
 
   def update
+    old_text = @comment.message
     @comment.message = comment_params[:message]
     respond_to do |format|
       format.json do
         if @comment.save
+
+          step_comment_annotation_notification(old_text)
           # Generate activity
           if @protocol.in_module?
             Activity.create(
@@ -198,4 +204,25 @@ class StepCommentsController < ApplicationController
   def comment_params
     params.require(:comment).permit(:message)
   end
+
+  def step_comment_annotation_notification(old_text = nil)
+    smart_annotation_notification(
+      old_text: (old_text if old_text),
+      new_text: comment_params[:message],
+      title: t('notifications.step_comment_annotation_title',
+               step: @step.name,
+               user: current_user.full_name),
+      message: t('notifications.step_annotation_message_html',
+                 project: link_to(@step.my_module.experiment.project.name,
+                                  project_url(@step.my_module
+                                                   .experiment
+                                                   .project)),
+                 my_module: link_to(@step.my_module.name,
+                                    protocols_my_module_url(
+                                      @step.my_module
+                                    )),
+                 step: link_to(@step.name,
+                               protocols_my_module_url(@step.my_module)))
+    )
+  end
 end

app/controllers/steps_controller.rb

@@ -1,6 +1,7 @@
 class StepsController < ApplicationController
   include ActionView::Helpers::TextHelper
   include ApplicationHelper
+  include StepsActions
 
   before_action :load_vars, only: [:edit, :update, :destroy, :show]
   before_action :load_vars_nested, only: [:new, :create]
@@ -56,6 +57,7 @@ class StepsController < ApplicationController
           asset.post_process_file(@protocol.team)
         end
 
+        create_annotation_notifications(@step)
         # Generate activity
         if @protocol.in_module?
           Activity.create(
@@ -129,6 +131,9 @@ class StepsController < ApplicationController
 
   def update
     respond_to do |format|
+      old_description = @step.description
+      old_checklists = fetch_old_checklists_data(@step)
+      new_checklists = fetch_new_checklists_data
       previous_size = @step.space_taken
 
       step_params_all = step_params
@@ -156,6 +161,12 @@ class StepsController < ApplicationController
       if @step.save
         @step.reload
 
+        # generates notification on step upadate
+        update_annotation_notifications(@step,
+                                        old_description,
+                                        new_checklists,
+                                        old_checklists)
+
         # Release team's space taken
         team = @protocol.team
         team.release_space(previous_size)

app/helpers/application_helper.rb

@@ -58,6 +58,50 @@ module ApplicationHelper
       !@experiment.nil?
   end
 
+  def smart_annotation_notification(options = {})
+    title = options.fetch(:title) { :title_must_be_present }
+    message = options.fetch(:message) { :message_must_be_present }
+    new_text = options.fetch(:new_text) { :new_text_must_be_present }
+    old_text = options[:old_text] || ''
+    sa_user = /\[\@(.*?)~([0-9a-zA-Z]+)\]/
+    # fetch user ids from the previous text
+    old_user_ids = []
+    old_text.gsub(sa_user) do |el|
+      match = el.match(sa_user)
+      old_user_ids << match[2].base62_decode
+    end
+    # fetch user ids from the new text
+    new_user_ids = []
+    new_text.gsub(sa_user) do |el|
+      match = el.match(sa_user)
+      new_user_ids << match[2].base62_decode
+    end
+    # check if the user has been already mentioned
+    annotated_users = []
+    new_user_ids.each do |el|
+      annotated_users << el unless old_user_ids.include?(el)
+    end
+    # restrict the list of ids and generate notification
+    annotated_users.uniq.each do |user_id|
+      target_user = User.find_by_id(user_id)
+      next unless target_user
+      generate_annotation_notification(target_user, title, message)
+    end
+  end
+
+  def generate_annotation_notification(target_user, title, message)
+    notification = Notification.create(
+      type_of: :assignment,
+      title:
+        ActionController::Base.helpers.sanitize(title),
+      message:
+        ActionController::Base.helpers.sanitize(message)
+    )
+    if target_user.assignments_notification
+      UserNotification.create(notification: notification, user: target_user)
+    end
+  end
+
   def smart_annotation_parser(text, team = nil)
     new_text = smart_annotation_filter_resources(text)
     new_text = smart_annotation_filter_users(new_text, team)

app/views/shared/_samples.html.erb

@@ -125,6 +125,7 @@
 
 <div class="samples-table">
   <table id="samples" class="table"
+    data-current-uri="<%= request.original_url %>"
     data-team-id="<%= @project.team.id %>"
     data-user-id="<%= @current_user.id %>"
     data-source="<%= @samples_index_link %>"

config/locales/en.yml

@@ -1516,6 +1516,22 @@ en:
       recent_changes: "Recent changes"
       system_message: "sciNote system message"
       deliver: 'Exportable content'
+    experiment_annotation_title: "%{user} mentioned you in %{experiment} experiment."
+    experiment_annotation_message_html: "Project: %{project} | Experiment: %{experiment}"
+    project_comment_annotation_title: "%{user} mentioned you in %{project} project comment."
+    project_annotation_message_html: "Project: %{project}"
+    my_module_comment_annotation_title: "%{user} mentioned you in %{my_module} task comment."
+    my_module_annotation_message_html: "Project: %{project} | Task: %{my_module}"
+    step_comment_annotation_title: "%{user} mentioned you in %{step} step comment."
+    step_description_title: "%{user} mentioned you in %{step} step description."
+    checklist_title: "%{user} mentioned you in %{step} step checklist."
+    step_annotation_message_html: "Project: %{project} | Task: %{my_module} | Step: %{step}"
+    result_annotation_title: "%{user} mentioned you in result %{result}."
+    result_comment_annotation_title: "%{user} mentioned you in result %{result} comment."
+    result_annotation_message_html: "Project: %{project} | Task: %{my_module}"
+    sample_annotation_title: "%{user} mentioned you in Column: %{column} of Sample %{sample}"
+    sample_annotation_message_html: "Sample: %{sample} | Column: %{column}"
+    protocol_step_annotation_message_html: "Protocol: %{protocol}"
     email_title: "You've received a sciNote notification!"
     assign_user_to_team: "<i>%{assigned_user}</i> was added as %{role} to team <strong>%{team}</strong> by <i>%{assigned_by_user}</i>."
     unassign_user_from_team: "<i>%{unassigned_user}</i> was removed from team <strong>%{team}</strong> by <i>%{unassigned_by_user}</i>."