Merge pull request #3027 from okriuchykhin/ok_SCI_5246

Remove Demo project and Samples inventory [SCI-5246][SCI-5248]

app/assets/demo_files/tables_content.yaml

@@ -1,18 +0,0 @@
-# Content for tables used in demo project.
-
-module1:
-  experimental_design_table: '{"data":[["group/time","1 dpi","6 dpi","",""],["PVYNTN","1","1","",""],["mock","1","1","",""],["","","","",""]]}'
-
-module2:
-  samples_table: '{"data":[["Name","Sample type"],["Mock 1dpi","potatoe leaves"],["Mock 6dpi","potatoe leaves"],["PVY NTN 1dpi","potatoe leaves"],["PVY NTN 6dpi","potatoe leaves"]]}'
-module3:
-  nanodrop: '{"data":[["Sample name","ng/ul ","260/280 ","260/230 "],["PVY NTN 6dpi","1.05","1.39","1.61"],["PVY NTN 1dpi","320.52","2.16","2.26"],["Mock 6dpi","906.19","2.15","2.26"],["Mock 1dpi","940.22","2.17","2.27"]]}'
-module4:
-  volumes: '{"data":[["Amount of starting material (mg)","Volume of Buffer RLT (µl)"],["<20","350"],["20 - 30","600"]]}'
-  dna_q: '{"data":[["Sample 1","Quantity "],["1","0,2"],["2","0,5"],["3","0,4"],["4","1,1"],["5","12,5"],["6","0,05"],["7","0"],["8","0"],["9","0"],["10","0"],["11","0"],["12","4,7"],["13","2,3"],["14","5,6"],["15","2,6"],["16","8,9"],["17","1,7"],["18","1"]]}'
-module6:
-  mastermix: '{"data":[["Date:","","","","","","","","","","","",""],["Reaction volume:","20 ul","","","","","","","","","","",""],["UMM/reaction:","10 µl","","","","","","","","","","",""],["sample/reaction:","6 µl","","","","","","","","","","",""],["","","","","","","","","","","","",""],["Chemistry","TaqMan","","","SYBR Green I","","","TaqMan","","","SYBR Green I","",""],["Gene","cox","","","cab4","","","PVY-NTN","","","PR-1","",""],["","conc.*","final conc.**","µl/reaction","conc.*","final conc.**","µl/reaction","conc.*","final conc.**","µl/reaction","conc.*","final conc.**","µl/reaction"],["Probe","10 µM","150 nM","0.3","/","/","/","5 µM","150 nM","0.6","/","/","/"],["FP","30 µM","300 nM","0.2","30 µM","300 nM ","0.2","10 µM","250 nM","0.5","30 µM","300 nM ","0.2"],["RP","30 µM","300 nM","0.2","30 µM","300 nM ","0.2","10 µM","250 nM","0.5","30 µM","300 nM ","0.2"]]}'
-  distribution: '{"data":[["%{sample0} (100x)\t","%{sample0} (100x)\t","%{sample0} (100x)\t","%{sample0} (100x)\t","%{sample0} (100x)\t","%{sample0} (100x)\t","%{sample0} (100x)\t","%{sample0} (100x)\t",null,null,"Mix smpl (10x)\t","Mix smpl (10x)\t"],["%{sample0} (1000x)\t","%{sample0} (1000x)\t","%{sample0} (1000x)\t","%{sample0} (1000x)\t","%{sample0} (1000x)\t","%{sample0} (1000x)\t","%{sample0} (1000x)\t","%{sample0} (1000x)\t",null,null,"Mix smpl (100x)\t","Mix smpl (100x)\t"],["%{sample1} (100x)\t","%{sample1} (100x)\t","%{sample1} (100x)\t","%{sample1} (100x)\t","%{sample1} (100x)\t","%{sample1} (100x)\t","%{sample1} (100x)\t","%{sample1} (100x)\t",null,null,"Mix smpl (1000x)\t","Mix smpl (1000x)\t"],["%{sample1} (1000x)\t","%{sample1} (1000x)\t","%{sample1} (1000x)\t","%{sample1} (1000x)\t","%{sample1} (1000x)\t","%{sample1} (1000x)\t","%{sample1} (1000x)\t","%{sample1} (1000x)\t",null,null,"Mix smpl (10000x)\t","Mix smpl (10000x)\t"],["%{sample2} (100x)\t","%{sample2} (100x)\t","%{sample2} (100x)\t","%{sample2} (100x)\t","%{sample2} (100x)\t","%{sample2} (100x)\t","%{sample2} (100x)\t","%{sample2} (100x)\t",null,null,"NTC1","NTC2"],["%{sample2} (1000x)\t","%{sample2} (1000x)\t","%{sample2} (1000x)\t","%{sample2} (1000x)\t","%{sample2} (1000x)\t","%{sample2} (1000x)\t","%{sample2} (1000x)\t","%{sample2} (1000x)\t",null,null,"NTC1","NTC2"],["%{sample3} (100x)\t","%{sample3} (100x)\t","%{sample3} (100x)\t","%{sample3} (100x)\t","%{sample3} (100x)\t","%{sample3} (100x)\t","%{sample3} (100x)\t","%{sample3} (100x)\t",null,null,"NTC1","NTC2"],["%{sample3} (1000x)\t","%{sample3} (1000x)\t","%{sample3} (1000x)\t","%{sample3} (1000x)\t","%{sample3} (1000x)\t","%{sample3} (1000x)\t","%{sample3} (1000x)\t","%{sample3} (1000x)\t",null,null,"NTC1","NTC2"],[null,null,null,null,null,null,null,null,null,null,null,null]]}'
-  qpcr_raw_data: '{"data":[["Sample 1","Quantity ","Column 3","Column 4"],["2","0,2","0,4","0,08"],["2","0,5","1","0,5"],["3","0,4","1,2","0,48"],["4","1,1","4,4","4,84"],["5","12,5","62,5","781,25"],["6","0,05","0,3","0,015"],["7","0","4","0"],["8","0","0","0"],["9","0","0","0"],["10","0","0","0"],["11","0","0","0"],["12","4,7","56,4","265,08"],["13","2,3","30","69"],["14","5,6","78,4","439,04"],["15","2,6","39","101,4"],["16","8,9","142,4","1267,36"],["17","1,7","28,9","49,13"],["18","1","18","18"],["","","",""]]}'
-module7:
-  qpcr_results: '{"data":[["Sample 1","Quantity ",null,null,null],["1","0,2",null,null,null],["2","0,5",null,null,null],["3","0,4",null,null,null],["4","1,1",null,null,null],["5","12,5",null,null,null],["6","0,05",null,null,null],["7","0",null,null,null],["8","0",null,null,null],["9","0",null,null,null],["10","0",null,null,null],["11","0",null,null,null],["12","4,7",null,null,null],["13","2,3",null,null,null],["14","5,6",null,null,null],["15","2,6",null,null,null],["16","8,9",null,null,null],["17","1,7",null,null,null],["18","1",null,null,null]]}'

app/controllers/repositories_controller.rb

@@ -26,7 +26,9 @@ class RepositoriesController < ApplicationController
 
   def index
     respond_to do |format|
-      format.html do; end
+      format.html do
+        render 'empty_index' if @repositories.blank?
+      end
       format.json do
         render json: prepare_repositories_datatable(@repositories, current_team, params)
       end

app/controllers/users/sessions_controller.rb

@@ -25,7 +25,7 @@ class Users::SessionsController < Devise::SessionsController
   def create
     super
 
-    generate_demo_project
+    generate_templates_project
   end
 
   def two_factor_recovery
@@ -80,7 +80,7 @@ class Users::SessionsController < Devise::SessionsController
       session.delete(:otp_user_id)
 
       sign_in(user)
-      generate_demo_project
+      generate_templates_project
       flash[:notice] = t('devise.sessions.signed_in')
       redirect_to stored_location_for(:user) || root_path
     else
@@ -100,7 +100,7 @@ class Users::SessionsController < Devise::SessionsController
     session.delete(:otp_user_id)
     if user.recover_2fa!(params[:recovery_code])
       sign_in(user)
-      generate_demo_project
+      generate_templates_project
       flash[:notice] = t('devise.sessions.signed_in')
       redirect_to root_path
     else
@@ -130,17 +130,9 @@ class Users::SessionsController < Devise::SessionsController
     end
   end
 
-  def generate_demo_project
+  def generate_templates_project
     # Schedule templates creation for user
     TemplatesService.new.schedule_creation_for_user(current_user)
-
-    # Schedule demo project creation for user
-    current_user.created_teams.each do |team|
-      FirstTimeDataGenerator.delay(
-        queue: :new_demo_project,
-        priority: 10
-      ).seed_demo_data_with_id(current_user.id, team.id)
-    end
   rescue StandardError => e
     Rails.logger.fatal("User ID #{current_user.id}: Error creating inital projects on sign_in: #{e.message}")
   end

app/models/team.rb

@@ -43,8 +43,6 @@ class Team < ApplicationRecord
   has_many :shared_repositories, through: :team_repositories, source: :repository
 
   attr_accessor :without_templates
-  attr_accessor :without_intro_demo
-  after_create :generate_intro_demo
 
   def default_view_state
     {
@@ -168,15 +166,4 @@ class Team < ApplicationRecord
     return if without_templates
     TemplatesService.new.delay(queue: :templates).update_team(self)
   end
-
-  include FirstTimeDataGenerator
-
-  def generate_intro_demo
-    return if without_intro_demo
-
-    user = User.find(created_by_id)
-    if user.created_teams.order(:created_at).first == self
-      seed_demo_data(user, self)
-    end
-  end
 end

app/services/team_importer.rb

@@ -57,7 +57,6 @@ class TeamImporter
       team_last_modified_by = team.last_modified_by_id
       team.last_modified_by_id = nil
       team.without_templates = true
-      team.without_intro_demo = true
       team.save!
 
       create_users(team_json['users'], team)

app/utilities/delayed_uploader_demo.rb

@@ -1,60 +0,0 @@
-# frozen_string_literal: true
-
-module DelayedUploaderDemo
-  # Get asset from demo_files folder
-  def self.get_asset(user, team, file_name)
-    asset = Asset.create(
-      created_by: user,
-      team: team,
-      last_modified_by: user
-    )
-    asset.file.attach(io: File.open("#{Rails.root}/app/assets/demo_files/#{file_name}", 'r'), filename: file_name)
-    asset
-  end
-
-  # Generates results asset for given module, file_name assumes file is located
-  # in demo_files.
-  def self.generate_result_asset(
-    my_module:,
-    current_user:,
-    current_team:,
-    result_name:,
-    created_at: Time.now,
-    file_name:,
-    comment: nil
-  )
-    temp_asset = get_asset(current_user, current_team, file_name)
-    temp_result = Result.new(
-      created_at: created_at,
-      user: current_user,
-      my_module: my_module,
-      name: result_name,
-      asset: temp_asset
-    )
-
-    temp_result.save
-
-    # Generate comment if it exists
-    generate_result_comment(temp_result, current_user, comment) if comment
-
-    temp_asset.post_process_file(my_module.experiment.project.team)
-  end
-
-  # Adds asset to existing step
-  def self.add_step_asset(step:, current_user:, current_team:, file_name:)
-    temp_asset =
-      DelayedUploaderDemo.get_asset(current_user, current_team, file_name)
-    step.assets << temp_asset
-    temp_asset.post_process_file(step.my_module.experiment.project.team)
-  end
-
-  def self.generate_result_comment(result, user, message, created_at = nil)
-    created_at ||= result.created_at
-    ResultComment.create(
-      user: user,
-      message: message,
-      created_at: created_at,
-      result: result
-    )
-  end
-end

app/views/repositories/empty_index.html.erb

@@ -0,0 +1,29 @@
+<% provide(:head_title, t('libraries.index.head_title')) %>
+<% provide(:container_class, 'no-second-nav-container') %>
+
+<%= render partial: 'sidebar', locals: { repositories: @repositories, archived: false } %>
+<div class="content-pane flexible repositories-index" data-readonly="<%= !current_user.is_admin_of_team?(current_team) %>">
+  <div class="content-header">
+    <h1 data-view-mode="active"><%= t('libraries.index.head_title') %></h1>
+  </div>
+  <div class="content-body">
+    <h1>
+      <%= t('repositories.index.empty_title') %>
+    </h1>
+    <% if can_create_repositories?(current_team) %>
+      <h5>
+        <%= t('repositories.index.empty_description_with_create') %>
+      </h5>
+      <a id="createRepoBtn" class="btn btn-primary create-new-repository" data-remote="true" href="<%= create_modal_team_repositories_path(current_team) %>">
+        <span class="fas fa-plus"></span>
+        <span class="hidden-xs"><%= t('libraries.index.no_libraries.create_new_button') %></span>
+      </a>
+    <% else %>
+      <h5>
+        <%= t('repositories.index.empty_description_no_create') %>
+      </h5>
+    <% end %>
+  </div>
+</div>
+
+<%= javascript_include_tag 'repositories/index' %>

config/locales/en.yml

@@ -1201,6 +1201,9 @@ en:
     index:
       head_title: "Inventories"
       title: "Inventories"
+      empty_title: "Your team has no inventories yet"
+      empty_description_no_create: "It would be a shame to waste all this space. Sadly you don’t have permission to add inventories. You can ask your team admin to grant you that permission."
+      empty_description_with_create: "It would be a shame to waste all this space. Create your first inventory now"
       add_new_repository_tab: "Add inventory"
       delete_flash: "\"%{name}\" inventory was successfully deleted!"
       rename_flash: "\"%{old_name}\" inventory was successfully renamed to \"%{new_name}\"!"

features/protocol.feature

@@ -13,7 +13,7 @@ Given default screen size2
      | name        | email              | password       | password_confirmation |
      | Karli Novak | nonadmin@myorg.com | mypassword1234 | mypassword1234 |
   And "nonadmin@myorg.com" is in "BioSistemika Process" team as a "admin"
-  Given Demo project exists for the "BioSistemika Process" team
+  Given Templates project exists for the "BioSistemika Process" team
   And "nonadmin@myorg.com" is signed in with "mypassword1234"
 
  @javascript

features/protocol_step.feature

@@ -13,7 +13,7 @@ Given the following users are registered
    | name        | email              | password       | password_confirmation |
    | Karli Novak | nonadmin@myorg.com | mypassword1234 | mypassword1234 |
 And "nonadmin@myorg.com" is in "BioSistemika Process" team as a "admin"
-Given Demo project exists for the "BioSistemika Process" team
+Given Templates project exists for the "BioSistemika Process" team
 And "nonadmin@myorg.com" is signed in with "mypassword1234"
 
 @javascript @wip

features/result.feature

@@ -12,7 +12,7 @@ Background:
      | name        | email              | password       | password_confirmation |
      | Karli Novak | nonadmin@myorg.com | mypassword1234 | mypassword1234 |
   And "nonadmin@myorg.com" is in "BioSistemika Process" team as a "admin"
-  Given Demo project exists for the "BioSistemika Process" team
+  Given Templates project exists for the "BioSistemika Process" team
   And "nonadmin@myorg.com" is signed in with "mypassword1234"
 
 @javascript

features/step_definitions/shared_steps.rb

@@ -85,12 +85,11 @@ Given(/^the "([^"]*)" team exists$/) do |team_name|
   FactoryBot.create(:team, name: team_name)
 end
 
-Given(/^Demo project exists for the "([^"]*)" team$/) do |team_name|
+Given(/^Templates project exists for the "([^"]*)" team$/) do |team_name|
   team = Team.find_by(name: team_name)
   user = team.user_teams.where(role: :admin).take.user
-  seed_demo_data(user, team)
+  TemplatesService.new.schedule_creation_for_user(user)
 end
-
 Given(/^I'm on the projects page of "([^"]*)" team$/) do |team_name|
   team = Team.find_by(name: team_name)
   @current_user.update(current_team_id: team.id)
@@ -238,5 +237,3 @@ Then('I delete downloaded file {string}') do |file_name|
   sleep 3
   FileUtils.rm_f(Rails.root.join(file_name))
 end
-
-

features/support/env.rb

@@ -16,8 +16,6 @@ require 'capybara/email'
 # require 'capybara/poltergeist'
 Capybara.javascript_driver = :poltergeist
 
-include FirstTimeDataGenerator
-
 Capybara.default_max_wait_time = 30
 #Capybara.asset_host = 'http://localhost:3001'
 Capybara.server_port = ENV['CAPYBARA_SERVER_PORT'] || 3000

lib/tasks/data.rake

@@ -151,33 +151,4 @@ namespace :data do
       end
     end
   end
-
-  desc 'Create demo project on existing users'
-  task :create_demo_project_on_existing_users,
-       %i(slice_size) => [:environment] do |_, args|
-    args.with_defaults(slice_size: 800)
-
-    require "#{Rails.root}/app/utilities/first_time_data_generator"
-    include FirstTimeDataGenerator
-
-    Rails.logger.info('Creating demo project on existing users')
-
-    Team.all.order(updated_at: :desc)
-        .each_slice(args[:slice_size]).with_index do |teams, i|
-      Rails.logger.info("Processing slice with index #{i}. " \
-                        "First team: #{teams.first.id}, " \
-                        "Last team: #{teams.last.id}.")
-
-      teams.each do |team|
-        owner_ut = team.user_teams.where(role: 2).first
-        next unless owner_ut
-
-        FirstTimeDataGenerator.delay(
-          run_at: i.hours.from_now,
-          queue: :new_demo_project,
-          priority: 10
-        ).seed_demo_data_with_id(owner_ut.user.id, team.id)
-      end
-    end
-  end
 end

spec/factories/teams.rb

@@ -7,7 +7,6 @@ FactoryBot.define do
     description { Faker::Lorem.sentence }
     space_taken { 1048576 }
     without_templates { true }
-    without_intro_demo { true }
     trait :with_members do
       users { create_list :user, 3 }
     end

spec/services/templates_service_spec.rb

@@ -4,7 +4,6 @@ require 'rails_helper'
 require 'fileutils'
 
 describe TemplatesService do
-  include FirstTimeDataGenerator
   let!(:main_team) { create :team }
   let!(:admin_user) { create :user }
 
@@ -12,84 +11,30 @@ describe TemplatesService do
     context 'update templates project' do
       it 'experiment is added to templates project' do
         create(:user_team, user: admin_user, team: main_team)
-        seed_demo_data(main_team.created_by, main_team)
         dj_worker = Delayed::Worker.new
-        # Two runs are needed to execute additional jobs which get generated
-        # during first run
-        Delayed::Job.all.each { |job| dj_worker.run(job) }
-        Delayed::Job.all.each { |job| dj_worker.run(job) }
-        demo_exp = main_team.projects.first.experiments.first
-        exp_exporter = ModelExporters::ExperimentExporter.new(demo_exp.id)
-        exp_dir = exp_exporter.export_template_to_dir
-        tmplts_dir = "#{Rails.root}/tmp/testing_templates"
-        FileUtils.remove_dir(tmplts_dir) if Dir.exist?(tmplts_dir)
-        FileUtils.mkdir(tmplts_dir)
-        FileUtils.mv(exp_dir, "#{tmplts_dir}/experiment_#{demo_exp.id}")
         templates_project =
           create :project, name: 'Templates', template: true, team: main_team
         create(
           :user_project, :owner, project: templates_project, user: admin_user
         )
-        ts = TemplatesService.new(tmplts_dir)
+        ts = TemplatesService.new
         ts.update_team(main_team)
         Delayed::Job.all.each { |job| dj_worker.run(job) }
-        tmpl_exp = templates_project.experiments.first
+        tmpl_exp = templates_project.experiments.find_by(name: 'Polymerase chain reaction')
 
-        expect(tmpl_exp.name).to eq(demo_exp.name)
         expect(tmpl_exp.uuid).to_not eq(nil)
         expect(tmpl_exp.my_modules.pluck(:name))
-          .to match_array(demo_exp.my_modules.active.pluck(:name))
+          .to match_array(['Data analysis - ddCq', 'Data quality control', 'Experiment design', 'qPCR',
+                           'Reverse transcription', 'RNA isolation', 'RNA quality & quantity - BIOANALYSER',
+                           'Sampling biological material'])
         tmpl_tasks = tmpl_exp.my_modules
-        demo_tasks = demo_exp.my_modules.active
+        tmpl_tasks.each do |tmpl_task|
-        demo_tasks.each do |demo_task|
+          tmpl_task.protocol.steps.each do |tmpl_step|
-          tmpl_task = tmpl_tasks.find_by_name(demo_task.name)
-          expect(tmpl_task.name).to eq(demo_task.name)
-          expect(tmpl_task.task_comments.size)
-            .to eq(demo_task.task_comments.size)
-          demo_task.results.each do |demo_res|
-            tmpl_res = tmpl_task.results.find_by_name(demo_res.name)
-            expect(tmpl_res.name).to eq(demo_res.name)
-            if demo_res.asset
-              expect(tmpl_res.asset.file.attached?).to eq(true)
-              expect(demo_res.asset.file_name)
-                .to eq(tmpl_res.asset.file_name)
-            elsif demo_res.table
-              expect(demo_res.table.contents).to eq(tmpl_res.table.contents)
-            elsif demo_res.result_text
-              expect(demo_res.result_text.text).to eq(tmpl_res.result_text.text)
-            end
-            expect(demo_res.result_comments.size)
-              .to eq(tmpl_res.result_comments.size)
-          end
-          unless demo_task.protocol.present? &&
-                 demo_task.protocol.steps.size.positive?
-            next
-          end
-
-          demo_task.protocol.steps.each do |demo_step|
-            tmpl_step = tmpl_task.protocol.steps.find_by_name(demo_step.name)
-            expect(demo_step.name).to eq(tmpl_step.name)
-            expect(demo_step.description).to eq(tmpl_step.description)
-            if demo_step.assets.present?
-              expect(demo_step.assets.map(&:file_name))
-                .to match_array(tmpl_step.assets.map(&:file_name))
-            end
             tmpl_step.assets.each do |asset|
               expect(asset.file.attached?).to eq(true)
             end
-            if demo_step.tables.present?
-              expect(demo_step.tables.pluck(:contents))
-                .to match_array(tmpl_step.tables.pluck(:contents))
-            end
-            if demo_step.checklists.present?
-              expect(demo_step.checklists.pluck(:name))
-                .to match_array(tmpl_step.checklists.pluck(:name))
-            end
-            expect(demo_step.step_comments.size)
-              .to eq(tmpl_step.step_comments.size)
           end
         end
-        FileUtils.remove_dir(tmplts_dir)
       end
     end
   end