Merge pull request #1114 from ZmagoD/zd_SCI_2304

removes samples from views [fixes SCI-2304]
2025-01-01 21:21:50 +08:00 · 2018-04-26 17:05:56 +02:00 · 2018-04-26 17:05:56 +02:00 · b277501e6d
commit b277501e6d
parent cb6fe50832 e9642cadad
13 changed files with 65 additions and 198 deletions
--- a/app/controllers/search_controller.rb
+++ b/app/controllers/search_controller.rb
@ -17,7 +17,6 @@ class SearchController < ApplicationController
    search_protocols if @search_category == :protocols
    search_steps if @search_category == :steps
    search_checklists if @search_category == :checklists
-    search_samples if @search_category == :samples
    if @search_category == :repositories && params[:repository]
      search_repository
    end
@ -254,12 +253,6 @@ class SearchController < ApplicationController
    @search_count = @checklist_search_count
  end

-  def search_samples
-    @sample_results = []
-    @sample_results = search_by_name(Sample) if @sample_search_count > 0
-    @search_count = @sample_search_count
-  end
-
  def search_repository
    @repository = Repository.find_by_id(params[:repository])
    render_403 unless can_read_team?(@repository.team)
--- a/app/views/canvas/full_zoom/_my_module.html.erb
+++ b/app/views/canvas/full_zoom/_my_module.html.erb
@ -64,14 +64,6 @@
            </span>
          </a>
        </li>
-        <li role="presentation">
-          <a class="btn btn-link task-card-view-samples" href="<%= my_module_sample_my_modules_url(my_module_id: my_module.id, format: :json) %>" aria-controls="<%= my_module.id %>_samples" role="tab" data-remote="true">
-            <span class="glyphicon glyphicon-tint" aria-hidden="true"></span>
-            <% if my_module.samples.count.positive? %>
-              <span class="badge badge-indicator"><%= my_module.samples.count %></span>
-            <% end %>
-          </a>
-        </li>
      <% end %>
    </ul>

@ -82,7 +74,6 @@
        <div role="tabpanel" class="tab-pane" id="<%= my_module.id %>_users" data-contents="users"></div>
        <div role="tabpanel" class="tab-pane" id="<%= my_module.id %>_activities" data-contents="activities"></div>
        <div role="tabpanel" class="tab-pane" id="<%= my_module.id %>_comments" data-contents="comments"></div>
-        <div role="tabpanel" class="tab-pane" id="<%= my_module.id %>_samples" data-contents="samples"></div>
      <% end %>
    </div>
  </div>
--- a/app/views/experiments/samples.html.erb
+++ b/app/views/experiments/samples.html.erb
@ -3,5 +3,5 @@
 <%= render partial: "shared/secondary_navigation" %>

 <div id="content">
-  <%= render partial: "shared/samples" %>
+  <%#= render partial: "shared/samples" %>
 </div>
--- a/app/views/my_modules/samples.html.erb
+++ b/app/views/my_modules/samples.html.erb
@ -3,5 +3,5 @@
 <%= render partial: "shared/secondary_navigation" %>

 <div id="content">
-	<%= render partial: "shared/samples" %>
+	<%#= render partial: "shared/samples" %>
 </div>
--- a/app/views/projects/samples.html.erb
+++ b/app/views/projects/samples.html.erb
@ -3,5 +3,5 @@
 <%= render partial: "shared/secondary_navigation" %>

 <div id="content">
-  <%= render partial: "shared/samples" %>
+  <%#= render partial: "shared/samples" %>
 </div>
--- a/app/views/reports/new/modal/_module_contents_inner.html.erb
+++ b/app/views/reports/new/modal/_module_contents_inner.html.erb
@ -66,9 +66,6 @@
        <li>
          <%= form.check_box :module_activity, label: t("projects.reports.elements.modals.module_contents_inner.activity") %>
        </li>
-        <li>
-          <%= form.check_box :module_samples, label: t("projects.reports.elements.modals.module_contents_inner.samples") %>
-        </li>
        <% # List all repositories, no matter whether rows are assigned or not %>
        <% Repository.where(team: @project.team).order(created_at: :asc).select(:id, :name).find_each do |repository| %>
          <li>
--- a/app/views/search/index.html.erb
+++ b/app/views/search/index.html.erb
@ -170,20 +170,6 @@
            <%= t'Checklists' %>
          </a>
        </li>
-        <li role="presentation"
-          class="
-          <%= "active" if @search_category.present? and @search_category == :samples %>
-          <%= "disabled" if @sample_search_count == 0 %>"
-        >
-          <a href="?<%= {category: 'samples', q: @search_query,
-                         whole_word: @search_whole_word, whole_phrase: @search_whole_phrase,
-                         match_case: @search_case, utf8: '✓',
-                         search_id: @search_id}.to_query %>">
-            <span class="badge pull-right"><%= @sample_search_count %></span>
-            <span class="glyphicon glyphicon-tint"></span>
-            <%= t'Samples' %>
-          </a>
-        </li>

        <li role="presentation"
          class="
@ -290,9 +276,6 @@
      <% if @search_category == :checklists and @checklist_search_count > 0 %>
        <%= render 'search/results/checklists', search_query: @search_query, results: @checklist_results %>
      <% end %>
-      <% if @search_category == :samples and @sample_search_count > 0 %>
-        <%= render 'search/results/samples', search_query: @search_query, results: @sample_results %>
-      <% end %>
      <% if @search_category == :repositories and @repository_search_count_total > 0 %>
        <%= render 'search/results/repositories', search_query: @search_query, results: @repository_results, repository: @repository %>
      <% end %>
--- a/app/views/search/results/partials/_my_module_text.html.erb
+++ b/app/views/search/results/partials/_my_module_text.html.erb
@ -14,10 +14,6 @@
 <% else %>
  <% if can_read_experiment?(my_module.experiment) %>
    <% case link_to_page %>
-      <% when :samples %>
-        <%= route_to_other_team samples_my_module_path(my_module),
-                                my_module.experiment.project.team,
-                                text %>
      <% when :repositories %>
        <%= route_to_other_team repository_my_module_path(my_module, repository),
                                my_module.experiment.project.team,
--- a/app/views/shared/_secondary_navigation.html.erb
+++ b/app/views/shared/_secondary_navigation.html.erb
@ -27,14 +27,6 @@
                <span class="hidden-xs hidden-lg glyphicon glyphicon-blackboard"></span>
              </a>
            </li>
-            <li id="project-samples-nav-tab" class="<%= "active" if is_project_samples? ||
-                                                                    sample_types_page_project? ||
-                                                                    sample_groups_page_project? %>">
-              <a href="<%= samples_project_url(@project) %>" title="<%=t "nav2.projects.samples" %>">
-                <span class="hidden-sm hidden-md"><%=t "nav2.projects.samples" %></span>
-                <span class="hidden-xs hidden-lg glyphicon glyphicon-tint"></span>
-              </a>
-            </li>
            <li id="project-archive-nav-tab" data-turbolinks="false" class="<%= "active" if is_project_archive? %>">
              <a href="<%= experiment_archive_project_url(@project) %>" title="<%=t "nav2.projects.archive" %>">
                <span class="glyphicon glyphicon-briefcase"></span>
@ -52,14 +44,6 @@
                <span class="hidden-xs hidden-lg glyphicon glyphicon-blackboard"></span>
              </a>
            </li>
-            <li id="experiment-samples-nav-tab" class="<%= "active" if is_experiment_samples? ||
-                                                                       sample_groups_page_experiment? ||
-                                                                       sample_types_page_expermient? %>">
-              <a href="<%= samples_experiment_url(@experiment) %>" title="<%=t "nav2.projects.samples" %>">
-                <span class="hidden-sm hidden-md"><%=t "nav2.projects.samples" %></span>
-                <span class="hidden-xs hidden-lg glyphicon glyphicon-tint"></span>
-              </a>
-            </li>
          <% end %>
          <% if can_read_project?(@experiment.project) %>
              <li id="project-archive-nav-tab" data-turbolinks="false" class="<%= "active" if is_experiment_archive? %>">
@ -94,17 +78,6 @@
          <% end %>

          <li data-hook="secondary-navigation-tabs"></li>
-
-          <% if can_read_experiment?(@my_module.experiment) %>
-            <li id="module-samples-nav-tab" class="<%= "active" if is_module_samples? ||
-                                                                   sample_types_page_my_module? ||
-                                                                   sample_groups_page_my_module? %>">
-              <a href="<%= samples_my_module_url(@my_module) %>" title="<%=t "nav2.modules.samples" %>">
-                <span class="hidden-sm hidden-md"><%=t "nav2.modules.samples" %></span>
-                <span class="hidden-xs hidden-lg glyphicon glyphicon-tint"></span>
-              </a>
-            </li>
-          <% end %>
          <% if can_read_team?(@my_module.experiment.project.team) &&
                @my_module.experiment.project.team.repositories.exists? %>
            <li id="repositories-nav-tab" class="<%= "active" if module_repository_page? %>">
--- a/config/initializers/assets.rb
+++ b/config/initializers/assets.rb
@ -41,10 +41,10 @@ Rails.application.config.assets.precompile += %w(jquery.ui.touch-punch.min.js)
 Rails.application.config.assets.precompile += %w(bootstrap-colorselector.js)
 Rails.application.config.assets.precompile += %w(eventPause-min.js)
 Rails.application.config.assets.precompile += %w(sidebar.js)
-Rails.application.config.assets.precompile += %w(samples/samples.js)
-Rails.application.config.assets.precompile += %w(samples/sample_datatable.js)
+# Rails.application.config.assets.precompile += %w(samples/samples.js)
+# Rails.application.config.assets.precompile += %w(samples/sample_datatable.js)
 Rails.application.config.assets.precompile += %w(projects/index.js)
-Rails.application.config.assets.precompile += %w(samples/samples_importer.js)
+# Rails.application.config.assets.precompile += %w(samples/samples_importer.js)
 Rails.application.config.assets.precompile += %w(projects/canvas.js)
 Rails.application.config.assets.precompile +=
  %w(experiments/dropdown_actions.js)
@ -73,7 +73,7 @@ Rails.application.config.assets.precompile += %w(comments.js)
 Rails.application.config.assets.precompile += %w(projects/show.js)
 Rails.application.config.assets.precompile += %w(notifications.js)
 Rails.application.config.assets.precompile += %w(users/invite_users_modal.js)
-Rails.application.config.assets.precompile += %w(samples/sample_types_groups.js)
+# Rails.application.config.assets.precompile += %w(samples/sample_types_groups.js)
 Rails.application.config.assets.precompile += %w(highlightjs-github-theme.css)
 Rails.application.config.assets.precompile += %w(search.js)
 Rails.application.config.assets.precompile += %w(repositories/index.js)
--- a/config/initializers/extends/report_extends.rb
+++ b/config/initializers/extends/report_extends.rb
@ -94,10 +94,6 @@ module ReportExtends
                      :activity,
                      false,
                      %i(my_module order)),
-    ModuleElement.new([:samples],
-                      :samples,
-                      false,
-                      %i(my_module order)),
    ModuleElement.new([:repository],
                      :repository,
                      false,
@ -113,14 +109,12 @@ module ReportExtends
  # adds :order local to listed elements views
  # ADD REPORT ELEMENT TYPE WHICH YOU WANT TO PASS 'ORDER' LOCAL IN THE PARTIAL
  SORTED_ELEMENTS = %w(my_module_activity
-                       my_module_samples
                       my_module_repository
                       step_comments
                       result_comments)
  # sets local :my_module to the listed my_module child elements
  MY_MODULE_ELEMENTS = %w(my_module
                          my_module_activity
-                          my_module_samples
                          my_module_repository)

  # sets local name to first element of the listed elements
--- a/config/routes.rb
+++ b/config/routes.rb
@ -27,15 +27,15 @@ Rails.application.routes.draw do
    # end

    # Save sample table state
-    post '/state_save/:team_id/:user_id',
-         to: 'user_samples#save_samples_table_status',
-         as: 'save_samples_table_status',
-         defaults: { format: 'json' }
-
-    post '/state_load/:team_id/:user_id',
-         to: 'user_samples#load_samples_table_status',
-         as: 'load_samples_table_status',
-         defaults: { format: 'json' }
+    # post '/state_save/:team_id/:user_id',
+    #      to: 'user_samples#save_samples_table_status',
+    #      as: 'save_samples_table_status',
+    #      defaults: { format: 'json' }
+    #
+    # post '/state_load/:team_id/:user_id',
+    #      to: 'user_samples#load_samples_table_status',
+    #      as: 'load_samples_table_status',
+    #      defaults: { format: 'json' }

    resources :activities, only: [:index]

@ -156,22 +156,22 @@ Rails.application.routes.draw do
        post 'copy', to: 'repositories#copy',
             defaults: { format: 'json' }
      end
-      resources :samples, only: [:new, :create]
-      resources :sample_types, except: [:show, :new] do
-        get 'sample_type_element', to: 'sample_types#sample_type_element'
-        get 'destroy_confirmation', to: 'sample_types#destroy_confirmation'
-      end
-      resources :sample_groups, except: [:show, :new] do
-        get 'sample_group_element', to: 'sample_groups#sample_group_element'
-        get 'destroy_confirmation', to: 'sample_groups#destroy_confirmation'
-      end
-      resources :custom_fields, only: [:create, :edit, :update, :destroy] do
-        get 'destroy_html'
-      end
+      # resources :samples, only: [:new, :create]
+      # resources :sample_types, except: [:show, :new] do
+      #   get 'sample_type_element', to: 'sample_types#sample_type_element'
+      #   get 'destroy_confirmation', to: 'sample_types#destroy_confirmation'
+      # end
+      # resources :sample_groups, except: [:show, :new] do
+      #   get 'sample_group_element', to: 'sample_groups#sample_group_element'
+      #   get 'destroy_confirmation', to: 'sample_groups#destroy_confirmation'
+      # end
+      # resources :custom_fields, only: [:create, :edit, :update, :destroy] do
+      #   get 'destroy_html'
+      # end
      member do
        post 'parse_sheet', defaults: { format: 'json' }
-        post 'import_samples'
-        post 'export_samples'
+        # post 'import_samples'
+        # post 'export_samples'
        post 'export_repository', to: 'repositories#export_repository'
        # Used for atwho (smart annotations)
        get 'atwho_users', to: 'at_who#users'
@ -254,15 +254,15 @@ Rails.application.routes.draw do
      member do
        # Notifications popup for individual project in projects index
        get 'notifications'
-        get 'samples' # Samples for single project
+        # get 'samples' # Samples for single project
        # Renders sample datatable for single project (ajax action)
-        post 'samples_index'
+        # post 'samples_index'
        get 'experiment_archive' # Experiment archive for single project
-        post :delete_samples,
-             constraints: CommitParamRouting.new(
-               ProjectsController::DELETE_SAMPLES
-             ),
-             action: :delete_samples
+        # post :delete_samples,
+        #      constraints: CommitParamRouting.new(
+        #        ProjectsController::DELETE_SAMPLES
+        #      ),
+        #      action: :delete_samples
      end

      # This route is defined outside of member block
@ -286,16 +286,16 @@ Rails.application.routes.draw do
        post 'clone' # clone experiment
        get 'move_modal' # return modal with move options
        post 'move' # move experiment
-        get 'samples' # Samples for single project
+        # get 'samples' # Samples for single project
        get 'updated_img' # Checks if the workflow image is updated
        get 'fetch_workflow_img' # Get udated workflow img
        # Renders sample datatable for single project (ajax action)
-        post 'samples_index'
-        post :delete_samples,
-             constraints: CommitParamRouting.new(
-               ExperimentsController::DELETE_SAMPLES
-             ),
-             action: :delete_samples
+      #   post 'samples_index'
+      #   post :delete_samples,
+      #        constraints: CommitParamRouting.new(
+      #          ExperimentsController::DELETE_SAMPLES
+      #        ),
+      #        action: :delete_samples
      end
    end

@ -308,7 +308,7 @@ Rails.application.routes.draw do
      resources :my_module_comments,
                path: '/comments',
                only: [:index, :create, :edit, :update, :destroy]
-      resources :sample_my_modules, path: '/samples_index', only: [:index]
+      # resources :sample_my_modules, path: '/samples_index', only: [:index]
      resources :result_texts, only: [:new, :create]
      resources :result_assets, only: [:new, :create]
      resources :result_tables, only: [:new, :create]
@ -321,7 +321,7 @@ Rails.application.routes.draw do
        get 'due_date'
        get 'protocols' # Protocols view for single module
        get 'results' # Results view for single module
-        get 'samples' # Samples view for single module
+        # get 'samples' # Samples view for single module
        # Repository view for single module
        get 'repository/:repository_id',
            to: 'my_modules#repository',
@ -339,22 +339,22 @@ Rails.application.routes.draw do
        get 'complete_my_module'
        post 'toggle_task_state'
        # Renders sample datatable for single module (ajax action)
-        post 'samples_index'
-        post :assign_samples,
-             constraints: CommitParamRouting.new(
-               MyModulesController::ASSIGN_SAMPLES
-             ),
-             action: :assign_samples
-        post :assign_samples,
-             constraints: CommitParamRouting.new(
-               MyModulesController::UNASSIGN_SAMPLES
-             ),
-             action: :unassign_samples
-        post :assign_samples,
-             constraints: CommitParamRouting.new(
-               MyModulesController::DELETE_SAMPLES
-             ),
-             action: :delete_samples
+        # post 'samples_index'
+        # post :assign_samples,
+        #      constraints: CommitParamRouting.new(
+        #        MyModulesController::ASSIGN_SAMPLES
+        #      ),
+        #      action: :assign_samples
+        # post :assign_samples,
+        #      constraints: CommitParamRouting.new(
+        #        MyModulesController::UNASSIGN_SAMPLES
+        #      ),
+        #      action: :unassign_samples
+        # post :assign_samples,
+        #      constraints: CommitParamRouting.new(
+        #        MyModulesController::DELETE_SAMPLES
+        #      ),
+        #      action: :delete_samples
      end

      # Those routes are defined outside of member block
@ -384,8 +384,8 @@ Rails.application.routes.draw do
                only: [:create, :index, :edit, :update, :destroy]
    end

-    resources :samples, only: [:edit, :update, :destroy]
-    get 'samples/:id', to: 'samples#show'
+    # resources :samples, only: [:edit, :update, :destroy]
+    # get 'samples/:id', to: 'samples#show'

    resources :result_texts, only: [:edit, :update, :destroy]
    get 'result_texts/:id/download' => 'result_texts#download',
@ -521,7 +521,7 @@ Rails.application.routes.draw do
      post 'auth/token', to: 'api#authenticate'
      scope '20170715', module: 'v20170715' do
        get 'tasks/tree', to: 'core_api#tasks_tree'
-        get 'tasks/:task_id/samples', to: 'core_api#task_samples'
+        # get 'tasks/:task_id/samples', to: 'core_api#task_samples'
      end
    end
  end
--- a/spec/controllers/api/v20170715/core_api_controller_spec.rb
+++ b/spec/controllers/api/v20170715/core_api_controller_spec.rb
@ -12,66 +12,6 @@ describe Api::V20170715::CoreApiController, type: :controller do
    UserProject.create!(user: user, project: task.experiment.project, role: 0)
  end

-  describe 'GET #task_samples' do
-    context 'When valid request' do
-      before do
-        request.headers['HTTP_ACCEPT'] = 'application/json'
-        request.headers['Authorization'] = 'Bearer ' + generate_token(user.id)
-        get :task_samples, params: { task_id: task.id }
-      end
-
-      it 'Returns HTTP success' do
-        expect(response).to have_http_status(200)
-      end
-
-      it 'Returns JSON body containing expected Samples' do
-        hash_body = nil
-        expect { hash_body = json }.not_to raise_exception
-        expect(hash_body).to match(
-          [{ 'sample_id' => sample1.id.to_s, 'name' => sample1.name },
-           { 'sample_id' => sample2.id.to_s, 'name' => sample2.name },
-           { 'sample_id' => sample3.id.to_s, 'name' => sample3.name }]
-        )
-      end
-    end
-
-    context 'When invalid request' do
-      context 'When invalid token' do
-        before do
-          request.headers['HTTP_ACCEPT'] = 'application/json'
-          request.headers['Authorization'] = 'Bearer WroNgToken'
-          get :task_samples, params: { task_id: task.id }
-        end
-
-        it 'Returns HTTP unauthorized' do
-          expect(response).to have_http_status(401)
-        end
-      end
-
-      context 'When valid token, but invalid request' do
-        before do
-          request.headers['HTTP_ACCEPT'] = 'application/json'
-          request.headers['Authorization'] = 'Bearer ' + generate_token(user.id)
-        end
-
-        it 'Returns HTTP not found' do
-          get :task_samples, params: { task_id: 1000 }
-          expect(response).to have_http_status(404)
-          expect(json).to match({})
-        end
-
-        it 'Returns HTTP access denied' do
-          UserProject.where(user: user, project: task.experiment.project)
-                     .first
-                     .destroy!
-          get :task_samples, params: { task_id: task.id }
-          expect(response).to have_http_status(403)
-          expect(json).to match({})
-        end
-      end
-    end
-  end
-
  describe 'GET #tasks_tree' do
    let!(:user_team) { create :user_team, team: team, user: user }
    context 'When valid request' do