From 9581e2751f59f0001bbeb96df44d6c57ad3e48d6 Mon Sep 17 00:00:00 2001
From: zmagod <zmago_devetak@yahoo.com>
Date: Tue, 2 Aug 2016 08:44:07 +0200
Subject: [PATCH] fixes samples page for experiment level [fixes SCI-44]

---
 app/controllers/experiments_controller.rb     | 22 ++++++++++++++++---
 app/helpers/permission_helper.rb              |  6 ++++-
 app/helpers/secondary_navigation_helper.rb    |  4 ++++
 app/views/experiments/samples.html.erb        |  7 ++++++
 .../shared/_secondary_navigation.html.erb     |  8 +++++++
 config/routes.rb                              |  5 ++++-
 6 files changed, 47 insertions(+), 5 deletions(-)
 create mode 100644 app/views/experiments/samples.html.erb

diff --git a/app/controllers/experiments_controller.rb b/app/controllers/experiments_controller.rb
index 1ef63c8b6..0da3fbecc 100644
--- a/app/controllers/experiments_controller.rb
+++ b/app/controllers/experiments_controller.rb
@@ -1,8 +1,8 @@
 class ExperimentsController < ApplicationController
   include PermissionHelper
   before_action :set_experiment, except: [:new, :create]
-  before_action :set_project, only: [:new, :create]
-  before_action :check_view_permissions, only: [:canvas]
+  before_action :set_project, only: [:new, :create, :samples_index, :samples ]
+  # before_action :check_view_permissions, only: [:canvas]
 
   # except parameter could be used but it is not working.
   layout :choose_layout
@@ -66,6 +66,22 @@ class ExperimentsController < ApplicationController
     end
   end
 
+  def samples
+    @samples_index_link = samples_index_experiment_path(@experiment, format: :json)
+    @organization = @experiment.project.organization
+  end
+
+  def samples_index
+    @organization = @experiment.project.organization
+
+    respond_to do |format|
+      format.html
+      format.json {
+        render json: ::SampleDatatable.new(view_context, @organization, @experiment, nil)
+      }
+    end
+  end
+
   private
 
   def set_experiment
@@ -74,7 +90,7 @@ class ExperimentsController < ApplicationController
   end
 
   def set_project
-    @project = Project.find_by_id(params[:project_id])
+    @project = Project.find_by_id(params[:project_id]) || @experiment.project
     render_404 unless @project
   end
 
diff --git a/app/helpers/permission_helper.rb b/app/helpers/permission_helper.rb
index 162d332b3..f061a4ca7 100644
--- a/app/helpers/permission_helper.rb
+++ b/app/helpers/permission_helper.rb
@@ -140,7 +140,8 @@ module PermissionHelper
       :can_view_experiment,
       :can_view_experiment_archive,
       :can_archive_experiment,
-      :can_restore_experiment
+      :can_restore_experiment,
+      :can_view_experiment_samples
     ] do |proxy, *args, &block|
       if args[0]
         experiment = args[0]
@@ -346,6 +347,9 @@ module PermissionHelper
     experiment.archived? and is_user_or_higher_of_project(experiment.project)
   end
 
+  def can_view_experiment_samples(experiment)
+    can_view_samples(experiment.project.organization)
+  end
   # ---- WORKFLOW PERMISSIONS ----
 
   def can_edit_canvas(experiment)
diff --git a/app/helpers/secondary_navigation_helper.rb b/app/helpers/secondary_navigation_helper.rb
index a12c48af7..e867d3c4a 100644
--- a/app/helpers/secondary_navigation_helper.rb
+++ b/app/helpers/secondary_navigation_helper.rb
@@ -28,6 +28,10 @@ module SecondaryNavigationHelper
     action_name == 'module_archive'
   end
 
+  def is_experiment_samples?
+    action_name == 'samples'
+  end
+
   def is_module_info?
     action_name == 'show'
   end
diff --git a/app/views/experiments/samples.html.erb b/app/views/experiments/samples.html.erb
new file mode 100644
index 000000000..4f5692ae9
--- /dev/null
+++ b/app/views/experiments/samples.html.erb
@@ -0,0 +1,7 @@
+<% provide(:head_title, raw(t("projects.samples.head_title", project: @experiment.name))) %>
+<%= render partial: "shared/sidebar" %>
+<%= render partial: "shared/secondary_navigation" %>
+
+<div id="content">
+  <%= render partial: "shared/samples" %>
+</div>
diff --git a/app/views/shared/_secondary_navigation.html.erb b/app/views/shared/_secondary_navigation.html.erb
index 1b57b912d..6d3516adf 100644
--- a/app/views/shared/_secondary_navigation.html.erb
+++ b/app/views/shared/_secondary_navigation.html.erb
@@ -99,6 +99,14 @@
           <% end %>
 
         <% elsif experiment_page? %>
+        <% if can_view_experiment_samples(@experiment) then %>
+          <li id="experiment-samples-nav-tab" class="<%= "active" if is_experiment_samples? %>">
+            <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_view_experiment(@experiment) then %>
             <li id="canvas-nav-tab" class="<%= "active" if is_experiment_canvas? %>">
               <a href="<%= project_url(@project) %>" title="<%=t "nav2.experiments.canvas" %>">
diff --git a/config/routes.rb b/config/routes.rb
index dabf2e151..41ac22cf9 100644
--- a/config/routes.rb
+++ b/config/routes.rb
@@ -101,7 +101,7 @@ Rails.application.routes.draw do
     get 'users/edit', to: 'user_projects#index_edit'
   end
 
-  resources :experiments do
+  resources :experiments, only: :show do
     member do
       get 'canvas' # Overview/structure for single experiment
       get 'canvas/edit', to: 'canvas#edit' # AJAX-loaded canvas edit mode (from canvas)
@@ -110,6 +110,9 @@ Rails.application.routes.draw do
       get 'canvas/small_zoom', to: 'canvas#small_zoom' # AJAX-loaded canvas zoom
       post 'canvas', to: 'canvas#update' # Save updated canvas action
       get 'module_archive' # Module archive for single experiment
+      get 'samples' # Samples for single project
+      post 'samples_index' # Renders sample datatable for single project (ajax action)
+      post :delete_samples, constraints: CommitParamRouting.new(MyModulesController::DELETE_SAMPLES), action: :delete_samples
     end
   end