Merge branch 'zd_SCI_44' of https://github.com/ZmagoD/scinote-web into ZmagoD-zd_SCI_44

app/controllers/experiments_controller.rb

@@ -1,7 +1,7 @@
 class ExperimentsController < ApplicationController
   include PermissionHelper
   before_action :set_experiment, except: [:new, :create]
-  before_action :set_project, only: [:new, :create]
+  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.
@@ -57,6 +57,7 @@ class ExperimentsController < ApplicationController
     if @experiment.save
       flash[:success] = t('experiments.update.success_flash',
                           experiment: @experiment.name)
+
       redirect_to canvas_experiment_path(@experiment)
     else
       flash[:alert] = t('experiments.update.error_flash')
@@ -71,6 +72,7 @@ class ExperimentsController < ApplicationController
     if @experiment.save
       flash[:success] = t('experiments.archive.success_flash',
                           experiment: @experiment.name)
+
       redirect_to project_path(@experiment.project)
     else
       flash[:alert] = t('experiments.archive.error_flash')
@@ -78,6 +80,27 @@ 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 do
+        render json: ::SampleDatatable.new(view_context,
+                                           @organization,
+                                           nil,
+                                           nil,
+                                           @experiment)
+      end
+    end
+  end
+
   private
 
   def set_experiment
@@ -86,7 +109,7 @@ 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
 

app/datatables/sample_datatable.rb

@@ -5,11 +5,16 @@ class SampleDatatable < AjaxDatatablesRails::Base
 
   ASSIGNED_SORT_COL = "assigned"
 
-  def initialize(view, organization, project = nil, my_module = nil)
+  def initialize(view,
+                 organization,
+                 project = nil,
+                 my_module = nil,
+                 experiment = nil)
     super(view)
     @organization = organization
     @project = project
     @my_module = my_module
+    @experiment = experiment
   end
 
   # Define sortable columns, so 1st column will be sorted by attribute in sortable_columns[0]
@@ -119,24 +124,29 @@ class SampleDatatable < AjaxDatatablesRails::Base
 
     if @my_module
       @assigned_samples = @my_module.samples
-      samples = samples
+
-      .joins(
+      samples = samples.joins("LEFT OUTER JOIN sample_my_modules ON
-        "LEFT OUTER JOIN sample_my_modules ON
                           (samples.id = sample_my_modules.sample_id AND
                           (sample_my_modules.my_module_id = #{@my_module.id.to_s} OR
-          sample_my_modules.id IS NULL))"
+                          sample_my_modules.id IS NULL))")
-      )
                           .references(:sample_my_modules)
     elsif @project
       @assigned_samples = @project.assigned_samples
-      ids = @project.my_modules.select(:id)
+      ids = @project.my_modules_ids
-      samples = samples
+
-      .joins(
+      samples = samples.joins("LEFT OUTER JOIN sample_my_modules ON
-        "LEFT OUTER JOIN sample_my_modules ON
+                              (samples.id = sample_my_modules.sample_id AND
+                              (sample_my_modules.my_module_id IN (#{ids}) OR
+                              sample_my_modules.id IS NULL))")
+                              .references(:sample_my_modules)
+    elsif @experiment
+      @assigned_samples = @experiment.assigned_samples
+      ids = @experiment.my_modules.select(:id)
+
+      samples = samples.joins("LEFT OUTER JOIN sample_my_modules ON
                           (samples.id = sample_my_modules.sample_id AND
                           (sample_my_modules.my_module_id IN (#{ids.to_sql}) OR
-          sample_my_modules.id IS NULL))"
+                          sample_my_modules.id IS NULL))")
-      )
                           .references(:sample_my_modules)
     end
 
@@ -172,6 +182,39 @@ class SampleDatatable < AjaxDatatablesRails::Base
           # Depending on the sort, order nulls first or
           # nulls last on sample_my_modules association
           records.order("sample_my_modules.id NULLS #{sort_null_direction(params[:order].values[0])}")
+        elsif @experiment
+          # A very elegant solution to sort assigned samples at a experiment level
+
+          # grabs the ids of samples which has a modules that belongs to this project
+          assigned = Sample
+            .joins('LEFT OUTER JOIN "sample_my_modules" ON "sample_my_modules"."sample_id" = "samples"."id"')
+            .joins('LEFT OUTER JOIN "my_modules" ON "my_modules"."id" = "sample_my_modules"."my_module_id"')
+            .where('"my_modules"."experiment_id" = ?', @experiment.id)
+            .where('"my_modules"."nr_of_assigned_samples" > 0')
+            .select('"samples"."id"')
+            .distinct
+
+          # grabs the ids that are not the previous one but are still of the same organization
+          unassigned = Sample
+            .where('"samples"."organization_id" = ?', @organization.id)
+            .where('"samples"."id" NOT IN (?)', assigned)
+            .select('"samples"."id"')
+            .distinct
+
+          # check the input param and merge the two arrays of ids
+          if params[:order].values[0]['dir'] == 'asc'
+            ids = assigned + unassigned
+          elsif params[:order].values[0]['dir'] == 'desc'
+            ids = unassigned + assigned
+          end
+          ids = ids.collect(&:id)
+
+          # order the records by input ids
+          order_by_index = ActiveRecord::Base.send(
+                                  :sanitize_sql_array,
+                                  ["position((',' || samples.id || ',') in ?)",
+                                  ids.join(',') + ','] )
+          records.where(id: ids).order(order_by_index)
         elsif @project
           # A very elegant solution to sort assigned samples at a project level
 
@@ -179,7 +222,8 @@ class SampleDatatable < AjaxDatatablesRails::Base
           assigned = Sample
             .joins('LEFT OUTER JOIN "sample_my_modules" ON "sample_my_modules"."sample_id" = "samples"."id"')
             .joins('LEFT OUTER JOIN "my_modules" ON "my_modules"."id" = "sample_my_modules"."my_module_id"')
-            .where('"my_modules"."project_id" = ?', @project.id)
+            .joins('LEFT OUTER JOIN "experiments" ON "experiments"."id" = "my_modules"."experiment_id"')
+            .where('"experiments"."project_id" = ?', @project.id)
             .where('"my_modules"."nr_of_assigned_samples" > 0')
             .select('"samples"."id"')
             .distinct

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? && 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)

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

app/models/project.rb

@@ -126,4 +126,17 @@ class Project < ActiveRecord::Base
     organization.log(final)
   end
 
+  def assigned_samples
+    Sample.joins(:my_modules).where(my_modules: {
+                                      id: my_modules_ids.split(',')
+                                    })
+  end
+
+  def my_modules_ids
+    ids = active_experiments.map do |exp|
+      exp.my_modules.pluck(:id) if exp.my_modules
+    end
+    ids.delete_if { |i| i.flatten.empty? }
+    ids.join(', ')
+  end
 end

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>

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" %>">

config/routes.rb

@@ -103,16 +103,26 @@ 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)
+      # AJAX-loaded canvas edit mode (from canvas)
+      get 'canvas/edit', to: 'canvas#edit'
       get 'canvas/full_zoom', to: 'canvas#full_zoom' # AJAX-loaded canvas zoom
-      get 'canvas/medium_zoom', to: 'canvas#medium_zoom' # AJAX-loaded canvas zoom
+      # AJAX-loaded canvas zoom
+      get 'canvas/medium_zoom', to: 'canvas#medium_zoom'
       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 'archive' # archive experiment
+      get 'samples' # Samples for single project
+      # Renders sample datatable for single project (ajax action)
+      post 'samples_index'
+      post :delete_samples,
+           constraints: CommitParamRouting.new(
+             MyModulesController::DELETE_SAMPLES
+           ),
+           action: :delete_samples
     end
   end