Merge pull request #39 from biosistemika/lm-explvl-routes

Additional fixes related to experiment level routes

app/controllers/experiments_controller.rb

@@ -2,6 +2,7 @@ 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]
 
   # except parameter could be used but it is not working.
   layout :choose_layout
@@ -9,13 +10,13 @@ class ExperimentsController < ApplicationController
   def new
     @experiment = Experiment.new
     respond_to do |format|
-      format.json  {
-        render json:{
-          html: render_to_string( {
-            partial: "new_modal.html.erb"
-          })
+      format.json do
+        render json: {
+          html: render_to_string(
+            partial: 'new_modal.html.erb'
+          )
         }
-      }
+      end
     end
   end
 
@@ -69,16 +70,22 @@ class ExperimentsController < ApplicationController
 
   def set_experiment
     @experiment = Experiment.find_by_id(params[:id])
+    render_404 unless @experiment
   end
 
   def set_project
     @project = Project.find_by_id(params[:project_id])
+    render_404 unless @project
   end
 
   def experiment_params
     params.require(:experiment).permit(:name, :description)
   end
 
+  def check_view_permissions
+    render_403 unless can_view_experiment(@experiment)
+  end
+
   def choose_layout
     action_name.in?(['index', 'archive']) ? 'main' : 'fluid'
   end

app/controllers/projects_controller.rb

@@ -2,16 +2,17 @@ class ProjectsController < ApplicationController
   include SampleActions
   include RenamingUtil
 
-  before_action :load_vars, only: [:show, :edit, :update, :canvas,
+  before_action :load_vars, only: [:show, :edit, :update,
                                    :notifications, :reports,
-                                   :samples, :module_archive,
+                                   :samples, :experiment_archive,
                                    :delete_samples, :samples_index]
-  before_action :check_view_permissions, only: [:show, :canvas, :reports,
-                                                :samples, :module_archive,
+  before_action :check_view_permissions, only: [:show, :reports,
+                                                :samples, :experiment_archive,
                                                 :samples_index]
   before_action :check_view_notifications_permissions, only: [ :notifications ]
   before_action :check_edit_permissions, only: [ :edit ]
-  before_action :check_module_archive_permissions, only: [:module_archive]
+  before_action :check_experiment_archive_permissions,
+                only: [:experiment_archive]
 
   filter_by_archived = false
 
@@ -238,10 +239,6 @@ class ProjectsController < ApplicationController
     # This is the "info" view
   end
 
-  def canvas
-    # This is the "structure/overview/canvas" view
-  end
-
   def notifications
     @modules = @project
       .assigned_modules(current_user)
@@ -263,8 +260,7 @@ class ProjectsController < ApplicationController
     @organization = @project.organization
   end
 
-  def module_archive
-
+  def experiment_archive
   end
 
   def samples_index
@@ -310,10 +306,8 @@ class ProjectsController < ApplicationController
     end
   end
 
-  def check_module_archive_permissions
-    unless can_restore_archived_modules(@project)
-      render_403
-    end
+  def check_experiment_archive_permissions
+    render_403 unless can_view_project_archive(@project)
   end
 
   def choose_layout

app/helpers/permission_helper.rb

@@ -118,7 +118,13 @@ module PermissionHelper
       :can_edit_result_asset_in_module,
       :can_archive_result_asset_in_module,
       :can_add_samples_to_module,
-      :can_delete_samples_from_module
+      :can_delete_samples_from_module,
+      :can_create_experiment,
+      :can_edit_experiment,
+      :can_view_experiment,
+      :can_view_experiment_archive,
+      :can_archive_experiment,
+      :can_restore_experiment
     ] do |proxy, *args, &block|
       if args[0]
         my_module = args[0]
@@ -313,6 +319,10 @@ module PermissionHelper
     can_view_project(experiment.project)
   end
 
+  def can_view_experiment_archive(experiment)
+    can_view_project(experiment.project)
+  end
+
   def can_archive_experiment(project)
     is_user_or_higher_of_project(project)
   end

app/helpers/sidebar_helper.rb

@@ -13,7 +13,7 @@ module SidebarHelper
     when "samples"
       return samples_project_path(project)
     when "archive"
-      return module_archive_project_url(project)
+      return experiment_archive_project_url(project)
     else
       return project_path(project)
     end

app/views/projects/show.html.erb

@@ -2,4 +2,4 @@
 <%= render partial: "shared/sidebar" %>
 <%= render partial: "shared/secondary_navigation" %>
 
-TODO
+<!-- TODO -->

app/views/search/results/_experiments.html.erb

@@ -14,7 +14,7 @@
     <span>
       <%=t "search.index.project" %>
       <%= render partial: "search/results/partials/project_text.html.erb",
-                  locals: { project: experiment.project, link_to_page: :canvas } %>
+                  locals: { project: experiment.project, link_to_page: :show } %>
     </span>
     <br>
     <span>

app/views/search/results/_projects.html.erb

@@ -2,7 +2,7 @@
   <h5>
     <span class="glyphicon glyphicon-blackboard"></span>
     <%= render partial: "search/results/partials/project_text.html.erb",
-               locals: { project: project, query: search_query, link_to_page: :canvas } %>
+               locals: { project: project, query: search_query, link_to_page: :show } %>
   </h5>
 
   <p>

app/views/search/results/_workflows.html.erb

@@ -19,7 +19,7 @@
     <span>
       <%=t "search.index.project" %>
       <%= render partial: "search/results/partials/project_text.html.erb",
-                  locals: { project: workflow.experiment.project, link_to_page: :canvas } %>
+                  locals: { project: workflow.experiment.project, link_to_page: :show } %>
     </span>
     <br>
     <span>

app/views/search/results/partials/_my_module_text.html.erb

@@ -4,8 +4,8 @@
 
 <% if my_module.archived? %>
   <span class="label label-warning"><%=t "search.index.archived" %></span>
-  <% if can_view_project_archive(my_module.experiment.project) and can_restore_module(my_module) %>
-    <a href="<%= module_archive_project_url(my_module.experiment.project) %>">
+  <% if can_view_experiment_archive(my_module.experiment) and can_restore_module(my_module) %>
+    <a href="<%= module_archive_experiment_url(my_module.experiment) %>">
       <%= text %>
     </a>
   <% else %>
@@ -23,7 +23,7 @@
           <%= text %>
         </a>
       <% when :canvas %>
-        <a href="<%= canvas_project_path(my_module.experiment.project) %>">
+        <a href="<%= canvas_experiment_path(my_module.experiment) %>">
           <%= text %>
         </a>
       <% when :results %>

app/views/search/results/partials/_project_text.html.erb

@@ -13,8 +13,8 @@
   <% end %>
 <% else %>
   <% if can_view_project(project) %>
-    <% if link_to_page == :canvas %>
-      <a href="<%= canvas_project_path(project) %>">
+    <% if link_to_page == :show %>
+      <a href="<%= project_path(project) %>">
         <%= text %>
       </a>
     <%  else %>

app/views/search/results/partials/_tag_text.html.erb

@@ -2,7 +2,7 @@
 <% text = query.present? ? highlight(tag.name, query.strip.split(/\s+/)) : tag.name %>
 
 <% if can_view_project(tag.project) %>
-  <a href="<%= canvas_project_path(tag.project) %>">
+  <a href="<%= project_path(tag.project) %>">
     <%= text %>
   </a>
 <% else %>

app/views/shared/_secondary_navigation.html.erb

@@ -17,7 +17,7 @@
           <li>
         <% end %>
            <% if can_view_project(@project) %>
-              <a href="<%= canvas_experiment_url(@experiment) %>">
+              <a href="<%= project_url(@project) %>">
             <% end %>
             <%= @project.name %>
             <% if can_view_project(@project) %>
@@ -48,7 +48,7 @@
           </li>-->
           <% if can_view_project(@project) then %>
             <li id="canvas-nav-tab" class="<%= "active" if is_project_canvas? %>">
-              <a href="<%= canvas_project_url(@project) %>" title="<%=t "nav2.projects.canvas" %>">
+              <a href="<%= project_url(@project) %>" title="<%=t "nav2.projects.canvas" %>">
                 <span class="hidden-sm hidden-md"><%=t "nav2.projects.canvas" %></span>
                 <span class="hidden-xs hidden-lg glyphicon glyphicon-blackboard"></span>
               </a>
@@ -76,7 +76,7 @@
           <% end %>
           <% if can_view_project_archive(@project) then %>
             <li id="project-archive-nav-tab" class="<%= "active" if is_project_archive? %>">
-              <a href="<%= module_archive_project_url(@project) %>"><span class="glyphicon glyphicon-briefcase"></span></a>
+              <a href="<%= experiment_archive_project_url(@project) %>"><span class="glyphicon glyphicon-briefcase"></span></a>
             </li>
           <% end %>
 
@@ -150,7 +150,7 @@
           <li>
         <% end %>
            <% if can_view_project(@project) %>
-              <a href="<%= canvas_experiment_url(@experiment) %>">
+              <a href="<%= project_url(@project) %>">
             <% end %>
             <%= truncate( @project.name, length: 20 ) %>
             <% if can_view_project(@project) %>

config/routes.rb

@@ -101,7 +101,7 @@ Rails.application.routes.draw do
     get 'users/edit', to: 'user_projects#index_edit'
   end
 
-  resources :experiments, only: [:show] do
+  resources :experiments do
     member do
       get 'canvas' # Overview/structure for single experiment
       get 'canvas/edit', to: 'canvas#edit' # AJAX-loaded canvas edit mode (from canvas)