Removed YUI, multiple improvements I can't remember since Xmas

.gitignore

@@ -15,3 +15,4 @@ vendor/cache/
 vendor/ruby
 public/assets
 config/deployvendor/ruby
+*.sublime*

Gemfile

@@ -14,7 +14,6 @@ gem 'jquery-ui-themes'
 gem 'jbuilder', '~> 2.0'
 gem 'highcharts-rails'
 gem 'jquery-tablesorter'
-gem 'yui-rails'
 gem 'jquery-cookie-rails'
 gem 'country-select'
 gem 'devise'

Gemfile.lock

@@ -250,8 +250,6 @@ GEM
       railties (>= 4.0)
       sprockets-rails (>= 2.0, < 4.0)
     will_paginate (3.1.5)
-    yui-rails (3.13.0.0.3.0)
-      rails (>= 3.1)
 
 PLATFORMS
   ruby
@@ -296,7 +294,6 @@ DEPENDENCIES
   uglifier (>= 1.3.0)
   web-console (~> 2.0)
   will_paginate
-  yui-rails
 
 RUBY VERSION
    ruby 2.3.0p0

app/assets/javascripts/application.js

@@ -11,5 +11,4 @@
 //= require jstree
 //= require tether
 //= require bootstrap
-//= require yui-min
 //= require_tree .

app/controllers/application_controller.rb

@@ -8,10 +8,12 @@ class ApplicationController < ActionController::Base
   before_action :authenticate_user!
 
   def layout_by_resource
-    if devise_controller? && resource_name == :client
-      'public'
-    else
+    if user_signed_in?
       'lims'
+    elsif client_signed_in?
+      'client'
+    else
+      'public'
     end
   end
 

app/helpers/application_helper.rb

@@ -72,25 +72,24 @@ def nah(value=nil, message="Not Available")
     end
   end
 
-
-  def destroy_link(params, title='delete')
+  def link_to_destroy(params, title='delete')
     link_to "#{icon(:remove)} #{title}".html_safe, params,
       data: { confirm: 'Are you sure you want to delete this entry?' },
       method: :delete, class: 'btn btn-outline-danger btn-sm',
       title: 'Delete Entry'
   end
 
-  def edit_link(params, title='edit')
+  def link_to_edit(params, title='edit')
     link_to "#{icon(:edit)} #{title}".html_safe, params,
       class: 'btn btn-sm btn-outline-primary', title: 'Edit Entry'
   end
 
-  def show_link(params, title='view')
+  def link_to_show(params, title='view')
     link_to "#{icon(:eye)} #{title}".html_safe, params,
       class: 'btn btn-sm btn-outline-primary', title: 'Show Entry'
   end
 
-  def new_link(title, params)
+  def link_to_new(title, params)
     title ||= 'new'
     link_to "#{icon(:'plus-square')} add #{title}".html_safe, params, class: 'btn btn-sm btn-outline-success'
   end

app/views/batches/batches/unprepped.html.erb

@@ -14,7 +14,7 @@
         <td><%= check_box_tag 'samples[]', s.id %></td>
         <td><%= s.barcode %></td>
         <td><%= s.collected_on %></td>
-        <%# show_link s.sample ? sample_sample_path(s.sample, s) : test_subject_sample_path(s.test_subject, s) %>
+        <%# link_to_show s.sample ? sample_sample_path(s.sample, s) : test_subject_sample_path(s.test_subject, s) %>
       </tr>
     <% end %>
 

app/views/bovine/index.html.erb

@@ -1,10 +1,10 @@
 <% title 'Home' %>
 <h1>Welcome to Metaboflo</h1>
 <p>
-	Welcome to the Metaboflo Laboratory Information Management System (LIMS). 
+	Welcome to the Metaboflo Laboratory Information Management System (LIMS).
 	Metaboflo is a central repository for study management and metabolomics scientific information.<br />
 </p>
-		
+
 <table class="list stats">
   <tr class="header">
     <th colspan="2">General Statistics</th>
@@ -37,9 +37,9 @@
   	<tr class="<%= cycle('odd', 'even') %>">
   		<td><%= experiment.name %></td>
   		<td><%= experiment.perform_on %></td>
-  		<td><%= show_link [experiment.sample, experiment] %></td>
-  		<td><%= edit_link edit_sample_experiment_path(experiment.sample, experiment) %></td>
-  		<td><%= destroy_link [experiment.sample, experiment] %></td>
+  		<td><%= link_to_show [experiment.sample, experiment] %></td>
+  		<td><%= link_to_edit edit_sample_experiment_path(experiment.sample, experiment) %></td>
+  		<td><%= link_to_destroy [experiment.sample, experiment] %></td>
   	</tr>
   	<% end %>
   </table>

app/views/data_file_types/edit.html.erb

@@ -2,4 +2,4 @@
 
 <%= render 'form' %>
 
-<%= show_link @data_file_type %>
+<%= link_to_show @data_file_type %>

app/views/data_file_types/index.html.erb

@@ -11,13 +11,13 @@
   <tr class="<%= cycle('odd', 'even') %>">
     <td><%= data_file_type.name %></td>
     <td><%= data_file_type.description %></td>
-    <td><%= show_link data_file_type %></td>
-    <td><%= edit_link edit_data_file_type_path(data_file_type) %></td>
-    <td><%= destroy_link(data_file_type) %></td>
+    <td><%= link_to_show data_file_type %></td>
+    <td><%= link_to_edit edit_data_file_type_path(data_file_type) %></td>
+    <td><%= link_to_destroy(data_file_type) %></td>
   </tr>
 <% end %>
 </table>
 
 <br />
 
-<%= new_link 'data file type', new_data_file_type_path %>
+<%= link_to_new 'data file type', new_data_file_type_path %>

app/views/data_file_types/show.html.erb

@@ -9,4 +9,4 @@
 </p>
 
 
-<%= edit_link edit_data_file_type_path(@data_file_type) %>
+<%= link_to_edit edit_data_file_type_path(@data_file_type) %>

app/views/data_files/index.html.erb

@@ -17,14 +17,14 @@
 		<td><%= link_to h(data_file.data_file_name), data_file.data.url %></td>
 		<td><%= number_to_human_size(data_file.data_file_size) %></td>
 		<td><%= link_to h(data_file.data_file_type.name), data_file_type_path(data_file.data_file_type) %></td>
-		<td><%= show_link experiment_data_file_path(data_file.experiment, data_file) %></td>
-		<td><%= destroy_link experiment_data_file_path(data_file.experiment, data_file) %></td>
+		<td><%= link_to_show experiment_data_file_path(data_file.experiment, data_file) %></td>
+		<td><%= link_to_destroy experiment_data_file_path(data_file.experiment, data_file) %></td>
 	</tr>
 	<% end %>
 </table>
 
 <br />
 
 <% if @experiment %>
-  <%= new_link 'data file for this experiment', new_experiment_data_file_path(@experiment) %>
+  <%= link_to_new 'data file for this experiment', new_experiment_data_file_path(@experiment) %>
 <% end %>

app/views/diets/edit.html.erb

@@ -1,5 +1,5 @@
 <h1>Editing diet</h1>
 
 <%= render :partial => 'form' %>
-	
-<%= show_link @diet %>
+
+<%= link_to_show @diet %>

app/views/diets/index.html.erb

@@ -9,13 +9,13 @@
 <% @diets.each do |diet| %>
   <tr>
     <td><%= diet.name %></td>
-    <td><%= show_link diet %></td>
-    <td><%= edit_link edit_diet_path(diet) %></td>
-    <td><%= destroy_link diet %></td>
+    <td><%= link_to_show diet %></td>
+    <td><%= link_to_edit edit_diet_path(diet) %></td>
+    <td><%= link_to_destroy diet %></td>
   </tr>
 <% end %>
 </table>
 
 <br />
 
-<%= new_link 'diet', new_diet_path %>
+<%= link_to_new 'diet', new_diet_path %>

app/views/diets/show.html.erb

@@ -10,7 +10,7 @@
 			<th>Name</th>
 			<th>Amount (%)</th>
 		</tr>
-		
+
 		<% @diet.diet_ingredients.each do |diet_ingredient| -%>
 		<tr>
 			<td><%= diet_ingredient.ingredient.name %></td>
@@ -29,7 +29,7 @@
 			<th>Name</th>
 			<th>Amount</th>
 		</tr>
-		
+
 		<% @diet.compositions.each do |composition| -%>
 		<tr>
 			<td><%= composition.nutrient.name %></td>
@@ -41,4 +41,4 @@
 
 <br />
 
-<%= edit_link edit_diet_path(@diet) %>
+<%= link_to_edit edit_diet_path(@diet) %>

app/views/experiments/edit.html.erb

@@ -2,4 +2,4 @@
 
 <%= render :partial => 'form' %>
 
-<%= show_link [@sample, @experiment] %>
+<%= link_to_show [@sample, @experiment] %>

app/views/experiments/index.html.slim

@@ -0,0 +1,46 @@
+h1= @sample.blank? ? 'Experiments' : "Experiments for sample # @sample "
+
+table.list
+  thead
+    tr
+      th= TestSubject.title
+      th Sample
+      th Title
+      th Type
+      th Description
+      th To be analyzed by
+      th To be analyzed on
+      th Analyzed by
+      th Analyzed on
+      th Data Files
+      th colspan="3"
+  tbody
+    - @experiments.each do |experiment|
+      tr
+        td= link_to(experiment.sample.root, experiment.sample.root)
+        td= link_to(experiment.sample, experiment.sample)
+        td= experiment.name
+        td= experiment.experiment_type.name unless experiment.experiment_type.nil?
+        td= truncate(experiment.description, :length => 50)
+        td= link_to(experiment.assigned_to.name, experiment.assigned_to) if experiment.assigned_to.present?
+        td= experiment.perform_on
+        td
+          - if experiment.performed_by
+            = link_to(experiment.performed_by.name, experiment.performed_by)
+          - else
+            = nah nil
+        td = nah experiment.performed_on
+        td
+          - if experiment.data_files.length > 0
+            ul
+              - experiment.data_files.each do |data_file|
+                li= link_to data_file.data_file_name, data_file.data.url
+          - else
+            = nah
+        td= link_to_show [experiment.sample, experiment]
+        td= link_to_edit edit_sample_experiment_path(experiment.sample, experiment)
+        td= link_to_destroy [experiment.sample, experiment]
+
+- if @sample.present?
+  = link_to_new 'experiment for this sample', new_sample_experiment_path(@sample)
+