Merge branch 'master' into value_constraints_batch_1

PecanProject · Jun 19, 2015 · b1f5891 · b1f5891
2 parents 9c30227 + 0d852fe
commit b1f5891
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Showing 28 changed files with 78 additions and 98 deletions.
diff --git a/app/models/db_file.rb b/app/models/db_file.rb
@@ -30,8 +30,6 @@ class DBFile < ActiveRecord::Base
   def setup(user_id, upload, args = nil)
     self[:created_user_id] = user_id
     self[:updated_user_id] = user_id
-    self[:parent_id] = args[:parent_id]
-    self[:file_id] = args[:file_id]
     if upload # Uploaded file
       self[:file_name] =  upload.original_filename
       self[:md5] = Digest::MD5.file(upload.path).hexdigest

diff --git a/app/views/citations/new.html.erb b/app/views/citations/new.html.erb
@@ -62,7 +62,7 @@
         <div class="form-actions">
           <div class="button-group">
             <%= link_to( citations_path ) do %>
-              <button class="button" type="button">Back</button>
+              <button class="button" type="button"><i class="icon-arrow-left"></i> All Records</button>
             <% end%>
           </div>
 		      <div class="button-group pull-right">
@@ -73,6 +73,3 @@
     </div>
   </div>
 </div>
-
-
-
diff --git a/app/views/covariates/new.html.erb b/app/views/covariates/new.html.erb
@@ -76,7 +76,7 @@
           <div class="form-actions">
             <div class="button-group">
               <%= link_to( covariates_path ) do %>
-                <button class="button" type="button">Back</button>
+                <button class="button" type="button"><i class="icon-arrow-left"></i> All Records</button>
               <% end%>
             </div>
             <div class="button-group pull-right">

diff --git a/app/views/cultivars/new.html.erb b/app/views/cultivars/new.html.erb
@@ -31,7 +31,7 @@
         <div class="form-actions">
           <div class="button-group">
             <%= link_to( cultivars_path ) do %>
-              <button class="button" type="button">Back</button>
+              <button class="button" type="button"><i class="icon-arrow-left"></i> All Records</button>
             <% end%>
           </div>
 		      <div class="button-group pull-right">

diff --git a/app/views/dbfiles/edit.html.erb b/app/views/dbfiles/edit.html.erb
@@ -1,21 +1,21 @@
 <div class="content">
   <div class="container">
-  	<div class="sixteen columns">
-  	  <header>
-    		<h1>Editing File</h1>
-  	  <hearder>
-  		<%= form_for @file, :url => dbfile_path(@file) do |f| %>
-  		  <%= f.error_messages %>
+    <div class="sixteen columns">
+      <header>
+        <h1>Editing File</h1>
+      </header>
+      <%= form_for @file, :url => dbfile_path(@file) do |f| %>
+        <%= f.error_messages %>
         <div class="row">
-    			<div class="eight columns alpha">
-        		<%= f.label :machine_id %><br />
-        		<%= f.select :machine_id, Machine.all.collect { |p| [p.select_default, p.id] }, :class => "input-full" %>
-    		  </div> 
+          <div class="eight columns alpha">
+            <%= f.label :machine_id %><br />
+            <%= f.select :machine_id, Machine.all.collect { |p| [p.select_default, p.id] }, {}, { :class => "input-full" } %>
+          </div> 
         </div>
         <div class="row">
           <div class="sixteen columns alpha">
-          	<%= f.label :file_path %><br />
-          	<%= f.text_field :file_path, :class => "input-full" %>
+            <%= f.label :file_path %><br />
+            <%= f.text_field :file_path, :class => "input-full" %>
           </div>
         </div>
         <div class="row">

diff --git a/app/views/dbfiles/new.html.erb b/app/views/dbfiles/new.html.erb
@@ -1,21 +1,41 @@
-<h1>New File</h1>
-<%= form_for @file, :url => dbfiles_path, :html => { :multipart => true } do |f| %>
-  <%= f.error_messages %>
+<div class="content">
+  <div class="container">
+    <div class="sixteen columns">
+      <header>
+        <h1>New File</h1>
+      </header>
+      <%= form_for @file, :url => dbfiles_path do |f| %>
+      <%= f.error_messages %>
+        <div class="row">
+          <div class="eight columns alpha">
+            <%= f.label :machine_id %><br />
+            <%= f.select :machine_id, Machine.all.collect { |p| [p.select_default, p.id] }, {}, { :class => "input-full" } %>
+          </div> 
+        </div>
+        <div class="row">
+          <div class="sixteen columns alpha">
+            <%= f.label :file_path %><br />
+            <%= f.text_field :file_path, :class => "input-full" %>
+          </div>
+        </div>
+        <div class="row">
+          <div class="sixteen columns alpha">
+            <%= f.label :file_name %><br />
+            <%= f.text_field :file_name, :class => "input-full" %>
+          </div>
+        </div>
 
-  <p>
-    <%= f.label :machine_id %><br />
-    <%= f.select :machine_id, Machine.all.collect { |p| [p.select_default, p.id] } %>
-  </p>
-  <p>
-    <%= f.label :file_path %><br />
-    <%= f.text_field :file_path %>
-  </p>
-  <p>
-    <%= f.label :file_name %><br />
-    <%= f.text_field :file_name %>
-  </p>
-
-  <p>
-    <%= f.submit 'Create' %>
-  </p>
-<% end %>
+        <div class="form-actions">
+          <div class="button-group">
+            <%= link_to( dbfiles_path ) do %>
+              <button class="button" type="button"><i class="icon-arrow-left"></i> All Records</button>
+            <% end%>
+          </div>
+          <div class="button-group pull-right">
+            <%= f.submit 'Create', :class => "button button-primary" %>
+          </div>
+        </div>
+      <% end %>
+    </div>
+  </div>
+</div>
diff --git a/app/views/entities/new.html.erb b/app/views/entities/new.html.erb
@@ -25,7 +25,7 @@
         <div class="form-actions">
           <div class="button-group">
             <%= link_to( entities_path ) do %>
-              <button class="button" type="button">Back</button>
+              <button class="button" type="button"><i class="icon-arrow-left"></i> All Records</button>
             <% end%>
           </div>
 		      <div class="button-group pull-right">

diff --git a/app/views/formats/new.html.erb b/app/views/formats/new.html.erb
@@ -51,7 +51,7 @@
         <div class="form-actions">
           <div class="button-group">
             <%= link_to( formats_path ) do %>
-              <button class="button" type="button">Back</button>
+              <button class="button" type="button"><i class="icon-arrow-left"></i> All Records</button>
             <% end%>
           </div>
 		      <div class="button-group pull-right">

diff --git a/app/views/machines/new.html.erb b/app/views/machines/new.html.erb
@@ -18,7 +18,7 @@
         <div class="form-actions">
           <div class="button-group">
             <%= link_to( machines_path ) do %>
-              <button class="button" type="button">Back</button>
+              <button class="button" type="button"><i class="icon-arrow-left"></i> All Records</button>
             <% end%>
           </div>
 		      <div class="button-group pull-right">

diff --git a/app/views/managements/new.html.erb b/app/views/managements/new.html.erb
@@ -51,7 +51,7 @@
         <div class="form-actions">
           <div class="button-group">
             <%= link_to( managements_path ) do %>
-              <button class="button" type="button">Back</button>
+              <button class="button" type="button"><i class="icon-arrow-left"></i> All Records</button>
             <% end%>
           </div>
 		      <div class="button-group pull-right">

diff --git a/app/views/methods/new.html.erb b/app/views/methods/new.html.erb
@@ -26,7 +26,7 @@
         <div class="form-actions">
           <div class="button-group">
             <%= link_to( methods_path ) do %>
-              <button class="button" type="button">Back</button>
+              <button class="button" type="button"><i class="icon-arrow-left"></i> All Records</button>
             <% end%>
           </div>
 		      <div class="button-group pull-right">

diff --git a/app/views/pfts/new.html.erb b/app/views/pfts/new.html.erb
@@ -27,7 +27,7 @@
         <div class="form-actions">
           <div class="button-group">
             <%= link_to( pfts_path ) do %>
-              <button class="button" type="button">Back</button>
+              <button class="button" type="button"><i class="icon-arrow-left"></i> All Records</button>
             <% end%>
           </div>
 		      <div class="button-group pull-right">

diff --git a/app/views/priors/new.html.erb b/app/views/priors/new.html.erb
@@ -56,7 +56,7 @@
         <div class="form-actions">
           <div class="button-group">
             <%= link_to( priors_path ) do %>
-              <button class="button" type="button">Back</button>
+              <button class="button" type="button"><i class="icon-arrow-left"></i> All Records</button>
             <% end%>
           </div>
 		      <div class="button-group pull-right">

diff --git a/app/views/sites/new.html.erb b/app/views/sites/new.html.erb
@@ -415,11 +415,8 @@
 
         <div class="form-actions">
           <div class="button-group">
-            <%= link_to( @site ) do %>
-              <button class="button" type="button">Show</button>
-            <% end%>
             <%= link_to( sites_path ) do %>
-              <button class="button" type="button">Back</button>
+              <button class="button" type="button"><i class="icon-arrow-left"></i> All Records</button>
             <% end%>
           </div>
 					<div class="button-group pull-right">
@@ -429,12 +426,6 @@
 
       <% end %>
     <% end %>
-
-<span id='search_term'></span>
-<div id="index_table" style="display: none;">
-</div>
-
-<%= link_to 'Back', sites_path %>
     </div>
   </div>
 </div>

diff --git a/app/views/species/new.html.erb b/app/views/species/new.html.erb
@@ -419,7 +419,7 @@
         <div class="form-actions">
           <div class="button-group">
             <%= link_to( species_index_path ) do %>
-              <button class="button" type="button">Back</button>
+              <button class="button" type="button"><i class="icon-arrow-left"></i> All Records</button>
             <% end%>
           </div>
           <div class="button-group pull-right">

diff --git a/app/views/traits/edit.html.erb b/app/views/traits/edit.html.erb
@@ -89,7 +89,7 @@
                 </div>
                 <div class="four columns omega">
                   <%= f.label :access_level %>
-                  <%= f.select :access_level, [["1.Restricted",1],['2.EBI Researchers',2],['3.External Researchers',3],['4.Public',4]], :selected => 2,:class => "input-full" %>
+                  <%= f.select :access_level, [["1.Restricted",1],['2.EBI Researchers',2],['3.External Researchers',3],['4.Public',4]], :class => "input-full" %>
                 </div>
               </div>
 

diff --git a/app/views/traits/new.html.erb b/app/views/traits/new.html.erb
@@ -123,7 +123,7 @@
       <div class="row form-actions">
         <div class="button-group">
             <%= link_to(traits_path) do %>
-              <button class="button" type="button">Back</button>
+              <button class="button" type="button"><i class="icon-arrow-left"></i> All Records</button>
             <% end%>
           </div>
           <div class="button-group pull-right">

diff --git a/app/views/treatments/new.html.erb b/app/views/treatments/new.html.erb
@@ -43,7 +43,7 @@
         <div class="form-actions">
           <div class="button-group">
             <%= link_to( treatments_path ) do %>
-              <button class="button" type="button">Back</button>
+              <button class="button" type="button"><i class="icon-arrow-left"></i> All Records</button>
             <% end%>
           </div>
 		      <div class="button-group pull-right">

diff --git a/app/views/users/new.html.erb b/app/views/users/new.html.erb
@@ -82,7 +82,7 @@
         <div class="form-actions">
           <div class="button-group">
             <%= link_to( users_path ) do %>
-              <button class="button" type="button">Back</button>
+              <button class="button" type="button"><i class="icon-arrow-left"></i> All Records</button>
             <% end%>
           </div>
 		      <div class="button-group pull-right">

diff --git a/app/views/variables/new.html.erb b/app/views/variables/new.html.erb
@@ -49,7 +49,7 @@
         <div class="form-actions">
           <div class="button-group">
             <%= link_to( variables_path ) do %>
-              <button class="button" type="button">Back</button>
+              <button class="button" type="button"><i class="icon-arrow-left"></i> All Records</button>
             <% end%>
           </div>
 		      <div class="button-group pull-right">

diff --git a/app/views/yields/_index_table.html.erb b/app/views/yields/_index_table.html.erb
@@ -30,13 +30,13 @@
           <td class="center"><%= link_to_if y.site, y.site, y.site %></td>
           <td class="center"><%= link_to_if y.treatment, y.treatment, y.treatment %></td>
 
-          <% if ( current_user.access_level < y.access_level ) or ( y.user_id == current_user.id ) or ( current_user.page_access_level <= 2 ) %>
+          <% if (current_user.page_access_level <= 3) %>
           <td class="center">
 <%= select_tag 'checked-'+y.id.to_s, options_for_select([["failed",-1],["unchecked",0],["passed",1]],y.checked) %> <span id='checked_notify-<%= y.id %>'></span>
           </td>
 
           <% else %>
-          <td class="center"><%= ["failed","unchecked","passed"][y.checked-1] %></td>
+          <td class="center"><%= ["failed","unchecked","passed"][y.checked + 1] %></td>
           <% end %>
 
           <% if ( current_user.access_level < y.access_level ) or ( current_user.access_level = y.access_level and y.checked ) or ( y.user_id == current_user.id ) or ( current_user.page_access_level <= 2 )%>

diff --git a/app/views/yields/edit.html.erb b/app/views/yields/edit.html.erb
@@ -78,7 +78,7 @@
             <%= f.select :dateloc, options_for_select($dateloc_drop.sort, f.object.dateloc || $dateloc_drop_default), :class => "input-full" %>
             <br />
             <%= f.label :access_level %>
-            <%= f.select :access_level, [["1.Restricted",1],['2.EBI',2],['3.External',3],['4.Public',4]], :selected => current_user.access_level, :class => "input-full" %>
+            <%= f.select :access_level, [["1.Restricted",1],['2.EBI',2],['3.External',3],['4.Public',4]], :class => "input-full" %>
           </div>
           <div class="eight columns omega">
             <%= f.label :notes %>

diff --git a/app/views/yields/new.html.erb b/app/views/yields/new.html.erb
@@ -88,7 +88,7 @@
         <div class="form-actions">
           <div class="button-group">
             <%= link_to( yields_path ) do %>
-              <button class="button" type="button">Back</button>
+              <button class="button" type="button"><i class="icon-arrow-left"></i> All Records</button>
             <% end%>
           </div>
   	      <%= f.hidden_field :citation_id, :value => session['citation'] %>

diff --git a/lib/data_access.rb b/lib/data_access.rb
@@ -48,7 +48,7 @@ def all_limited(current_user)
       access_level = 4
     end
 
-    if respond_to?("checked") and respond_to?("user_id")
+    if column_names.include?("checked") and column_names.include?("user_id")
       where("(#{table_name}.checked >= ? and #{table_name}.access_level >= ?) or #{table_name}.user_id = ?",
             checked, access_level, user)
     else

diff --git a/spec/features/management_integration_spec.rb b/spec/features/management_integration_spec.rb
@@ -67,12 +67,12 @@
     end
     it 'should display the new management form' do
       visit(treatments_path)
-      first(:xpath, ".//a[text() = 'New Management for this treatment']").click
+      first(:xpath, ".//a[text() = 'Create a New Management for this Treatment']").click
       page.should_not have_content "We're sorry"
     end
     it 'should not have a citations select box' do
       visit(treatments_path)
-      first(:xpath, ".//a[text() = 'New Management for this treatment']").click
+      first(:xpath, ".//a[text() = 'Create a New Management for this Treatment']").click
       page.should_not have_selector(:xpath, '//select[@name="management[citation_id]"]')
     end      
   end

diff --git a/spec/features/pft_integration_spec.rb b/spec/features/pft_integration_spec.rb
@@ -139,7 +139,7 @@
   # test for redmine bug #1784
   it 'should not create a new PFT when the Back button is clicked' do
     visit '/pfts/new'
-    click_button 'Back'
+    click_button 'All Records'
     page.should_not have_content 'Pft was successfully created.'
   end
 

diff --git a/spec/features/treatment_integration_spec.rb b/spec/features/treatment_integration_spec.rb
@@ -47,7 +47,7 @@
 
     before :each do
       visit '/treatments/'
-      first(:xpath,".//a[@alt='edit' and contains(@href,'/edit')]").click
+      first(:xpath,".//a[@title='edit' and contains(@href,'/edit')]").click
     end
 
     it 'following edit link should return content "Editing Treatment" ' do

diff --git a/spec/views/treatments/index.html.erb_spec.rb b/spec/views/treatments/index.html.erb_spec.rb