Fixes bug with unreplaceable avatar. Removes obsolete rake tasks. Removes solr from serverscript. Slightly refactors edit page.

Gemfile.lock

@@ -191,7 +191,7 @@ GEM
     mime-types (2.6.2)
     mimemagic (0.3.0)
     mini_portile (0.6.2)
-    minitest (5.8.1)
+    minitest (5.8.2)
     mocha (1.1.0)
       metaclass (~> 0.0.1)
     multi_json (1.11.2)
@@ -451,6 +451,3 @@ DEPENDENCIES
   webmock
   whenever
   will_paginate
-
-BUNDLED WITH
-   1.10.6

app/controllers/users_controller.rb

@@ -262,6 +262,17 @@ class UsersController < ApplicationController
       :email,
       :password,
       :password_confirmation,
+      :avatar,
+      :delete_avatar,
+      :sex,
+      :yearofbirth,
+      :description,
+      :homepages_attributes,
+      :message_on_newsletter,
+      :message_on_message,
+      :message_on_new_phenotype,
+      :message_on_phenotype_comment_reply,
+      :message_on_snp_comment_reply,
     )
   end
 end

app/models/user.rb

@@ -2,14 +2,14 @@ class User < ActiveRecord::Base
   include PgSearchCommon
 
   has_attached_file :avatar,
-    styles: { medium: "300x300>", thumb: "100x100>#", head: "32x32#" },
+    styles: { medium: "300x300>", thumb: "100x100>", head: "32x32#" },
     default_url: 'standard_:style.png'
 
   before_validation :clear_avatar
 
   validates_attachment_size :avatar, less_than: 1.megabyte
   validates_attachment_content_type :avatar,
-    content_type: ['image/jpeg', 'image/png', 'image/gif']
+    content_type: /\Aimage\/.*\Z/
   # call on authlogic
   acts_as_authentic do |c| 
     # replace SHA512 by bcrypt

app/views/users/_edit.html.erb

@@ -1,6 +1,6 @@
-<% # helper thing so we don't have to put up fields into every page %>
-<%= nested_form_for(@user, :remote => true, :url => user_path, :html => { :class => "form-stacked",:multipart => true  } ) do |f| %>
-<%= render 'shared/error_messages', :target => @user %>
+<%= nested_form_for(@user, url: user_path, html: { multipart: true, class: "horizontal" }) do |f| %>
+
+<%= render 'shared/error_messages', target: @user %>
 <div id="post_errors" style="display:none"></div>
 <div id="tab-container">
   <ul class="nav nav-tabs">
@@ -14,37 +14,34 @@
 <div id="general">
 	<div class="well">
 		<h2>General Information</h2>
-		<%= image_tag @user.avatar.url(:thumb) %>
-		<%if @user.avatar_file_name != nil%>
-		<%= f.label(:delete_avatar, 'Delete current avatar') %><%= f.check_box(:delete_avatar) %>
-		<%end%>
-	<div class="clearfix">
-		<%= f.label :avatar, "Upload new avatar"%>
-		<%=f.file_field :avatar%>
-	</div>
-	
-	<div class="clearfix">
-		<%= f.label :name %>
+		<%= f.label :name, "Your username" %>
 		<%= f.text_field :name %>
-	</div>
+
+        <%= f.label :avatar, "Your current avatar" %>
+		<%= image_tag @user.avatar.url(:thumb) %>
+		<% if @user.avatar_file_name != nil %>
+            <div class="checkbox">
+            <%= f.check_box(:delete_avatar) %> Delete current avatar?
+            </div>
+		<% end %>
+
+		<%= f.label :avatar, "Upload new avatar"%>
+		<%= f.file_field :avatar %>
+
 	
-    <h5><%=link_to "Change eMail/Password",{ :controller => "users", :action => "changepassword",:id => @user.id }%></h5>
+    <h5><%= link_to "Change eMail/Password", {controller: "users", action: "changepassword", id: @user.id} %></h5>
 	            
-    <% if current_user.genotypes.length >= 1%><%= link_to "Add another genotyping!", :controller => "genotypes", :action => "new"%><% end %>
+    <% if current_user.genotypes.length >= 1%><%= link_to "Add another genotyping!", controller: "genotypes", action: "new"%><% end %>
 	</div>
 </div>
 
 <div id="phenotypes">
 	<div class="well">
 		<h2>Your Phenotypes</h2>
-		<div class="clearfix">
 		<%= f.label :sex, "Chromosomal Sex"%>
-		<%= f.select :sex, options_for_select(["XX", "XY", "other", "rather not say"], :selected => @user.sex) %>
-		</div>
-		<div class="clearfix">
+		<%= f.select :sex, options_for_select(["XX", "XY", "other", "rather not say"], selected: @user.sex) %>
 		<%= f.label :yearofbirth, "Year of Birth"%>
-		<%= f.select :yearofbirth, options_for_select(((1900..2011).to_a << "rather not say").reverse, :selected => @user.yearofbirth) %>
-		</div>
+		<%= f.select :yearofbirth, options_for_select(((1900..2015).to_a << "rather not say").reverse, selected: @user.yearofbirth) %>
        <h2>Additional phenotypes</h2>
 		<%= f.fields_for :user_phenotypes do |p| %>
             <% @phenotype = Phenotype.find_by_id(p.object.phenotype_id) %>
@@ -62,22 +59,18 @@
 	 	</div>
 <%end %>
 
- <%= link_to "Add a new phenotype", :controller => "phenotypes", :action => "new" %>
+ <%= link_to "Add a new phenotype", controller: "phenotypes", action: "new" %>
  	</div>
 </div>
 
 <div id="details">
 <div class="well">
 <h2>Details</h2>
-<div class="clearfix">
-	<p>Add or edit a description of yourself:<br/><%= f.text_area  :description, :size => "1x10" %></p>
-</div>
+	<p>Add or edit a description of yourself:<br/><%= f.text_area  :description, size: "1x10" %></p>
 <p>Please provide at least one homepage (or Twitter, Blog etc.) </p>
 <%= f.fields_for :homepages do |h| %>
-	<div class="clearfix">
 		Description <%= h.text_field :description %>
 		URL <%= h.url_field :url %><%= h.link_to_remove "Remove"%>
-	</div>
 <% end %>
 <%= f.link_to_add "Add a page", :homepages %>
 </div>
@@ -121,6 +114,6 @@
 </div>
 
 <div class="actions">
-	<%= f.submit "Update Information", :class => "btn btn-primary", :id => "update_user" %>
+	<%= f.submit "Update Information", class: "btn btn-primary", id: "update_user" %>
 </div>
 <% end %> 

app/views/users/edit.html.erb

@@ -1,4 +1,3 @@
 <legend>Edit your details</legend>
 <br/>
 <%= render 'edit' %>
-

lib/tasks/clean_snpedia.rake

@@ -1,14 +0,0 @@
-namespace :snpedia do
-	desc "kick out those nasty extra-crap things"
-	task :clean => :environment do
-		SnpediaPaper.all.each do |paper|
-			if paper.summary.index("}}") != nil
-				puts "OLD"
-				puts paper.summary
-				paper.update_attributes(:summary => paper.summary[0...paper.summary.index("}}")-1])
-				puts "NEW"
-				puts paper.summary
-			end
-		end
-	end
-end

lib/tasks/delete_brokensnps.rake

@@ -1,15 +0,0 @@
-# delete broken snps of user 
-
-namespace :snps do
-  desc "delete broken snps"
-  task :delete => :environment do
-    Snp.where("id >= 1941594 and id <= 1956090").find_each do |s|
-      s.user_snps.each do |us|
-        puts "delete user-snp: " + us.snp_name
-        UserSnp.delete(us)
-      end
-      puts "delete snp: " + s.name
-      Snp.delete(s)
-    end
-  end
-end

turnoffserver

@@ -1,5 +1,4 @@
 #/bin/bash
 screen -X -S Server quit
-screen -X -S Solr quit
 killall -9 redis-server
 screen -X -S Sidekiq quit