fixed some minor bugs, added user-chrom.sex and user-yearofbirth

app/controllers/phenotypes_controller.rb

@@ -37,7 +37,7 @@ class PhenotypesController < ApplicationController
 	    @phenotype = Phenotype.find_by_characteristic(params[:phenotype][:characteristic])
 		end
 
-		unless @phenotype.known_phenotypes.include?(params[:user_phenotype][:variation])
+		if @phenotype.known_phenotypes.include?(params[:user_phenotype][:variation]) == false
 		  @phenotype.known_phenotypes << params[:user_phenotype][:variation]
 	  end
 	  

app/jobs/zipgenotypingfiles.rb

@@ -10,7 +10,7 @@ class Zipgenotypingfiles
       @user = User.find_by_id(up.user_id)
       print @user
       if @user.genotypes[0] != nil
-        @genotyping_files << @user.genotypes[0].fs_filename
+        @genotyping_files << @user.genotypes[0]
       end
     end
 
@@ -19,7 +19,7 @@ class Zipgenotypingfiles
       if File.exists?(::Rails.root.to_s+"/public/data/zip/"+phenotype_id.to_s+"."+@time.to_s.gsub(" ","_")+".zip") == false
         Zip::ZipFile.open(::Rails.root.to_s+"/public/data/zip/"+phenotype_id.to_s+"."+@time.to_s.gsub(" ","_")+".zip", Zip::ZipFile::CREATE) do |zipfile| 
           @genotyping_files.each do |gen_file|
-            zipfile.add(gen_file, "#{RAILS_ROOT}/public/data/"+ gen_file)
+            zipfile.add("user"+gen_file.user_id.to_s+"_file"+gen_file.id.to_s+"_yearofbirth"+gen_file.user.yearofbirth+"_sex"+gen_file.user.sex+"."+gen_file.filetype+".txt", "#{RAILS_ROOT}/public/data/"+ gen_file.fs_filename)
           end
         end
       end

app/models/phenotype.rb

@@ -9,7 +9,10 @@ class Phenotype < ActiveRecord::Base
 	   text :characteristic
    end
    
-   def known_phenotypes
-     read_attribute(:known_phenotypes) || []
+   after_create :default_array
+   
+   def default_array
+     self.known_phenotypes ||= []
    end
+   
 end

app/models/user.rb

@@ -1,7 +1,7 @@
 class User < ActiveRecord::Base
   has_attached_file :avatar, :styles => { :medium => "300x300>", :thumb => "100x100>#", :head => "32x32#" }, :default_url => '/images/standard_:style.png'
   
-  attr_accessible :user_phenotypes_attributes, :variation, :characteristic, :name, :password_confirmation, :password, :email, :description, :homepages, :homepages_attributes,:avatar, :phenotype_creation_counter, :phenotype_additional_counter,:delete_avatar
+  attr_accessible :user_phenotypes_attributes, :variation, :characteristic, :name, :password_confirmation, :password, :email, :description, :homepages, :homepages_attributes,:avatar, :sex, :yearofbirth, :phenotype_creation_counter, :phenotype_additional_counter,:delete_avatar
 	before_validation :clear_avatar
 	
 	validates_attachment_size :avatar, :less_than=>1.megabyte

app/views/users/_edit.html.erb

@@ -42,6 +42,14 @@
 <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.label :yearofbirth, "Year of Birth"%>
+		<%= f.select :yearofbirth, options_for_select(((1900..2011).to_a << "rather not say").reverse, :selected => @user.yearofbirth) %>
+		</div>
 		<%= f.fields_for :user_phenotypes do |p| %>
 		<div class="field">
 		

db/migrate/20110926172905_add_sex_age_columns_to_user.rb

@@ -0,0 +1,11 @@
+class AddSexAgeColumnsToUser < ActiveRecord::Migration
+  def self.up
+    add_column :users, :sex,    :string, :default => "rather not say"
+    add_column :users, :yearofbirth, :string, :default => "rather not say"
+  end
+
+  def self.down
+    remove_column :users, :sex
+    remove_column :users, :yearofbirth
+  end
+end

db/schema.rb

@@ -11,7 +11,7 @@
 #
 # It's strongly recommended to check this file into your version control system.
 
-ActiveRecord::Schema.define(:version => 20110926092220) do
+ActiveRecord::Schema.define(:version => 20110926172905) do
 
   create_table "achievements", :force => true do |t|
     t.text     "award"
@@ -30,18 +30,18 @@ ActiveRecord::Schema.define(:version => 20110926092220) do
   end
 
   create_table "homepages", :force => true do |t|
-    t.string   "url"
-    t.string   "description"
+    t.text     "url"
+    t.text     "description"
     t.datetime "created_at"
     t.datetime "updated_at"
     t.integer  "user_id"
   end
 
   create_table "mendeley_papers", :force => true do |t|
-    t.string   "first_author"
-    t.string   "title"
-    t.string   "mendeley_url"
-    t.string   "doi"
+    t.text     "first_author"
+    t.text     "title"
+    t.text     "mendeley_url"
+    t.text     "doi"
     t.integer  "pub_year"
     t.string   "uuid"
     t.boolean  "open_access"
@@ -52,7 +52,7 @@ ActiveRecord::Schema.define(:version => 20110926092220) do
   end
 
   create_table "messages", :force => true do |t|
-    t.string   "subject"
+    t.text     "subject"
     t.integer  "user_id"
     t.text     "body"
     t.boolean  "sent"
@@ -64,8 +64,8 @@ ActiveRecord::Schema.define(:version => 20110926092220) do
   end
 
   create_table "phenotype_comments", :force => true do |t|
-    t.string   "comment_text"
-    t.string   "subject"
+    t.text     "comment_text"
+    t.text     "subject"
     t.integer  "user_id"
     t.integer  "phenotype_id"
     t.integer  "reply_to_id"
@@ -83,9 +83,9 @@ ActiveRecord::Schema.define(:version => 20110926092220) do
   end
 
   create_table "plos_papers", :force => true do |t|
-    t.string   "first_author"
-    t.string   "title"
-    t.string   "doi"
+    t.text     "first_author"
+    t.text     "title"
+    t.text     "doi"
     t.datetime "pub_date"
     t.datetime "created_at"
     t.datetime "updated_at"
@@ -94,8 +94,8 @@ ActiveRecord::Schema.define(:version => 20110926092220) do
   end
 
   create_table "snp_comments", :force => true do |t|
-    t.string   "comment_text"
-    t.string   "subject"
+    t.text     "comment_text"
+    t.text     "subject"
     t.integer  "user_id"
     t.integer  "snp_id"
     t.datetime "created_at"
@@ -105,7 +105,7 @@ ActiveRecord::Schema.define(:version => 20110926092220) do
 
   create_table "snpedia_papers", :force => true do |t|
     t.string   "url"
-    t.string   "summary"
+    t.text     "summary"
     t.datetime "created_at"
     t.datetime "updated_at"
     t.integer  "snp_id"
@@ -119,15 +119,9 @@ ActiveRecord::Schema.define(:version => 20110926092220) do
     t.string   "allele_frequency"
     t.integer  "ranking"
     t.integer  "number_of_users",    :default => 0
-<<<<<<< HEAD
-    t.datetime "mendeley_updated",   :default => '2011-08-22 15:25:47'
-    t.datetime "plos_updated",       :default => '2011-08-22 15:25:47'
-    t.datetime "snpedia_updated",    :default => '2011-08-22 15:25:47'
-=======
-    t.datetime "mendeley_updated",   :default => '2011-08-13 15:18:53'
-    t.datetime "plos_updated",       :default => '2011-08-13 15:18:53'
-    t.datetime "snpedia_updated",    :default => '2011-08-13 15:18:53'
->>>>>>> baa3387dcbb11ce042acb224478742b6f726d077
+    t.datetime "mendeley_updated",   :default => '2011-08-22 23:08:27'
+    t.datetime "plos_updated",       :default => '2011-08-22 23:08:27'
+    t.datetime "snpedia_updated",    :default => '2011-08-22 23:08:27'
     t.datetime "created_at"
     t.datetime "updated_at"
   end
@@ -181,6 +175,8 @@ ActiveRecord::Schema.define(:version => 20110926092220) do
     t.boolean  "help_one",                     :default => false
     t.boolean  "help_two",                     :default => false
     t.boolean  "help_three",                   :default => false
+    t.string   "sex",                          :default => "rather not say"
+    t.string   "yearofbirth",                  :default => "rather not say"
   end
 
   add_index "users", ["email"], :name => "index_users_on_email", :unique => true