WORK IN PROGRESS - Show genotype parsing status to users

.rubocop.yml

@@ -28,3 +28,7 @@ Style/FrozenStringLiteralComment:
 
 Metrics/LineLength:
   Max: 100
+
+Metrics/BlockLength:
+  Exclude:
+    - 'spec/**/*.rb'

.travis.yml

@@ -5,6 +5,7 @@ addons:
   apt:
     packages:
     - libhiredis-dev
+  chrome: stable
   postgresql: '9.3'
 services:
   - redis-server

Gemfile

@@ -71,7 +71,8 @@ group :test do
   gem 'webmock'
   gem 'vcr'
   gem 'capybara'
-  gem 'poltergeist'
+  gem 'selenium-webdriver', require: false
+  gem 'chromedriver-helper'
   gem 'database_cleaner'
   gem 'timecop'
 end

Gemfile.lock

@@ -62,6 +62,8 @@ GEM
       tzinfo (~> 1.1)
     addressable (2.5.1)
       public_suffix (~> 2.0, >= 2.0.2)
+    archive-zip (0.7.0)
+      io-like (~> 0.3.0)
     arel (6.0.4)
     ast (2.3.0)
     authlogic (3.6.0)
@@ -86,9 +88,13 @@ GEM
       rack (>= 1.0.0)
       rack-test (>= 0.5.4)
       xpath (~> 2.0)
+    childprocess (0.8.0)
+      ffi (~> 1.0, >= 1.0.11)
+    chromedriver-helper (1.1.0)
+      archive-zip (~> 0.7.0)
+      nokogiri (~> 1.6)
     chronic (0.10.2)
     climate_control (0.2.0)
-    cliver (0.3.2)
     cocaine (0.5.8)
       climate_control (>= 0.0.3, < 1.0)
     coderay (1.1.1)
@@ -146,6 +152,7 @@ GEM
     http-cookie (1.0.3)
       domain_name (~> 0.5)
     i18n (0.8.1)
+    io-like (0.3.0)
     jquery-rails (4.3.1)
       rails-dom-testing (>= 1, < 3)
       railties (>= 4.2.0)
@@ -212,10 +219,6 @@ GEM
     plos (0.0.7)
       nokogiri
       rest-client
-    poltergeist (1.15.0)
-      capybara (~> 2.1)
-      cliver (~> 0.3.1)
-      websocket-driver (>= 0.2.0)
     power_assert (1.0.2)
     powerpack (0.1.1)
     pry (0.10.4)
@@ -317,6 +320,9 @@ GEM
       tilt (>= 1.1, < 3)
     scrypt (3.0.5)
       ffi-compiler (>= 1.0, < 2.0)
+    selenium-webdriver (3.8.0)
+      childprocess (~> 0.5)
+      rubyzip (~> 1.0)
     sentry-raven (2.7.1)
       faraday (>= 0.7.6, < 1.0)
     shellany (0.0.1)
@@ -376,9 +382,6 @@ GEM
       addressable (>= 2.3.6)
       crack (>= 0.3.2)
       hashdiff
-    websocket-driver (0.6.5)
-      websocket-extensions (>= 0.1.0)
-    websocket-extensions (0.1.2)
     whenever (0.9.7)
       chronic (>= 0.6.3)
     will_paginate (3.1.5)
@@ -397,6 +400,7 @@ DEPENDENCIES
   bcrypt-ruby
   capistrano (~> 2.0)
   capybara
+  chromedriver-helper
   composite_primary_keys (~> 8.0)
   database_cleaner
   dotenv-rails
@@ -420,7 +424,6 @@ DEPENDENCIES
   pg
   pg_search
   plos
-  poltergeist
   pry-rails
   rails (~> 4.2)
   rails3-generators
@@ -432,6 +435,7 @@ DEPENDENCIES
   rvm-capistrano (= 1.4.4)
   sanitize
   sass-rails
+  selenium-webdriver
   sentry-raven
   shoulda-context
   sidekiq

app/controllers/genotypes_controller.rb

@@ -6,10 +6,10 @@ class GenotypesController < ApplicationController
 
   def index
     @title = "Listing all genotypings"
-    @genotypes =
-      Genotype
-      .includes(:user)
-      .order("#{sort_column} #{sort_direction}")
+    @genotypes = Genotype
+                 .successfully_parsed
+                 .includes(:user)
+                 .order("#{sort_column} #{sort_direction}")
     @genotypes_paginate = @genotypes.paginate(page: params[:page], per_page: 20)
   end
 
@@ -19,8 +19,9 @@ def new
   end
 
   def create
-    @genotype = Genotype.create(genotype_params)
+    @genotype = Genotype.new(genotype_params)
     @genotype.user = current_user
+    @genotype.parse_status = 'queued'
     if @genotype.valid? && @genotype.save
       Preparsing.perform_async(@genotype.id)
       # award for genotyping-upload
@@ -36,7 +37,11 @@ def create
       if current_user.has_sequence == false
         current_user.toggle!(:has_sequence)
       end
-      redirect_to(current_user, notice: 'Genotype was successfully uploaded! Parsing and annotating might take a couple of <strike>hours</strike> days.')
+
+      redirect_to(
+        edit_user_path(current_user, anchor: 'genotypes'),
+        notice: t('.uploaded_successfully')
+      )
     else
       render action: 'new'
     end
@@ -61,6 +66,14 @@ def destroy
     redirect_to current_user
   end
 
+  def download
+    genotype = Genotype.find(params[:id])
+    send_data(
+      File.open(genotype.genotype.path),
+      filename: genotype.genotype_file_name
+    )
+  end
+
   private
 
   def sort_column
@@ -74,5 +87,4 @@ def sort_direction
   def genotype_params
     params.require(:genotype).permit(:genotype, :filetype)
   end
-
 end

app/helpers/application_helper.rb

@@ -17,4 +17,27 @@ def page_navigation_links(pages)
   def table_row_sequence_number(paginated, current_page_index)
     paginated.per_page * (paginated.current_page - 1) + current_page_index + 1
   end
+
+  def download_button(url)
+    link_to(url, class: 'btn btn-default btn-sm', title: t('download')) do
+      glyphicon('download-alt')
+    end
+  end
+
+  def delete_button(url, opts = {})
+    opts = {
+      method: 'delete',
+      class: 'btn btn-danger btn-sm',
+      title: t('delete'),
+      data: {
+        confirm: t('.confirm_delete', default: t('confirm_delete'))
+      }
+    }.deep_merge(opts)
+
+    link_to(url, opts) { glyphicon('trash') }
+  end
+
+  def glyphicon(name)
+    tag('span', class: "glyphicon glyphicon-#{name}")
+  end
 end

app/helpers/users_helper.rb

@@ -0,0 +1,13 @@
+# frozen_string_literal: true
+
+module UsersHelper
+  def genotype_parse_status_label(parse_status)
+    label_class = case parse_status
+                  when 'queued' then 'label-default'
+                  when 'parsing' then 'label-warning'
+                  when 'done' then 'label-success'
+                  when 'error' then 'label-danger'
+                  end
+    content_tag('span', parse_status, class: "label #{label_class}")
+  end
+end

app/models/genotype.rb

@@ -5,6 +5,8 @@ class Genotype < ActiveRecord::Base
   belongs_to :user
   has_many :user_snps, dependent: :delete_all
   validates_presence_of :user
+  validates :parse_status, inclusion: { in: %w[queued parsing done error] },
+                           allow_nil: true
 
   has_attached_file :genotype, url: '/data/:fs_filename',
                                path: "#{Rails.root}/public/data/:fs_filename"
@@ -14,6 +16,10 @@ class Genotype < ActiveRecord::Base
     size: { in: 0..400.megabytes }
   do_not_validate_attachment_file_type :genotype
 
+  def self.successfully_parsed
+    where("parse_status IS NULL OR parse_status = 'done'")
+  end
+
   def is_image?
     false
   end

app/views/genotypes/index.html.erb

@@ -31,7 +31,7 @@
         <td class="table-cell vertical-centered"><%= g.id %></td>
         <td class="table-cell vertical-centered"><%= g.created_at%></td>
         <td class="table-cell vertical-centered"><%= g.filetype %></td>
-        <td class="table-cell vertical-centered"><%= link_to "Download", '../data/' + g.fs_filename, class: "btn btn-default" %></td>
+        <td class="table-cell vertical-centered"><%= download_button(download_genotype_path(g)) %></td>
       </tr>
       <% end %>
     </table>

app/views/users/_edit.html.erb

@@ -4,12 +4,41 @@
   <div id="post_errors" style="display:none"></div>
 
   <ul class="nav nav-tabs" role="tablist">
-    <li role="presentation" class="active"><a href="#general" aria-controls="general" role="tab" data-toggle="tab">General</a></li>
-    <li role="presentation"><a href="#phenotypes" aria-controls="phenotypes" role="tab" data-toggle="tab">Your phenotypes</a></li>
-    <li role="presentation"><a href="#details" aria-controls="details" role="tab" data-toggle="tab">Details</a></li>
-    <li role="presentation"><a href="#openhumans" aria-controls="openhumans" role="tab" data-toggle="tab">Open Humans</a></li>
-    <li role="presentation"><a href="#notifications" aria-controls="notifications" role="tab" data-toggle="tab">Notifications</a></li>
-    <li role="presentation"><a href="#deleting" aria-controls="deleting" role="tab" data-toggle="tab">Deleting</a></li>
+    <li role="presentation" class="active">
+      <a href="#general" aria-controls="general" role="tab" data-toggle="tab">
+        General
+      </a>
+    </li>
+    <li role="presentation">
+      <a href="#genotypes" aria-controls="genotypes" role="tab" data-toggle="tab">
+        Your genotypes
+      </a>
+    </li>
+    <li role="presentation">
+      <a href="#phenotypes" aria-controls="phenotypes" role="tab" data-toggle="tab">
+        Your phenotypes
+      </a>
+    </li>
+    <li role="presentation">
+      <a href="#details" aria-controls="details" role="tab" data-toggle="tab">
+        Details
+      </a>
+    </li>
+    <li role="presentation">
+      <a href="#openhumans" aria-controls="openhumans" role="tab" data-toggle="tab">
+        Open Humans
+      </a>
+    </li>
+    <li role="presentation">
+      <a href="#notifications" aria-controls="notifications" role="tab" data-toggle="tab">
+        Notifications
+      </a>
+    </li>
+    <li role="presentation">
+      <a href="#deleting" aria-controls="deleting" role="tab" data-toggle="tab">
+        Deleting
+      </a>
+    </li>
   </ul>
 
   <div class="tab-content">
@@ -39,8 +68,48 @@
       </div>
     </div>
 
+    <div role="tabpanel" class="tab-pane well tabs__one-tab settings__genotypes" id="genotypes">
+      <h2 class="tabs__one-tab-title">Your Genotypes</h2>
+      <%= link_to(t('.genotypes.upload_new'), new_genotype_path, class: 'btn btn-default pull-right') %>
+      <table class="table">
+        <thead>
+          <tr>
+            <th><%= Genotype.human_attribute_name(:filetype) %></th>
+            <th><%= Genotype.human_attribute_name(:filename) %></th>
+            <th><%= Genotype.human_attribute_name(:created_at) %></th>
+            <th><%= Genotype.human_attribute_name(:parse_status) %></th>
+            <th><%= t('.genotypes.imported_snps') %></th>
+            <th></th>
+          </tr>
+        </thead>
+        <tbody>
+          <% @user.genotypes.order('created_at DESC').each do |genotype| %>
+            <tr>
+              <td><%= genotype.filetype %></td>
+              <td><%= genotype.genotype_file_name %></td>
+              <td><%= genotype.created_at %></td>
+              <td><%= genotype_parse_status_label(genotype.parse_status) %></td>
+              <td><%= genotype.user_snps.count %></td>
+              <td class="pull-right">
+                <%= download_button(download_genotype_path(genotype)) %>
+                <%= delete_button(
+                  genotype,
+                  data: {
+                    confirm: t('.genotypes.confirm_delete', file_name: genotype.genotype_file_name)
+                  }
+                ) %>
+              </td>
+            </tr>
+          <% end %>
+        </tbody>
+      </table>
+      <div class="well well-sm">
+        <%= t('.genotypes.parse_error_info', error_label: genotype_parse_status_label('error')).html_safe %>
+      </div>
+    </div>
+
     <div role="tabpanel" class="tab-pane well tabs__one-tab settings__phenotypes" id="phenotypes">
-  		<h2 class="tabs__one-tab-title">Your Phenotypes</h2>
+      <h2 class="tabs__one-tab-title">Your Phenotypes</h2>
       <div class="row settings__phenotypes-options">
         <div class="col-md-offset-1 col-md-4 settings__phenotypes-options-sex">
           <h4 class="text-center"><%= f.label :sex, "Chromosomal Sex"%></h4>
@@ -74,7 +143,7 @@
           <%= link_to "Add phenotype", {controller: "phenotypes", action: "new"}, class:"btn btn-default center-block settings__add-phenotype-button" %>
         </div>
       </div>
-   	</div>
+    </div>
 
     <div role="tabpanel" class="tab-pane well tabs__one-tab settings__details" id="details">
       <div class="clearfix">
@@ -118,14 +187,7 @@
       </dl>
     </div>
     <div role="tabpanel" class="tab-pane well tabs__one-tab settings__deleting" id="deleting">
-      <h2 class="tabs__one-tab-title">Deleting</h2>
-      <h3>Genotypes</h3>
-      <% if not @user.genotypes.empty? %>
-        <% @user.genotypes.each do |ug| %>
-          <p><%= link_to "Genotype #{ug.genotype_file_name}", ug, method: "delete", confirm: "Are you sure you want to delete genotype #{ug.genotype_file_name.to_s}?", class: "btn btn-default settings__deleting-button" %> </p>
-        <% end %>
-      <% end %>
-      <h3>Account</h3>
+      <h2 class="tabs__one-tab-title">Delete account</h2>
       <p><%= link_to "Delete this account", @user, method: "delete", class: "btn btn-default settings__deleting-button", data: { confirm: 'Are you sure you want to delete your account?' } %></p>
     </div>