From 8aec988fbf4de7afb72e32328fef22f0f6d6b03f Mon Sep 17 00:00:00 2001
From: Helge Rausch <helge@rausch.io>
Date: Fri, 23 Oct 2015 08:05:46 +0200
Subject: [PATCH 01/11] Move configuration into environment

---
 .env.example                                  | 14 +++++++++++
 .gitignore                                    |  1 +
 .travis.yml                                   | 13 +++-------
 Gemfile                                       |  2 ++
 Gemfile.lock                                  |  8 ++++++
 README.md                                     |  9 ++-----
 Rakefile                                      |  3 ++-
 app/controllers/fitbit_profiles_controller.rb |  6 +++--
 app/workers/fitbit_edit.rb                    |  3 ++-
 app/workers/fitbit_endsubscription.rb         |  3 ++-
 app/workers/fitbit_init.rb                    |  3 ++-
 app/workers/fitbit_notification.rb            |  3 ++-
 app/workers/plos_search.rb                    |  3 +--
 config/app_config.yml.example                 | 25 -------------------
 config/application.rb                         |  6 +----
 config/initializers/0_load_app_config.rb      |  2 --
 config/initializers/airbrake.rb               |  4 +--
 config/initializers/mendeley.rb               |  2 +-
 config/initializers/recaptcha.rb              |  4 +--
 config/initializers/secret_token.rb           | 11 +++-----
 config/initializers/sidekiq.rb                |  6 ++---
 21 files changed, 57 insertions(+), 74 deletions(-)
 create mode 100644 .env.example
 delete mode 100644 config/app_config.yml.example
 delete mode 100644 config/initializers/0_load_app_config.rb

diff --git a/.env.example b/.env.example
new file mode 100644
index 0000000..b71f09b
--- /dev/null
+++ b/.env.example
@@ -0,0 +1,14 @@
+export SECRET_KEY_BASE=foo
+export SECRET_TOKEN=bar
+export RAILS_ENV=development
+export POSTGRES_URL="postgres://localhost/snpr_$RAILS_ENV"
+#export REDIS_URL=
+export FITBIT_CONSUMER_KEY=foo
+export FITBIT_CONSUMER_SECRET=bar
+export PLOS_API_KEY=foo
+export RECAPTCHA_PRIVATE_KEY=foo
+export RECAPTCHA_PUBLIC_KEY=bar
+export SIDEKIQ_PASSWORD=foo
+export MENDELEY_CONSUMER_KEY=foo
+export ERRBIT_API_KEY=foo
+export ERRBIT_HOST=localhost
diff --git a/.gitignore b/.gitignore
index c553a73..0cd3f4f 100644
--- a/.gitignore
+++ b/.gitignore
@@ -31,3 +31,4 @@ tmp/pids/server.pid
 vendor/bundle
 vendor/cache
 logfile
+.env
diff --git a/.travis.yml b/.travis.yml
index 4339df2..13d846c 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -1,11 +1,11 @@
-language: ruby # Defaults to ruby, but travis-ci recommends making this explicit.
+language: ruby
 sudo: false
 cache: bundler
 addons:
   apt:
     packages:
     - libhiredis-dev
-  postgresql: "9.2"
+  postgresql: '9.3'
 services:
   - redis-server
 rvm:
@@ -14,11 +14,6 @@ env: DB=postgres CI=1
 bundler_args: --without development debug
 before_script:
   - cp config/database.yml.ci config/database.yml
-  - cp config/app_config.yml.example config/app_config.yml
-  - echo "foo" > mail_username.txt
-  - echo "bar" > mail_password.txt
-  - echo "secret-token" > secret_token
-  - echo "secret-key-base" > secret_key_base
-  - psql -c 'create database snpr_test;' -U postgres
+  - cp .env.example .env
   - bundle exec rake db:setup
-script: "bundle exec rake test"
+script: bundle exec rake
diff --git a/Gemfile b/Gemfile
index 2eea1e3..67761a8 100644
--- a/Gemfile
+++ b/Gemfile
@@ -1,5 +1,7 @@
 source 'http://rubygems.org'
 
+gem 'dotenv-rails', groups: %i(development test)
+
 gem 'rails', '~> 4.2.0'
 gem 'authlogic' # lots of user-related magic
 gem 'i18n', '>= 0.6.6'
diff --git a/Gemfile.lock b/Gemfile.lock
index ddbc1f8..075f94d 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -106,6 +106,10 @@ GEM
     docile (1.1.5)
     domain_name (0.5.24)
       unf (>= 0.0.5, < 1.0.0)
+    dotenv (2.0.2)
+    dotenv-rails (2.0.2)
+      dotenv (= 2.0.2)
+      railties (~> 4.0)
     dynamic_form (1.1.4)
     erubis (2.7.0)
     execjs (2.6.0)
@@ -375,6 +379,7 @@ DEPENDENCIES
   capybara
   composite_primary_keys (~> 8.0)
   database_cleaner
+  dotenv-rails
   dynamic_form
   execjs
   factory_girl_rails
@@ -426,3 +431,6 @@ DEPENDENCIES
   whenever
   will_paginate
   yui-compressor
+
+BUNDLED WITH
+   1.10.6
diff --git a/README.md b/README.md
index e5585ce..50e1987 100644
--- a/README.md
+++ b/README.md
@@ -38,13 +38,7 @@ rake db:seed OR rake db:setup (which also sets up the entire db)
 # edit database.yml to point to your postgresql database
 cp config/database.yml.example config/database.yml
 
-cp config/app_config.yml.example config/app_config.yml
-```
-
-## Generate Secret Token
-
-```
-bundle rake secret > secret_token
+cp .env.example .env
 ```
 
 ## Initialize Database
@@ -58,6 +52,7 @@ bundle exec rake db:setup
 ```
 bundle exec rake
 ```
+This runs RSpec tests as well as the **legacy** test/unit ones.
 
 # Usage
 
diff --git a/Rakefile b/Rakefile
index f32fb01..7aff7d5 100644
--- a/Rakefile
+++ b/Rakefile
@@ -6,4 +6,5 @@ require 'rake'
 
 Snpr::Application.load_tasks
 
-task :test => :spec
+task test: :spec
+task default: :test
diff --git a/app/controllers/fitbit_profiles_controller.rb b/app/controllers/fitbit_profiles_controller.rb
index 772bf28..822516a 100644
--- a/app/controllers/fitbit_profiles_controller.rb
+++ b/app/controllers/fitbit_profiles_controller.rb
@@ -162,7 +162,8 @@ class FitbitProfilesController < ApplicationController
     print @user
     @fitbit_profile = @user.fitbit_profile 
     print @fitbit_profile
-    client = Fitgem::Client.new({:consumer_key => APP_CONFIG[:fitbit_consumer_key], :consumer_secret => APP_CONFIG[:fitbit_consumer_secret]})
+    client = Fitgem::Client.new(consumer_key: ENV.fetch('FITBIT_CONSUMER_KEY'),
+                                consumer_secret: ENV.fetch('FITBIT_CONSUMER_SECRET'))
     request_token = client.request_token
     @fitbit_profile.request_token = request_token.token
     @fitbit_profile.request_secret = request_token.secret
@@ -174,7 +175,8 @@ class FitbitProfilesController < ApplicationController
     @user = current_user
     @fitbit_profile = @user.fitbit_profile
     if params[:oauth_token] && params[:oauth_verifier]
-      @client = Fitgem::Client.new(:consumer_key => APP_CONFIG[:fitbit_consumer_key], :consumer_secret => APP_CONFIG[:fitbit_consumer_secret])
+      @client = Fitgem::Client.new(consumer_key: ENV.fetch('FITBIT_CONSUMER_KEY'),
+                                   consumer_secret: ENV.fetch('FITBIT_CONSUMER_SECRET'))
       token = params[:oauth_token]
       secret = @fitbit_profile.request_secret
       verifier = params[:oauth_verifier]
diff --git a/app/workers/fitbit_edit.rb b/app/workers/fitbit_edit.rb
index fd746c2..15e1bcd 100644
--- a/app/workers/fitbit_edit.rb
+++ b/app/workers/fitbit_edit.rb
@@ -6,7 +6,8 @@ class FitbitEdit
 
    def perform(fitbit_profile_id)
      @fitbit_profile = FitbitProfile.find_by_id(fitbit_profile_id)
-     @client = Fitgem::Client.new(:consumer_key => APP_CONFIG[:fitbit_consumer_key], :consumer_secret => APP_CONFIG[:fitbit_consumer_secret])
+     @client = Fitgem::Client.new(consumer_key: ENV.fetch('FITBIT_CONSUMER_KEY'),
+                                  consumer_secret: ENV.fetch('FITBIT_CONSUMER_SECRET'))
      @client.reconnect(@fitbit_profile.access_token, @fitbit_profile.access_secret)
      @return_value = @client.create_subscription({:type => :all, :subscription_id => @fitbit_profile.id})
      puts "subscription returned: "+ @return_value[0]
diff --git a/app/workers/fitbit_endsubscription.rb b/app/workers/fitbit_endsubscription.rb
index 1b06991..18e0046 100644
--- a/app/workers/fitbit_endsubscription.rb
+++ b/app/workers/fitbit_endsubscription.rb
@@ -6,7 +6,8 @@ class FitbitEndSubscription
 
    def perform(fitbit_profile_id)
      @fitbit_profile = FitbitProfile.find_by_id(fitbit_profile_id)
-     @client = Fitgem::Client.new(:consumer_key => APP_CONFIG[:fitbit_consumer_key], :consumer_secret => APP_CONFIG[:fitbit_consumer_secret])
+     @client = Fitgem::Client.new(consumer_key: ENV.fetch('FITBIT_CONSUMER_KEY'),
+                                  consumer_secret: ENV.fetch('FITBIT_CONSUMER_SECRET'))
      @client.reconnect(@fitbit_profile.access_token, @fitbit_profile.access_secret)
      @client.remove_subscription({:type => :all, :subscriber_id => "general", :subscription_id => @fitbit_profile.id})
      @fitbit_profile.destroy()
diff --git a/app/workers/fitbit_init.rb b/app/workers/fitbit_init.rb
index 8c06ad1..d1f36c4 100644
--- a/app/workers/fitbit_init.rb
+++ b/app/workers/fitbit_init.rb
@@ -5,7 +5,8 @@ class FitbitInit
    sidekiq_options :queue => :fitbit, :retry => 5, :unique => true
 
    def perform(fitbit_profile_id)
-     @client = Fitgem::Client.new(:consumer_key => APP_CONFIG[:fitbit_consumer_key], :consumer_secret => APP_CONFIG[:fitbit_consumer_secret])
+     @client = Fitgem::Client.new(consumer_key: ENV.fetch('FITBIT_CONSUMER_KEY'),
+                                  consumer_secret: ENV.fetch('FITBIT_CONSUMER_SECRET'))
      fitbit_profile = FitbitProfile.find_by_id(fitbit_profile_id)
      @client.reconnect(fitbit_profile.access_token, fitbit_profile.access_secret)
      fitbit_id = @client.user_info["user"]["encodedId"]
diff --git a/app/workers/fitbit_notification.rb b/app/workers/fitbit_notification.rb
index 71a813c..4d2fe81 100644
--- a/app/workers/fitbit_notification.rb
+++ b/app/workers/fitbit_notification.rb
@@ -9,7 +9,8 @@ class FitbitNotification
      notification.each do |n|
        @fitbit_profile = FitbitProfile.find_by_id(n["subscriptionId"])
        if @fitbit_profile != nil
-         @client = Fitgem::Client.new(:consumer_key => APP_CONFIG[:fitbit_consumer_key], :consumer_secret => APP_CONFIG[:fitbit_consumer_secret])
+         @client = Fitgem::Client.new(consumer_key: ENV.fetch('FITBIT_CONSUMER_KEY'),
+                                      consumer_secret: ENV.fetch('FITBIT_CONSUMER_SECRET'))
          @client.reconnect(@fitbit_profile.access_token, @fitbit_profile.access_secret)
          puts n
          puts n["collectionType"]
diff --git a/app/workers/plos_search.rb b/app/workers/plos_search.rb
index bb51aeb..01136b8 100644
--- a/app/workers/plos_search.rb
+++ b/app/workers/plos_search.rb
@@ -84,7 +84,6 @@ class PlosSearch
   end
 
   def self.api_key
-    # TODO: put in APP_CONFIG
-    File.read(Rails.root.join("key_plos.txt")).strip
+    ENV.fetch('PLOS_API_KEY')
   end
 end
diff --git a/config/app_config.yml.example b/config/app_config.yml.example
deleted file mode 100644
index d9e1536..0000000
--- a/config/app_config.yml.example
+++ /dev/null
@@ -1,25 +0,0 @@
-default: &default
-  fitbit_consumer_key:
-  fitbit_consumer_secret:
-  mendeley:
-    consumer_key:
-  recaptcha:
-    public_key: foo
-    private_key: bar
-  sidekiq:
-    user: admin
-    password: password
-  devise: password
-  errbit:
-    api_key: gobbledigook
-    host: url
-
-production:
-  <<: *default
-
-development:
-  <<: *default
-
-test:
-  <<: *default
-
diff --git a/config/application.rb b/config/application.rb
index 2419059..48e1f03 100644
--- a/config/application.rb
+++ b/config/application.rb
@@ -2,11 +2,7 @@ require File.expand_path('../boot', __FILE__)
 
 require 'rails/all'
 
-if defined?(Bundler)
-  # Require the gems listed in Gemfile, including any gems
-  # you've limited to :test, :development, or :production.
-  Bundler.require(*Rails.groups)
-end
+Bundler.require(*Rails.groups)
 
 module Snpr
   class Application < Rails::Application
diff --git a/config/initializers/0_load_app_config.rb b/config/initializers/0_load_app_config.rb
deleted file mode 100644
index 4e5bbdd..0000000
--- a/config/initializers/0_load_app_config.rb
+++ /dev/null
@@ -1,2 +0,0 @@
-raw_config = File.read("#{Rails.root}/config/app_config.yml")
-APP_CONFIG = YAML.load(raw_config)[Rails.env].symbolize_keys
diff --git a/config/initializers/airbrake.rb b/config/initializers/airbrake.rb
index 8f6f488..c644ca1 100644
--- a/config/initializers/airbrake.rb
+++ b/config/initializers/airbrake.rb
@@ -1,7 +1,7 @@
 # This is the config to talk to opensnperr.herokuapp.com
 Airbrake.configure do |config|
-  config.api_key = APP_CONFIG[:errbit]['api_key']
-  config.host    = APP_CONFIG[:errbit]['host']
+  config.api_key = ENV.fetch('ERRBIT_API_KEY')
+  config.host    = ENV.fetch('ERRBIT_HOST')
   config.port    = 80
   config.secure  = config.port == 443
   config.environment_name = Rails.env.production? ? `hostname` : Rails.env
diff --git a/config/initializers/mendeley.rb b/config/initializers/mendeley.rb
index 86a5cff..7fe405b 100644
--- a/config/initializers/mendeley.rb
+++ b/config/initializers/mendeley.rb
@@ -1 +1 @@
-Mendeley.consumer_key = APP_CONFIG[:mendeley]['consumer_key']
+Mendeley.consumer_key = ENV.fetch('MENDELEY_CONSUMER_KEY')
diff --git a/config/initializers/recaptcha.rb b/config/initializers/recaptcha.rb
index 301b881..489ec65 100644
--- a/config/initializers/recaptcha.rb
+++ b/config/initializers/recaptcha.rb
@@ -1,4 +1,4 @@
 Recaptcha.configure do |config|
-  config.public_key  = APP_CONFIG[:recaptcha]['public_key']
-  config.private_key = APP_CONFIG[:recaptcha]['private_key']
+  config.public_key  = ENV.fetch('RECAPTCHA_PUBLIC_KEY')
+  config.private_key = ENV.fetch('RECAPTCHA_PRIVATE_KEY')
 end
diff --git a/config/initializers/secret_token.rb b/config/initializers/secret_token.rb
index 188ec87..4927177 100644
--- a/config/initializers/secret_token.rb
+++ b/config/initializers/secret_token.rb
@@ -1,9 +1,4 @@
-# TODO: Move to environment variables
-begin 
-  Snpr::Application.configure do
-    config.secret_token = File.read(Rails.root.join('secret_token'))
-    config.secret_key_base = File.read(Rails.root.join('secret_key_base'))
-  end
-rescue LoadError, Errno::ENOENT => e
-  raise "Secret token couldn't be loaded! Error: #{e}"
+Snpr::Application.configure do
+  config.secret_token = ENV.fetch('SECRET_TOKEN')
+  config.secret_key_base = ENV.fetch('SECRET_KEY_BASE')
 end
diff --git a/config/initializers/sidekiq.rb b/config/initializers/sidekiq.rb
index 3f61644..a6b8553 100644
--- a/config/initializers/sidekiq.rb
+++ b/config/initializers/sidekiq.rb
@@ -3,8 +3,6 @@ require 'sidekiq/web'
 require 'sidekiq/limit_fetch'
 
 
-Sidekiq::Web.use(Rack::Auth::Basic) do |user, password|
-  u = (APP_CONFIG[:sidekiq].try(:[], "user") || "admin")
-  p = (APP_CONFIG[:sidekiq].try(:[], "password") || "password")
-  [user, password] == [u, p]
+Sidekiq::Web.use(Rack::Auth::Basic) do |_user, password|
+  password == ENV.fetch('SIDEKIQ_PASSWORD')
 end

From e5428701ce3d491c03fd4b2ead32d3a368740734 Mon Sep 17 00:00:00 2001
From: Helge Rausch <helge@rausch.io>
Date: Fri, 23 Oct 2015 21:19:52 +0200
Subject: [PATCH 02/11] Add script for extracting env vars for nginx

---
 bin/extract_env_var_names_for_nginx      | 7 +++++++
 {script => bin}/munin/parse_queue_length | 0
 {script => bin}/munin/requests.sh        | 0
 {script => bin}/munin/response_time.sh   | 0
 {script => bin}/munin/sidekiq_workers.sh | 0
 script/rails                             | 6 ------
 6 files changed, 7 insertions(+), 6 deletions(-)
 create mode 100755 bin/extract_env_var_names_for_nginx
 rename {script => bin}/munin/parse_queue_length (100%)
 rename {script => bin}/munin/requests.sh (100%)
 rename {script => bin}/munin/response_time.sh (100%)
 rename {script => bin}/munin/sidekiq_workers.sh (100%)
 delete mode 100644 script/rails

diff --git a/bin/extract_env_var_names_for_nginx b/bin/extract_env_var_names_for_nginx
new file mode 100755
index 0000000..f66bc29
--- /dev/null
+++ b/bin/extract_env_var_names_for_nginx
@@ -0,0 +1,7 @@
+#!/usr/bin/env ruby
+
+env_file_name = ARGV[0] || '.env.example'
+puts File.read(env_file_name)
+         .split(/ |=/)
+         .grep(/\A[_A-Z0-9]+\z/)
+         .map { |var| "env #{var};" }
diff --git a/script/munin/parse_queue_length b/bin/munin/parse_queue_length
similarity index 100%
rename from script/munin/parse_queue_length
rename to bin/munin/parse_queue_length
diff --git a/script/munin/requests.sh b/bin/munin/requests.sh
similarity index 100%
rename from script/munin/requests.sh
rename to bin/munin/requests.sh
diff --git a/script/munin/response_time.sh b/bin/munin/response_time.sh
similarity index 100%
rename from script/munin/response_time.sh
rename to bin/munin/response_time.sh
diff --git a/script/munin/sidekiq_workers.sh b/bin/munin/sidekiq_workers.sh
similarity index 100%
rename from script/munin/sidekiq_workers.sh
rename to bin/munin/sidekiq_workers.sh
diff --git a/script/rails b/script/rails
deleted file mode 100644
index f8da2cf..0000000
--- a/script/rails
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env ruby
-# This command will automatically be run when you run "rails" with Rails 3 gems installed from the root of your application.
-
-APP_PATH = File.expand_path('../../config/application',  __FILE__)
-require File.expand_path('../../config/boot',  __FILE__)
-require 'rails/commands'

From 08583082109408e40cd7fecbcaa936f66ec7bb93 Mon Sep 17 00:00:00 2001
From: Helge Rausch <helge@rausch.io>
Date: Fri, 23 Oct 2015 21:43:25 +0200
Subject: [PATCH 03/11] Use sass-rails for CSS compression

---
 Gemfile                           | 17 ++++++++---------
 Gemfile.lock                      | 12 ++++++++----
 config/environments/production.rb |  2 +-
 3 files changed, 17 insertions(+), 14 deletions(-)

diff --git a/Gemfile b/Gemfile
index 67761a8..d010335 100644
--- a/Gemfile
+++ b/Gemfile
@@ -6,10 +6,10 @@ gem 'rails', '~> 4.2.0'
 gem 'authlogic' # lots of user-related magic
 gem 'i18n', '>= 0.6.6'
 gem 'rails3-generators'
-gem "jquery-rails"
-gem 'bcrypt-ruby', :require => "bcrypt"
+gem 'jquery-rails'
+gem 'bcrypt-ruby', :require => 'bcrypt'
 gem 'sanitize'
-gem "recaptcha", :require => "recaptcha/rails"
+gem 'recaptcha', :require => 'recaptcha/rails'
 gem 'dynamic_form'
 gem 'lograge'
 gem 'slop'
@@ -34,13 +34,13 @@ gem 'pg_search'
 # so we can create zip-files for genotypes
 gem 'rubyzip'
 
-gem "will_paginate"
+gem 'will_paginate'
 gem 'nested_form', github: 'ryanb/nested_form'
 gem 'json'
 gem 'mediawiki-gateway'
 gem 'paperclip', '~> 4.0 '
 gem 'friendly_id'
-gem 'recommendify', github: 'paulasmuth/recommendify', :ref => "34308c4"
+gem 'recommendify', github: 'paulasmuth/recommendify', :ref => '34308c4'
 
 # background jobs
 gem 'sidekiq'
@@ -55,10 +55,9 @@ gem 'whenever', require: false
 gem 'therubyracer'
 gem 'execjs'
 gem 'uglifier'
-gem 'yui-compressor'
-gem "twitter-bootstrap-rails"
-gem "jquery-ui-rails"
-gem "sass"
+gem 'twitter-bootstrap-rails'
+gem 'jquery-ui-rails'
+gem 'sass-rails'
 
 #group :production do
 #	gem 'rpm_contrib'
diff --git a/Gemfile.lock b/Gemfile.lock
index 075f94d..0877b70 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -293,7 +293,13 @@ GEM
       crass (~> 1.0.2)
       nokogiri (>= 1.4.4)
       nokogumbo (= 1.4.1)
-    sass (3.4.13)
+    sass (3.4.19)
+    sass-rails (5.0.4)
+      railties (>= 4.0.0, < 5.0)
+      sass (~> 3.1)
+      sprockets (>= 2.8, < 4.0)
+      sprockets-rails (>= 2.0, < 4.0)
+      tilt (>= 1.1, < 3)
     scrypt (1.2.1)
       ffi-compiler (>= 0.0.2)
       rake
@@ -365,7 +371,6 @@ GEM
     xpath (2.0.0)
       nokogiri (~> 1.3)
     yajl-ruby (1.2.1)
-    yui-compressor (0.12.0)
 
 PLATFORMS
   ruby
@@ -410,7 +415,7 @@ DEPENDENCIES
   rubyzip
   rvm-capistrano (= 1.4.4)
   sanitize
-  sass
+  sass-rails
   shoulda-context
   sidekiq
   sidekiq-limit_fetch
@@ -430,7 +435,6 @@ DEPENDENCIES
   webmock
   whenever
   will_paginate
-  yui-compressor
 
 BUNDLED WITH
    1.10.6
diff --git a/config/environments/production.rb b/config/environments/production.rb
index 0f261e0..7ff7b3a 100644
--- a/config/environments/production.rb
+++ b/config/environments/production.rb
@@ -52,7 +52,7 @@ Snpr::Application.configure do
   # Compress JavaScript and CSS
   config.assets.compress = true
   config.assets.js_compressor = :uglifier
-  config.assets.css_compressor = :yui
+  #config.assets.css_compressor = :yui
 
   # Don't fallback to assets pipeline
   config.assets.compile = false

From eeaf3bd847ec993bc535b358343f25618a98cf27 Mon Sep 17 00:00:00 2001
From: Helge Rausch <helge@rausch.io>
Date: Sat, 24 Oct 2015 12:05:05 +0200
Subject: [PATCH 04/11] Add comment to .env.example

---
 .env.example | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/.env.example b/.env.example
index b71f09b..572ec16 100644
--- a/.env.example
+++ b/.env.example
@@ -1,3 +1,9 @@
+# This file serves as a template for configuration through environment
+# variables. It should always be sufficient for use in development and
+# testing. It should also be always complete in a sense that all
+# variables that can be set are included. It is used to extract a list
+# of permitted variables for production during deployment, commented out
+# or not.
 export SECRET_KEY_BASE=foo
 export SECRET_TOKEN=bar
 export RAILS_ENV=development

From e4c268f5c83043df8eed1959a1219a61af0b0017 Mon Sep 17 00:00:00 2001
From: Helge Rausch <helge@rausch.io>
Date: Fri, 23 Oct 2015 21:28:48 +0200
Subject: [PATCH 05/11] Trigger docker build when tests pass

---
 .travis.yml | 5 +++++
 bin/deploy  | 5 +++++
 2 files changed, 10 insertions(+)
 create mode 100755 bin/deploy

diff --git a/.travis.yml b/.travis.yml
index 13d846c..5b85cb6 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -17,3 +17,8 @@ before_script:
   - cp .env.example .env
   - bundle exec rake db:setup
 script: bundle exec rake
+deploy:
+  provider: script
+  script: bin/deploy
+  on:
+    branch: dockerize
diff --git a/bin/deploy b/bin/deploy
new file mode 100755
index 0000000..e5012a5
--- /dev/null
+++ b/bin/deploy
@@ -0,0 +1,5 @@
+#!/usr/bin/env sh
+
+curl -X POST \
+     -d "build=true&source_type=Branch&source_name=dockerize" \
+     https://registry.hub.docker.com/u/opensnp/rails/trigger/$DOCKERHUB_TRIGGER_TOKEN/ 

From eb4fbc5a1b2489aa983923181fa6ab6826935848 Mon Sep 17 00:00:00 2001
From: Helge Rausch <helge@rausch.io>
Date: Fri, 23 Oct 2015 21:28:48 +0200
Subject: [PATCH 06/11] Update gems

---
 Gemfile.lock | 214 +++++++++++++++++++++++++++------------------------
 1 file changed, 115 insertions(+), 99 deletions(-)

diff --git a/Gemfile.lock b/Gemfile.lock
index 0877b70..50639ac 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -24,87 +24,102 @@ GIT
 GEM
   remote: http://rubygems.org/
   specs:
-    actionmailer (4.2.2)
-      actionpack (= 4.2.2)
-      actionview (= 4.2.2)
-      activejob (= 4.2.2)
+    actionmailer (4.2.4)
+      actionpack (= 4.2.4)
+      actionview (= 4.2.4)
+      activejob (= 4.2.4)
       mail (~> 2.5, >= 2.5.4)
       rails-dom-testing (~> 1.0, >= 1.0.5)
-    actionpack (4.2.2)
-      actionview (= 4.2.2)
-      activesupport (= 4.2.2)
+    actionpack (4.2.4)
+      actionview (= 4.2.4)
+      activesupport (= 4.2.4)
       rack (~> 1.6)
       rack-test (~> 0.6.2)
       rails-dom-testing (~> 1.0, >= 1.0.5)
-      rails-html-sanitizer (~> 1.0, >= 1.0.1)
-    actionview (4.2.2)
-      activesupport (= 4.2.2)
+      rails-html-sanitizer (~> 1.0, >= 1.0.2)
+    actionview (4.2.4)
+      activesupport (= 4.2.4)
       builder (~> 3.1)
       erubis (~> 2.7.0)
       rails-dom-testing (~> 1.0, >= 1.0.5)
-      rails-html-sanitizer (~> 1.0, >= 1.0.1)
-    activejob (4.2.2)
-      activesupport (= 4.2.2)
+      rails-html-sanitizer (~> 1.0, >= 1.0.2)
+    activejob (4.2.4)
+      activesupport (= 4.2.4)
       globalid (>= 0.3.0)
-    activemodel (4.2.2)
-      activesupport (= 4.2.2)
+    activemodel (4.2.4)
+      activesupport (= 4.2.4)
       builder (~> 3.1)
-    activerecord (4.2.2)
-      activemodel (= 4.2.2)
-      activesupport (= 4.2.2)
+    activerecord (4.2.4)
+      activemodel (= 4.2.4)
+      activesupport (= 4.2.4)
       arel (~> 6.0)
-    activerecord-import (0.7.0)
+    activerecord-import (0.10.0)
       activerecord (>= 3.0)
-    activesupport (4.2.2)
+    activesupport (4.2.4)
       i18n (~> 0.7)
       json (~> 1.7, >= 1.7.7)
       minitest (~> 5.1)
       thread_safe (~> 0.3, >= 0.3.4)
       tzinfo (~> 1.1)
     addressable (2.3.8)
-    airbrake (4.1.0)
+    airbrake (4.3.3)
       builder
       multi_json
-    arel (6.0.0)
-    authlogic (3.4.5)
+    arel (6.0.3)
+    authlogic (3.4.6)
       activerecord (>= 3.2)
       activesupport (>= 3.2)
       request_store (~> 1.0)
-      scrypt (~> 1.2)
+      scrypt (>= 1.2, < 3.0)
     bcrypt (3.1.10)
     bcrypt-ruby (3.1.5)
       bcrypt (>= 3.1.3)
     builder (3.2.2)
-    capistrano (2.15.5)
+    capistrano (2.15.6)
       highline
       net-scp (>= 1.0.0)
       net-sftp (>= 2.0.0)
       net-ssh (>= 2.0.14)
       net-ssh-gateway (>= 1.1.0)
-    capybara (2.4.4)
+    capybara (2.5.0)
       mime-types (>= 1.16)
       nokogiri (>= 1.3.3)
       rack (>= 1.0.0)
       rack-test (>= 0.5.4)
       xpath (~> 2.0)
-    celluloid (0.16.0)
-      timers (~> 4.0.0)
+    celluloid (0.17.2)
+      celluloid-essentials
+      celluloid-extras
+      celluloid-fsm
+      celluloid-pool
+      celluloid-supervision
+      timers (>= 4.1.1)
+    celluloid-essentials (0.20.5)
+      timers (>= 4.1.1)
+    celluloid-extras (0.20.5)
+      timers (>= 4.1.1)
+    celluloid-fsm (0.20.5)
+      timers (>= 4.1.1)
+    celluloid-pool (0.20.5)
+      timers (>= 4.1.1)
+    celluloid-supervision (0.20.5)
+      timers (>= 4.1.1)
     chronic (0.10.2)
     climate_control (0.0.3)
       activesupport (>= 3.0)
     cocaine (0.5.7)
       climate_control (>= 0.0.3, < 1.0)
     coderay (1.1.0)
-    composite_primary_keys (8.1.0)
+    composite_primary_keys (8.1.1)
       activerecord (~> 4.2.0)
     connection_pool (2.2.0)
     crack (0.4.2)
       safe_yaml (~> 1.0.0)
     crass (1.0.2)
-    database_cleaner (1.4.1)
+    database_cleaner (1.5.1)
     diff-lcs (1.2.5)
     docile (1.1.5)
-    domain_name (0.5.24)
+    domain_name (0.5.25)
       unf (>= 0.0.5, < 1.0.0)
     dotenv (2.0.2)
     dotenv-rails (2.0.2)
@@ -118,20 +133,20 @@ GEM
     factory_girl_rails (4.5.0)
       factory_girl (~> 4.5.0)
       railties (>= 3.0.0)
-    ffi (1.9.8)
+    ffi (1.9.10)
     ffi-compiler (0.1.3)
       ffi (>= 1.0.0)
       rake
-    fitgem (0.10.0)
+    fitgem (0.12.1)
       oauth
     formatador (0.2.5)
     friendly_id (5.1.0)
       activerecord (>= 4.0.0)
-    globalid (0.3.5)
+    globalid (0.3.6)
       activesupport (>= 4.1.0)
-    guard (2.12.5)
+    guard (2.13.0)
       formatador (>= 0.2.4)
-      listen (~> 2.7)
+      listen (>= 2.7, <= 4.0)
       lumberjack (~> 1.0)
       nenv (~> 0.1)
       notiffany (~> 0.0)
@@ -139,32 +154,32 @@ GEM
       shellany (~> 0.0)
       thor (>= 0.18.1)
     guard-compat (1.2.1)
-    guard-rspec (4.5.0)
+    guard-rspec (4.6.4)
       guard (~> 2.1)
       guard-compat (~> 1.1)
       rspec (>= 2.99.0, < 4.0)
-    highline (1.7.2)
+    hashdiff (0.2.2)
+    highline (1.7.8)
     hitimes (1.2.3)
     http-cookie (1.0.2)
       domain_name (~> 0.5)
     i18n (0.7.0)
-    jquery-rails (4.0.4)
+    jquery-rails (4.0.5)
       rails-dom-testing (~> 1.0)
       railties (>= 4.2.0)
       thor (>= 0.14, < 2.0)
     jquery-ui-rails (5.0.5)
       railties (>= 3.2.16)
     json (1.8.3)
-    libv8 (3.16.14.7)
-    listen (2.10.0)
-      celluloid (~> 0.16.0)
+    libv8 (3.16.14.13)
+    listen (3.0.3)
       rb-fsevent (>= 0.9.3)
       rb-inotify (>= 0.9)
-    lograge (0.3.2)
+    lograge (0.3.4)
       actionpack (>= 3)
       activesupport (>= 3)
       railties (>= 3)
-    loofah (2.0.2)
+    loofah (2.0.3)
       nokogiri (>= 1.5.9)
     lumberjack (1.0.9)
     mail (2.6.3)
@@ -173,71 +188,71 @@ GEM
       rest-client (~> 1.7)
     metaclass (0.0.4)
     method_source (0.8.2)
-    mime-types (2.6.1)
+    mime-types (2.6.2)
     mimemagic (0.3.0)
     mini_portile (0.6.2)
-    minitest (5.7.0)
+    minitest (5.8.1)
     mocha (1.1.0)
       metaclass (~> 0.0.1)
-    multi_json (1.11.0)
+    multi_json (1.11.2)
     nenv (0.2.0)
     net-scp (1.2.1)
       net-ssh (>= 2.6.5)
     net-sftp (2.1.2)
       net-ssh (>= 2.6.5)
-    net-ssh (2.9.2)
+    net-ssh (3.0.1)
     net-ssh-gateway (1.2.0)
       net-ssh (>= 2.6.5)
     netrc (0.10.3)
-    newrelic_rpm (3.12.0.288)
+    newrelic_rpm (3.14.0.305)
     nokogiri (1.6.6.2)
       mini_portile (~> 0.6.0)
     nokogumbo (1.4.1)
       nokogiri
-    notiffany (0.0.6)
+    notiffany (0.0.8)
       nenv (~> 0.1)
       shellany (~> 0.0)
     oauth (0.4.7)
-    paperclip (4.3.0)
+    paperclip (4.3.1)
       activemodel (>= 3.2.0)
       activesupport (>= 3.2.0)
       cocaine (~> 0.5.5)
       mime-types
       mimemagic (= 0.3.0)
-    pg (0.18.2)
-    pg_search (1.0.3)
+    pg (0.18.3)
+    pg_search (1.0.5)
       activerecord (>= 3.1)
       activesupport (>= 3.1)
       arel
     plos (0.0.7)
       nokogiri
       rest-client
-    power_assert (0.2.3)
-    pry (0.10.1)
+    power_assert (0.2.4)
+    pry (0.10.3)
       coderay (~> 1.1.0)
       method_source (~> 0.8.1)
       slop (~> 3.4)
     pry-rails (0.3.4)
       pry (>= 0.9.10)
-    rack (1.6.2)
+    rack (1.6.4)
     rack-protection (1.5.3)
       rack
     rack-test (0.6.3)
       rack (>= 1.0)
-    rails (4.2.2)
-      actionmailer (= 4.2.2)
-      actionpack (= 4.2.2)
-      actionview (= 4.2.2)
-      activejob (= 4.2.2)
-      activemodel (= 4.2.2)
-      activerecord (= 4.2.2)
-      activesupport (= 4.2.2)
+    rails (4.2.4)
+      actionmailer (= 4.2.4)
+      actionpack (= 4.2.4)
+      actionview (= 4.2.4)
+      activejob (= 4.2.4)
+      activemodel (= 4.2.4)
+      activerecord (= 4.2.4)
+      activesupport (= 4.2.4)
       bundler (>= 1.3.0, < 2.0)
-      railties (= 4.2.2)
+      railties (= 4.2.4)
       sprockets-rails
     rails-deprecated_sanitizer (1.0.3)
       activesupport (>= 4.2.0.alpha)
-    rails-dom-testing (1.0.6)
+    rails-dom-testing (1.0.7)
       activesupport (>= 4.2.0.beta, < 5.0)
       nokogiri (~> 1.6.0)
       rails-deprecated_sanitizer (>= 1.0.1)
@@ -245,46 +260,46 @@ GEM
       loofah (~> 2.0)
     rails3-generators (1.0.0)
       railties (>= 3.0.0)
-    railties (4.2.2)
-      actionpack (= 4.2.2)
-      activesupport (= 4.2.2)
+    railties (4.2.4)
+      actionpack (= 4.2.4)
+      activesupport (= 4.2.4)
       rake (>= 0.8.7)
       thor (>= 0.18.1, < 2.0)
     rake (10.4.2)
-    rb-fsevent (0.9.4)
+    rb-fsevent (0.9.6)
     rb-inotify (0.9.5)
       ffi (>= 0.5.0)
     recaptcha (0.4.0)
     redis (3.2.1)
     redis-namespace (1.5.2)
       redis (~> 3.0, >= 3.0.4)
-    ref (1.0.5)
-    request_store (1.1.0)
+    ref (2.0.0)
+    request_store (1.2.0)
     rest-client (1.8.0)
       http-cookie (>= 1.0.2, < 2.0)
       mime-types (>= 1.16, < 3.0)
       netrc (~> 0.7)
-    rspec (3.2.0)
-      rspec-core (~> 3.2.0)
-      rspec-expectations (~> 3.2.0)
-      rspec-mocks (~> 3.2.0)
-    rspec-core (3.2.3)
-      rspec-support (~> 3.2.0)
-    rspec-expectations (3.2.1)
+    rspec (3.3.0)
+      rspec-core (~> 3.3.0)
+      rspec-expectations (~> 3.3.0)
+      rspec-mocks (~> 3.3.0)
+    rspec-core (3.3.2)
+      rspec-support (~> 3.3.0)
+    rspec-expectations (3.3.1)
       diff-lcs (>= 1.2.0, < 2.0)
-      rspec-support (~> 3.2.0)
-    rspec-mocks (3.2.1)
+      rspec-support (~> 3.3.0)
+    rspec-mocks (3.3.2)
       diff-lcs (>= 1.2.0, < 2.0)
-      rspec-support (~> 3.2.0)
-    rspec-rails (3.2.1)
+      rspec-support (~> 3.3.0)
+    rspec-rails (3.3.3)
       actionpack (>= 3.0, < 4.3)
       activesupport (>= 3.0, < 4.3)
       railties (>= 3.0, < 4.3)
-      rspec-core (~> 3.2.0)
-      rspec-expectations (~> 3.2.0)
-      rspec-mocks (~> 3.2.0)
-      rspec-support (~> 3.2.0)
-    rspec-support (3.2.2)
+      rspec-core (~> 3.3.0)
+      rspec-expectations (~> 3.3.0)
+      rspec-mocks (~> 3.3.0)
+      rspec-support (~> 3.3.0)
+    rspec-support (3.3.0)
     rubyzip (1.1.7)
     rvm-capistrano (1.4.4)
       capistrano (>= 2.15.4)
@@ -300,13 +315,13 @@ GEM
       sprockets (>= 2.8, < 4.0)
       sprockets-rails (>= 2.0, < 4.0)
       tilt (>= 1.1, < 3)
-    scrypt (1.2.1)
+    scrypt (2.0.2)
       ffi-compiler (>= 0.0.2)
       rake
     shellany (0.0.1)
     shoulda-context (1.2.1)
-    sidekiq (3.4.2)
-      celluloid (~> 0.16.0)
+    sidekiq (3.5.1)
+      celluloid (~> 0.17.2)
       connection_pool (~> 2.2, >= 2.2.0)
       json (~> 1.0)
       redis (~> 3.2, >= 3.2.1)
@@ -326,17 +341,17 @@ GEM
       temple (~> 0.6.3)
       tilt (~> 1.3, >= 1.3.3)
     slop (3.6.0)
-    spring (1.3.6)
+    spring (1.4.0)
     spring-commands-rspec (1.0.4)
       spring (>= 0.9.1)
-    sprockets (3.2.0)
-      rack (~> 1.0)
-    sprockets-rails (2.3.1)
+    sprockets (3.4.0)
+      rack (> 1, < 3)
+    sprockets-rails (2.3.3)
       actionpack (>= 3.0)
       activesupport (>= 3.0)
       sprockets (>= 2.8, < 4.0)
     temple (0.6.10)
-    test-unit (3.0.9)
+    test-unit (3.1.5)
       power_assert
     therubyracer (0.12.2)
       libv8 (~> 3.16.14.0)
@@ -344,8 +359,8 @@ GEM
     thor (0.19.1)
     thread_safe (0.3.5)
     tilt (1.4.1)
-    timecop (0.7.3)
-    timers (4.0.4)
+    timecop (0.8.0)
+    timers (4.1.1)
       hitimes
     twitter-bootstrap-rails (3.2.0)
       actionpack (~> 4.1)
@@ -362,9 +377,10 @@ GEM
     unf_ext (0.0.7.1)
     uuidtools (2.1.5)
     vcr (2.9.3)
-    webmock (1.21.0)
+    webmock (1.22.1)
       addressable (>= 2.3.6)
       crack (>= 0.3.2)
+      hashdiff
     whenever (0.9.4)
       chronic (>= 0.6.3)
     will_paginate (3.0.7)

From 9e609fa24c40e686d5e0ffc51b37c95a0052cabe Mon Sep 17 00:00:00 2001
From: Helge Rausch <helge@rausch.io>
Date: Fri, 23 Oct 2015 21:28:48 +0200
Subject: [PATCH 07/11] Load dotenv in production

---
 .env.example | 2 +-
 Gemfile      | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.env.example b/.env.example
index 572ec16..6ab7e29 100644
--- a/.env.example
+++ b/.env.example
@@ -8,7 +8,7 @@ export SECRET_KEY_BASE=foo
 export SECRET_TOKEN=bar
 export RAILS_ENV=development
 export POSTGRES_URL="postgres://localhost/snpr_$RAILS_ENV"
-#export REDIS_URL=
+export REDIS_URL=redis://localhost
 export FITBIT_CONSUMER_KEY=foo
 export FITBIT_CONSUMER_SECRET=bar
 export PLOS_API_KEY=foo
diff --git a/Gemfile b/Gemfile
index d010335..4e176da 100644
--- a/Gemfile
+++ b/Gemfile
@@ -1,6 +1,6 @@
 source 'http://rubygems.org'
 
-gem 'dotenv-rails', groups: %i(development test)
+gem 'dotenv-rails'
 
 gem 'rails', '~> 4.2.0'
 gem 'authlogic' # lots of user-related magic

From f53593fe71dfd204f5a10470b3ad91a6db2bf72e Mon Sep 17 00:00:00 2001
From: Helge Rausch <helge@rausch.io>
Date: Fri, 23 Oct 2015 21:28:48 +0200
Subject: [PATCH 08/11] Log to stdout by default in production

---
 config/environments/production.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/config/environments/production.rb b/config/environments/production.rb
index 7ff7b3a..02ac95b 100644
--- a/config/environments/production.rb
+++ b/config/environments/production.rb
@@ -23,7 +23,7 @@ Snpr::Application.configure do
   config.log_level = :info
 
   # Use a different logger for distributed setups
-  # config.logger = SyslogLogger.new
+  config.logger = Logger.new($stdout)
 
   # Use a different cache store in production
   # config.cache_store = :mem_cache_store

From bb2d6d5ea476de88005424780d8a670b6456adec Mon Sep 17 00:00:00 2001
From: Helge Rausch <helge@rausch.io>
Date: Thu, 29 Oct 2015 08:31:17 +0100
Subject: [PATCH 09/11] Deploy master branch

---
 .travis.yml | 2 +-
 bin/deploy  | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 5b85cb6..ac4f84b 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -21,4 +21,4 @@ deploy:
   provider: script
   script: bin/deploy
   on:
-    branch: dockerize
+    branch: master
diff --git a/bin/deploy b/bin/deploy
index e5012a5..f397599 100755
--- a/bin/deploy
+++ b/bin/deploy
@@ -1,5 +1,5 @@
 #!/usr/bin/env sh
 
 curl -X POST \
-     -d "build=true&source_type=Branch&source_name=dockerize" \
+     -d "build=true&source_type=Branch&source_name=master" \
      https://registry.hub.docker.com/u/opensnp/rails/trigger/$DOCKERHUB_TRIGGER_TOKEN/ 

From 0d95a9632db34f02de863603254829fd29900735 Mon Sep 17 00:00:00 2001
From: Helge Rausch <helge@rausch.io>
Date: Thu, 29 Oct 2015 08:51:11 +0100
Subject: [PATCH 10/11] Use new hash syntax

---
 Gemfile | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/Gemfile b/Gemfile
index 4e176da..46d9921 100644
--- a/Gemfile
+++ b/Gemfile
@@ -7,9 +7,9 @@ gem 'authlogic' # lots of user-related magic
 gem 'i18n', '>= 0.6.6'
 gem 'rails3-generators'
 gem 'jquery-rails'
-gem 'bcrypt-ruby', :require => 'bcrypt'
+gem 'bcrypt-ruby', require: 'bcrypt'
 gem 'sanitize'
-gem 'recaptcha', :require => 'recaptcha/rails'
+gem 'recaptcha', require: 'recaptcha/rails'
 gem 'dynamic_form'
 gem 'lograge'
 gem 'slop'
@@ -40,7 +40,7 @@ gem 'json'
 gem 'mediawiki-gateway'
 gem 'paperclip', '~> 4.0 '
 gem 'friendly_id'
-gem 'recommendify', github: 'paulasmuth/recommendify', :ref => '34308c4'
+gem 'recommendify', github: 'paulasmuth/recommendify', ref: '34308c4'
 
 # background jobs
 gem 'sidekiq'

From bde8095716455f497ff312d313c3df064a46d1c7 Mon Sep 17 00:00:00 2001
From: Helge Rausch <helge@rausch.io>
Date: Sat, 31 Oct 2015 12:02:41 +0100
Subject: [PATCH 11/11] Add more text about how to set up the environment

---
 README.md | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/README.md b/README.md
index 50e1987..4e90939 100644
--- a/README.md
+++ b/README.md
@@ -34,12 +34,14 @@ rake db:seed OR rake db:setup (which also sets up the entire db)
 
 ## Setup Config
 
-```
-# edit database.yml to point to your postgresql database
-cp config/database.yml.example config/database.yml
+All configuration is done via environment variables. A file with a
+working environment for development can be found at `.env.example`.
+Simply copy it to `.env` to use it as is. The
+[dotenv](https://github.com/bkeepers/dotenv) gem will pick it up
+and set the environment variables.
 
-cp .env.example .env
-```
+Copy `config/database.yml.example` to `config/database.yml` and adapt to
+your database setup.
 
 ## Initialize Database