From 996c99e2c78c7c5e991897bf7258ccb1cdf76298 Mon Sep 17 00:00:00 2001
From: Scott Rohde <srohde@igb.illinois.edu>
Date: Wed, 31 Jan 2018 16:01:43 -0600
Subject: [PATCH 01/44] Start update to Rails 5.

.ruby-version:

Set to ruby-2.3.0 since Rails 5 requires Ruby 2.2.2+.

Gemfile:

Set rails version to 5.0.6.

Comment out prototype-rails for now at least.

Remove version restriction from multi_json.

Change Gem "protected_attributes" to "protected_attributes_continued" until we
start using strong parameters.

Comment out prototype_legacy_helper for now.

Gemfile.lock:

Generated by doing
> rails activerecord-session_store activerecord-postgis-adapter multi_json

application_controller.rb:

In #log_searches, call #permit! on params before calling #inspect.

application_helper.rb:

In the "sortable" helper, call #permit on params before calling #merge.

In "link_to_submit" helper, replace the call to "link_to_function" with a
suitable "link_to" call.
---
 .ruby-version                             |   2 +-
 Gemfile                                   |  10 +-
 Gemfile.lock                              | 156 ++++++++++------------
 app/controllers/application_controller.rb |   2 +-
 app/helpers/application_helper.rb         |   4 +-
 5 files changed, 83 insertions(+), 91 deletions(-)

diff --git a/.ruby-version b/.ruby-version
index d427c89b6..a831048a2 100644
--- a/.ruby-version
+++ b/.ruby-version
@@ -1 +1 @@
-ruby-2.1.5
+ruby-2.3.0
diff --git a/Gemfile b/Gemfile
index 48345bbd6..090c363fa 100644
--- a/Gemfile
+++ b/Gemfile
@@ -1,8 +1,8 @@
 source "http://rubygems.org"
 
-gem "rails", "4.2.10"
+gem "rails", "5.0.6"
 # needed for rails 3.1 and above until we phase out prototype:
-gem 'prototype-rails', github: 'rails/prototype-rails', branch: '4.2' # see https://github.com/rails/prototype-rails/issues/37
+## gem 'prototype-rails', github: 'rails/prototype-rails', branch: '4.2' # see https://github.com/rails/prototype-rails/issues/37
 gem "query_reviewer", "0.1.6"
 gem "nokogiri"
 gem "narray", "0.6.0.4"
@@ -10,7 +10,7 @@ gem "choice", "0.1.6"
 gem "comma", "3.0.4"
 gem "json"
 gem "rgeo", "~> 0.5.0"
-gem "multi_json", "1.3.6"
+gem "multi_json"
 gem "railroad", "0.5.0"
 gem "recaptcha", "0.3.4", :require => "recaptcha/rails"
 gem "ruby-graphviz", "1.0.8"
@@ -25,10 +25,10 @@ gem 'rabl'
 gem 'yajl-ruby', '~> 1.3.1'
 gem 'rubyzip', '~> 1.2.1'
 gem 'activerecord-session_store' # no longer part of Rails proper
-gem 'protected_attributes' # Use this until and unless we start using Strong Parameters.
+gem 'protected_attributes_continued' # Use this until and unless we start using Strong Parameters.
 
 # to-do: remove prototype dependencies so we no longer need this gem
-gem 'prototype_legacy_helper', '0.0.0', :git => 'git://github.com/rails/prototype_legacy_helper.git'
+#gem 'prototype_legacy_helper', '0.0.0', :git => 'git://github.com/rails/prototype_legacy_helper.git'
 
 gem 'memoist'
 
diff --git a/Gemfile.lock b/Gemfile.lock
index 56820fce7..d4c88ecff 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -1,67 +1,58 @@
-GIT
-  remote: git://github.com/rails/prototype-rails.git
-  revision: 0fed929ff48c10c3b978edd3baa983a81f404dbf
-  branch: 4.2
-  specs:
-    prototype-rails (4.0.0)
-      rails (~> 4.0)
-
-GIT
-  remote: git://github.com/rails/prototype_legacy_helper.git
-  revision: a2cd95c3e3c1a4f7a9566efdab5ce59c886cb05f
-  specs:
-    prototype_legacy_helper (0.0.0)
-
 GEM
   remote: http://rubygems.org/
   specs:
-    actionmailer (4.2.10)
-      actionpack (= 4.2.10)
-      actionview (= 4.2.10)
-      activejob (= 4.2.10)
+    actioncable (5.0.6)
+      actionpack (= 5.0.6)
+      nio4r (>= 1.2, < 3.0)
+      websocket-driver (~> 0.6.1)
+    actionmailer (5.0.6)
+      actionpack (= 5.0.6)
+      actionview (= 5.0.6)
+      activejob (= 5.0.6)
       mail (~> 2.5, >= 2.5.4)
-      rails-dom-testing (~> 1.0, >= 1.0.5)
-    actionpack (4.2.10)
-      actionview (= 4.2.10)
-      activesupport (= 4.2.10)
-      rack (~> 1.6)
-      rack-test (~> 0.6.2)
-      rails-dom-testing (~> 1.0, >= 1.0.5)
+      rails-dom-testing (~> 2.0)
+    actionpack (5.0.6)
+      actionview (= 5.0.6)
+      activesupport (= 5.0.6)
+      rack (~> 2.0)
+      rack-test (~> 0.6.3)
+      rails-dom-testing (~> 2.0)
       rails-html-sanitizer (~> 1.0, >= 1.0.2)
-    actionview (4.2.10)
-      activesupport (= 4.2.10)
+    actionview (5.0.6)
+      activesupport (= 5.0.6)
       builder (~> 3.1)
       erubis (~> 2.7.0)
-      rails-dom-testing (~> 1.0, >= 1.0.5)
+      rails-dom-testing (~> 2.0)
       rails-html-sanitizer (~> 1.0, >= 1.0.3)
-    activejob (4.2.10)
-      activesupport (= 4.2.10)
-      globalid (>= 0.3.0)
-    activemodel (4.2.10)
-      activesupport (= 4.2.10)
-      builder (~> 3.1)
-    activerecord (4.2.10)
-      activemodel (= 4.2.10)
-      activesupport (= 4.2.10)
-      arel (~> 6.0)
-    activerecord-postgis-adapter (3.1.5)
-      activerecord (~> 4.2)
-      rgeo-activerecord (>= 4.0.4)
-    activerecord-session_store (0.1.2)
-      actionpack (>= 4.0.0, < 5)
-      activerecord (>= 4.0.0, < 5)
-      railties (>= 4.0.0, < 5)
-    activesupport (4.2.10)
+    activejob (5.0.6)
+      activesupport (= 5.0.6)
+      globalid (>= 0.3.6)
+    activemodel (5.0.6)
+      activesupport (= 5.0.6)
+    activerecord (5.0.6)
+      activemodel (= 5.0.6)
+      activesupport (= 5.0.6)
+      arel (~> 7.0)
+    activerecord-postgis-adapter (4.0.5)
+      activerecord (~> 5.0.0)
+      rgeo-activerecord (~> 5.0.0)
+    activerecord-session_store (1.1.0)
+      actionpack (>= 4.0, < 5.2)
+      activerecord (>= 4.0, < 5.2)
+      multi_json (~> 1.11, >= 1.11.2)
+      rack (>= 1.5.2, < 3)
+      railties (>= 4.0, < 5.2)
+    activesupport (5.0.6)
+      concurrent-ruby (~> 1.0, >= 1.0.2)
       i18n (~> 0.7)
       minitest (~> 5.1)
-      thread_safe (~> 0.3, >= 0.3.4)
       tzinfo (~> 1.1)
     addressable (2.5.2)
       public_suffix (>= 2.0.2, < 4.0)
     apipie-rails (0.4.0)
       json
       rails (>= 4.0)
-    arel (6.0.4)
+    arel (7.1.4)
     bootstrap-will_paginate (1.0.0)
       will_paginate
     builder (3.2.3)
@@ -106,17 +97,18 @@ GEM
     mini_mime (1.0.0)
     mini_portile2 (2.3.0)
     minitest (5.11.3)
-    multi_json (1.3.6)
+    multi_json (1.13.1)
     mustache (1.0.5)
     narray (0.6.0.4)
-    nokogiri (1.8.1)
+    nio4r (2.2.0)
+    nokogiri (1.8.2)
       mini_portile2 (~> 2.3.0)
-    passenger (5.1.12)
+    passenger (5.2.0)
       rack
       rake (>= 0.8.1)
     pg (0.21.0)
-    protected_attributes (1.1.4)
-      activemodel (>= 4.0.1, < 5.0)
+    protected_attributes_continued (1.3.0)
+      activemodel (~> 5.0)
     pry (0.11.3)
       coderay (~> 1.1.0)
       method_source (~> 0.9.0)
@@ -124,40 +116,39 @@ GEM
     query_reviewer (0.1.6)
     rabl (0.13.1)
       activesupport (>= 2.3.14)
-    rack (1.6.8)
+    rack (2.0.4)
     rack-test (0.6.3)
       rack (>= 1.0)
     railroad (0.5.0)
-    rails (4.2.10)
-      actionmailer (= 4.2.10)
-      actionpack (= 4.2.10)
-      actionview (= 4.2.10)
-      activejob (= 4.2.10)
-      activemodel (= 4.2.10)
-      activerecord (= 4.2.10)
-      activesupport (= 4.2.10)
-      bundler (>= 1.3.0, < 2.0)
-      railties (= 4.2.10)
-      sprockets-rails
-    rails-deprecated_sanitizer (1.0.3)
-      activesupport (>= 4.2.0.alpha)
-    rails-dom-testing (1.0.9)
-      activesupport (>= 4.2.0, < 5.0)
-      nokogiri (~> 1.6)
-      rails-deprecated_sanitizer (>= 1.0.1)
+    rails (5.0.6)
+      actioncable (= 5.0.6)
+      actionmailer (= 5.0.6)
+      actionpack (= 5.0.6)
+      actionview (= 5.0.6)
+      activejob (= 5.0.6)
+      activemodel (= 5.0.6)
+      activerecord (= 5.0.6)
+      activesupport (= 5.0.6)
+      bundler (>= 1.3.0)
+      railties (= 5.0.6)
+      sprockets-rails (>= 2.0.0)
+    rails-dom-testing (2.0.3)
+      activesupport (>= 4.2.0)
+      nokogiri (>= 1.6)
     rails-html-sanitizer (1.0.3)
       loofah (~> 2.0)
     rails3-restful-authentication (3.0.1)
-    railties (4.2.10)
-      actionpack (= 4.2.10)
-      activesupport (= 4.2.10)
+    railties (5.0.6)
+      actionpack (= 5.0.6)
+      activesupport (= 5.0.6)
+      method_source
       rake (>= 0.8.7)
       thor (>= 0.18.1, < 2.0)
     rake (12.3.0)
     recaptcha (0.3.4)
-    rgeo (0.5.3)
-    rgeo-activerecord (4.0.5)
-      activerecord (~> 4.2)
+    rgeo (0.5.0)
+    rgeo-activerecord (5.0.1)
+      activerecord (~> 5.0.0)
       rgeo (~> 0.3)
     rspec (3.7.0)
       rspec-core (~> 3.7.0)
@@ -204,6 +195,9 @@ GEM
     trollop (2.1.2)
     tzinfo (1.2.4)
       thread_safe (~> 0.1)
+    websocket-driver (0.6.5)
+      websocket-extensions (>= 0.1.0)
+    websocket-extensions (0.1.3)
     will_paginate (3.1.6)
     xpath (2.1.0)
       nokogiri (~> 1.3)
@@ -227,19 +221,17 @@ DEPENDENCIES
   json
   json-schema
   memoist
-  multi_json (= 1.3.6)
+  multi_json
   narray (= 0.6.0.4)
   nokogiri
   passenger
   pg
-  protected_attributes
-  prototype-rails!
-  prototype_legacy_helper (= 0.0.0)!
+  protected_attributes_continued
   pry
   query_reviewer (= 0.1.6)
   rabl
   railroad (= 0.5.0)
-  rails (= 4.2.10)
+  rails (= 5.0.6)
   rails3-restful-authentication (~> 3.0.1)
   recaptcha (= 0.3.4)
   rgeo (~> 0.5.0)
diff --git a/app/controllers/application_controller.rb b/app/controllers/application_controller.rb
index 97ff8ada3..dfb418383 100644
--- a/app/controllers/application_controller.rb
+++ b/app/controllers/application_controller.rb
@@ -117,7 +117,7 @@ def log_searches(m, arg = params[:search])
     search_info += "\nsearch string: \"" + (params['search'] || "") + "\""
     search_info += "\nformat: " + (params['format'] || 'html')
     search_info += "\nSQL query: " + sql # method_object.call(arg).send(additional_method).to_sql
-    search_info += "\nall parameters: " + params.inspect
+    search_info += "\nall parameters: " + params.permit!.inspect
 
     logger.info(search_info)
 
diff --git a/app/helpers/application_helper.rb b/app/helpers/application_helper.rb
index 3033d5e39..8eb186b50 100644
--- a/app/helpers/application_helper.rb
+++ b/app/helpers/application_helper.rb
@@ -44,7 +44,7 @@ def sortable(column, title = nil)
     title ||= column.titleize
     css_class = (column == sort_column) ? "current #{sort_direction}" : nil
     direction = (column == sort_column && sort_direction == "asc") ? "desc" : "asc"
-    link_to title, params.merge(:sort => column, :direction => direction, :page => nil), {:class => css_class}
+    link_to title, params.permit(:sort, :direction, :page, :_).merge(:sort => column, :direction => direction, :page => nil), {:class => css_class}
   end
 
   def format_stat(record)
@@ -65,7 +65,7 @@ def format_stat(record)
 
 # Call this to make a link inside a form that submits the form.
 def link_to_submit(*args, &block)
-  link_to_function (block_given? ? capture(&block) : args[0]), "jQuery(this).closest('form').submit()", args.extract_options!
+  link_to (block_given? ? capture(&block) : args[0]), "#", args.extract_options!.merge(onclick: "jQuery(this).closest('form').submit(); return false")
 end
 
 # Given a FormBuilder object `f`, a string `label`, an SQL table name

From 1a9d9452b5cad2aab944a7a6f1d6a168d191e864 Mon Sep 17 00:00:00 2001
From: Scott Rohde <srohde@igb.illinois.edu>
Date: Fri, 2 Feb 2018 11:28:43 -0600
Subject: [PATCH 02/44] Set PhusionPassenger version to 5.1.12 until we find
 out how to work with the latest (5.2.0) version.

---
 Gemfile      | 2 +-
 Gemfile.lock | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/Gemfile b/Gemfile
index 090c363fa..84d4bbc98 100644
--- a/Gemfile
+++ b/Gemfile
@@ -82,7 +82,7 @@ end
 
 group :production do
   #  gem "rmagick", "2.13.1"
-  gem "passenger"
+  gem "passenger", "5.1.12"
 end
 
 # API-related Gems:
diff --git a/Gemfile.lock b/Gemfile.lock
index d4c88ecff..936ab9069 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -103,7 +103,7 @@ GEM
     nio4r (2.2.0)
     nokogiri (1.8.2)
       mini_portile2 (~> 2.3.0)
-    passenger (5.2.0)
+    passenger (5.1.12)
       rack
       rake (>= 0.8.1)
     pg (0.21.0)
@@ -224,7 +224,7 @@ DEPENDENCIES
   multi_json
   narray (= 0.6.0.4)
   nokogiri
-  passenger
+  passenger (= 5.1.12)
   pg
   protected_attributes_continued
   pry

From 4a4de926255e5190915c93e54ca75af09f1e3c14 Mon Sep 17 00:00:00 2001
From: Scott Rohde <srohde@igb.illinois.edu>
Date: Fri, 2 Feb 2018 14:25:34 -0600
Subject: [PATCH 03/44] Make some changes to config files suggested by
 app:update task.

---
 config/application.rb              |  2 +-
 config/boot.rb                     |  2 +-
 config/environment.rb              |  2 +-
 config/environments/development.rb | 32 ++++++++++++++++----
 config/environments/production.rb  | 48 +++++++++++++++---------------
 config/environments/test.rb        |  9 ++++--
 config/initializers/assets.rb      | 10 +++----
 7 files changed, 64 insertions(+), 41 deletions(-)

diff --git a/config/application.rb b/config/application.rb
index 4d7430fc5..572a1da6b 100644
--- a/config/application.rb
+++ b/config/application.rb
@@ -1,4 +1,4 @@
-require File.expand_path('../boot', __FILE__)
+require_relative 'boot'
 
 require 'rails/all'
 
diff --git a/config/boot.rb b/config/boot.rb
index 6b750f00b..30f5120df 100644
--- a/config/boot.rb
+++ b/config/boot.rb
@@ -1,3 +1,3 @@
-ENV['BUNDLE_GEMFILE'] ||= File.expand_path('../../Gemfile', __FILE__)
+ENV['BUNDLE_GEMFILE'] ||= File.expand_path('../Gemfile', __dir__)
 
 require 'bundler/setup' # Set up gems listed in the Gemfile.
diff --git a/config/environment.rb b/config/environment.rb
index 01de3b5bb..0448b3ca0 100644
--- a/config/environment.rb
+++ b/config/environment.rb
@@ -1,5 +1,5 @@
 # Load the Rails application.
-require File.expand_path('../application', __FILE__)
+require_relative 'application'
 
 # Initialize the Rails application.
 Rails.application.initialize!
diff --git a/config/environments/development.rb b/config/environments/development.rb
index b55e2144b..fb101a451 100644
--- a/config/environments/development.rb
+++ b/config/environments/development.rb
@@ -9,13 +9,28 @@
   # Do not eager load code on boot.
   config.eager_load = false
 
-  # Show full error reports and disable caching.
-  config.consider_all_requests_local       = true
-  config.action_controller.perform_caching = false
+  # Show full error reports.
+  config.consider_all_requests_local = true
+
+  # Enable/disable caching. By default caching is disabled.
+  if Rails.root.join('tmp/caching-dev.txt').exist?
+    config.action_controller.perform_caching = true
+
+    config.cache_store = :memory_store
+    config.public_file_server.headers = {
+      'Cache-Control' => 'public, max-age=172800'
+    }
+  else
+    config.action_controller.perform_caching = false
+
+    config.cache_store = :null_store
+  end
 
   # Don't care if the mailer can't send.
   config.action_mailer.raise_delivery_errors = false
 
+  config.action_mailer.perform_caching = false
+
   # Print deprecation notices to the Rails logger.
   config.active_support.deprecation = :log
 
@@ -29,13 +44,20 @@
 
   # Asset digests allow you to set far-future HTTP expiration dates on all assets,
   # yet still be able to expire them through the digest params.
-  config.assets.digest = true
+  ## config.assets.digest = true
 
   # Adds additional error checking when serving assets at runtime.
   # Checks for improperly declared sprockets dependencies.
   # Raises helpful error messages.
-  config.assets.raise_runtime_errors = true
+  ## config.assets.raise_runtime_errors = true
+
+  # Suppress logger output for asset requests.
+  config.assets.quiet = true
 
   # Raises error for missing translations
   # config.action_view.raise_on_missing_translations = true
+
+  # Use an evented file watcher to asynchronously detect changes in source code,
+  # routes, locales, etc. This feature depends on the listen gem.
+  # config.file_watcher = ActiveSupport::EventedFileUpdateChecker
 end
diff --git a/config/environments/production.rb b/config/environments/production.rb
index 96103997d..fc143dda9 100644
--- a/config/environments/production.rb
+++ b/config/environments/production.rb
@@ -1,7 +1,6 @@
 Rails.application.configure do
   # Settings specified here will take precedence over those in config/application.rb.
 
-  # The production environment is meant for finished, "live" apps.
   # Code is not reloaded between requests.
   config.cache_classes = true
 
@@ -15,18 +14,9 @@
   config.consider_all_requests_local       = false
   config.action_controller.perform_caching = true
 
-  # Enable Rack::Cache to put a simple HTTP cache in front of your application
-  # Add `rack-cache` to your Gemfile before enabling this.
-  # For large-scale production use, consider using a caching reverse proxy like
-  # NGINX, varnish or squid.
-  # config.action_dispatch.rack_cache = true
-
   # Disable serving static files from the `/public` folder by default since
   # Apache or NGINX already handles this.
-  config.serve_static_files = ENV['RAILS_SERVE_STATIC_FILES'].present?
-
-  # Compress JavaScripts and CSS
-  ## config.assets.compress = true
+  config.public_file_server.enabled = ENV['RAILS_SERVE_STATIC_FILES'].present?
 
   # Compress JavaScripts and CSS.
   config.assets.js_compressor = :uglifier
@@ -35,16 +25,20 @@
   # Do not fallback to assets pipeline if a precompiled asset is missed.
   ## config.assets.compile = false
 
-  # Asset digests allow you to set far-future HTTP expiration dates on all assets,
-  # yet still be able to expire them through the digest params.
-  config.assets.digest = true
-
   # `config.assets.precompile` and `config.assets.version` have moved to config/initializers/assets.rb
 
+  # Enable serving of images, stylesheets, and JavaScripts from an asset server.
+  # config.action_controller.asset_host = 'http://assets.example.com'
+
   # Specifies the header that your server uses for sending files.
   # config.action_dispatch.x_sendfile_header = 'X-Sendfile' # for Apache
   # config.action_dispatch.x_sendfile_header = 'X-Accel-Redirect' # for NGINX
 
+  # Mount Action Cable outside main process or domain
+  # config.action_cable.mount_path = nil
+  # config.action_cable.url = 'wss://example.com/cable'
+  # config.action_cable.allowed_request_origins = [ 'http://example.com', /http:\/\/example.*/ ]
+
   # Force all access to the app over SSL, use Strict-Transport-Security, and use secure cookies.
   # config.force_ssl = true
 
@@ -53,10 +47,7 @@
   config.log_level = :debug
 
   # Prepend all log lines with the following tags.
-  # config.log_tags = [ :subdomain, :uuid ]
-
-  # Use a different logger for distributed setups.
-  # config.logger = ActiveSupport::TaggedLogging.new(SyslogLogger.new)
+  config.log_tags = [ :request_id ]
 
   # Use a different cache store in production.
   # config.cache_store = :mem_cache_store
@@ -64,8 +55,10 @@
   # set assets path
   ## config.assets.prefix = (ENV['RAILS_RELATIVE_URL_ROOT'] || "") + "/assets"
 
-  # Enable serving of images, stylesheets, and JavaScripts from an asset server.
-  # config.action_controller.asset_host = 'http://assets.example.com'
+  # Use a real queuing backend for Active Job (and separate queues per environment)
+  # config.active_job.queue_adapter     = :resque
+  # config.active_job.queue_name_prefix = "bety_rails3_#{Rails.env}"
+  config.action_mailer.perform_caching = false
 
   # Ignore bad email addresses and do not raise email delivery errors.
   # Set this to true and configure the email server for immediate delivery to raise delivery errors.
@@ -78,12 +71,19 @@
   # Send deprecation notices to registered listeners.
   config.active_support.deprecation = :notify
 
-  # Disable automatic flushing of the log to improve performance.
-  # config.autoflush_log = false
-
   # Use default logging formatter so that PID and timestamp are not suppressed.
   config.log_formatter = ::Logger::Formatter.new
 
+  # Use a different logger for distributed setups.
+  # require 'syslog/logger'
+  # config.logger = ActiveSupport::TaggedLogging.new(Syslog::Logger.new 'app-name')
+
+  if ENV["RAILS_LOG_TO_STDOUT"].present?
+    logger           = ActiveSupport::Logger.new(STDOUT)
+    logger.formatter = config.log_formatter
+    config.logger = ActiveSupport::TaggedLogging.new(logger)
+  end
+
   # Do not dump schema after migrations.
   config.active_record.dump_schema_after_migration = false
 end
diff --git a/config/environments/test.rb b/config/environments/test.rb
index 2acb5eb97..ff7c69fda 100644
--- a/config/environments/test.rb
+++ b/config/environments/test.rb
@@ -12,9 +12,11 @@
   # preloads Rails for running tests, you may have to set it to true.
   config.eager_load = false
 
-  # Configure static file server for tests with Cache-Control for performance.
-  config.serve_static_files   = true
-  config.static_cache_control = 'public, max-age=3600'
+  # Configure public file server for tests with Cache-Control for performance.
+  config.public_file_server.enabled = true
+  config.public_file_server.headers = {
+    'Cache-Control' => 'public, max-age=3600'
+  }
 
   # Show full error reports and disable caching.
   config.consider_all_requests_local       = true
@@ -25,6 +27,7 @@
 
   # Disable request forgery protection in test environment.
   config.action_controller.allow_forgery_protection = false
+  config.action_mailer.perform_caching = false
 
   # Tell Action Mailer not to deliver emails to the real world.
   # The :test delivery method accumulates sent emails in the
diff --git a/config/initializers/assets.rb b/config/initializers/assets.rb
index a459b7d5f..ff2d2299a 100644
--- a/config/initializers/assets.rb
+++ b/config/initializers/assets.rb
@@ -3,11 +3,9 @@
 # Version of your assets, change this if you want to expire all your assets.
 # Rails.application.config.assets.version = '1.0'
 
+# Add additional assets to the asset load path
+# Rails.application.config.assets.paths << Emoji.images_path
+
 # Precompile additional assets.
 # application.js, application.css, and all non-JS/CSS in app/assets folder are already added.
-Rails.application.config.assets.precompile += %w(
-  prototype.js
-  effects.js
-  controls.js
-  dragdrop.js
-)
+# Rails.application.config.assets.precompile += %w( search.js )

From 9aafb78af61d85d962c2be4e8e79074b67c06cc6 Mon Sep 17 00:00:00 2001
From: Scott Rohde <srohde@igb.illinois.edu>
Date: Mon, 5 Feb 2018 13:51:07 -0600
Subject: [PATCH 04/44] A few changes to get some more spec to pass:
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

app/controllers/api/v1/traits_controller.rb:

Api::V1::TraitsController#create used to set the response content_type to
“application/xml”.  It seemed that this was overridden by the type of the
template rendered but is no longer.  So we should just not set it.

Gemfile, Gemfile.lock:

Had to add the “rails-controller-testing” to support tests which use the
“assigns” method.

app/controllers/bulk_upload_controller.rb:

In the BulkUploadController#display_csv_file, we have to replace the test “if
uploaded_io” with “if !uploaded_io.blank?” because the call "post
'display_csv_file', { 'CSV file' => nil }” in the bulk upload controller spec
now results in the value of the “CSV file” parameter being “”:String instead of
NilClass.
---
 Gemfile                                     | 1 +
 Gemfile.lock                                | 5 +++++
 app/controllers/api/v1/traits_controller.rb | 2 +-
 app/controllers/bulk_upload_controller.rb   | 2 +-
 4 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/Gemfile b/Gemfile
index 84d4bbc98..742fa6901 100644
--- a/Gemfile
+++ b/Gemfile
@@ -60,6 +60,7 @@ group :test do
   # gem "webrat", "0.7.1"
   gem "capybara"
   gem "database_cleaner"
+  gem "rails-controller-testing" # TO-DO: rewrite the specs that rely on this
 end
 
 # If you have difficulty installing or don't wish to install capybara-webkit,
diff --git a/Gemfile.lock b/Gemfile.lock
index 936ab9069..ac61c05f8 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -132,6 +132,10 @@ GEM
       bundler (>= 1.3.0)
       railties (= 5.0.6)
       sprockets-rails (>= 2.0.0)
+    rails-controller-testing (1.0.2)
+      actionpack (~> 5.x, >= 5.0.1)
+      actionview (~> 5.x, >= 5.0.1)
+      activesupport (~> 5.x)
     rails-dom-testing (2.0.3)
       activesupport (>= 4.2.0)
       nokogiri (>= 1.6)
@@ -232,6 +236,7 @@ DEPENDENCIES
   rabl
   railroad (= 0.5.0)
   rails (= 5.0.6)
+  rails-controller-testing
   rails3-restful-authentication (~> 3.0.1)
   recaptcha (= 0.3.4)
   rgeo (~> 0.5.0)
diff --git a/app/controllers/api/v1/traits_controller.rb b/app/controllers/api/v1/traits_controller.rb
index 9d5221092..e38c3bd93 100644
--- a/app/controllers/api/v1/traits_controller.rb
+++ b/app/controllers/api/v1/traits_controller.rb
@@ -38,7 +38,7 @@ def create
     end
     create_from_xml_string(xml_data)
 
-    render status: 201, content_type: "application/xml"
+    render status: 201
 
   rescue Nokogiri::XML::SyntaxError, InvalidDocument, InvalidData,
     Yajl::ParseError, Api::CsvHandler::BadHeading
diff --git a/app/controllers/bulk_upload_controller.rb b/app/controllers/bulk_upload_controller.rb
index da331e7de..1486a103e 100644
--- a/app/controllers/bulk_upload_controller.rb
+++ b/app/controllers/bulk_upload_controller.rb
@@ -173,7 +173,7 @@ def choose_global_citation
   def display_csv_file
 
     uploaded_io = params["CSV file"]
-    if uploaded_io
+    if !uploaded_io.blank?
       # we got here via the "upload file" button
       @data_set = BulkUploadDataSet.new(session, uploaded_io)
     elsif session[:csvpath]

From 271c6c35cd8f50edc4264963a681ee7ee1e86741 Mon Sep 17 00:00:00 2001
From: Rob Kooper <kooper@illinois.edu>
Date: Wed, 7 Feb 2018 09:53:49 -0600
Subject: [PATCH 05/44] unicorn and bety root path

Added gem + configuration to run bety using unicorn. This is a frontend to
multiple instances of bety running, which will speed up the response time.

Added ability to set the path to the bety application using an environment
variable.
---
 Dockerfile           | 18 +++++---
 Gemfile              |  4 ++
 config.ru            |  5 ++-
 config/unicorn.rb    | 97 ++++++++++++++++++++++++++++++++++++++++++++
 docker/entrypoint.sh |  7 +++-
 5 files changed, 123 insertions(+), 8 deletions(-)
 create mode 100644 config/unicorn.rb

diff --git a/Dockerfile b/Dockerfile
index e2fa2de5b..f485e4ac1 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,5 +1,4 @@
-FROM ruby:2.1
-MAINTAINER Max Burnette <mburnet2@illinois.edu>
+FROM ruby:2.3
 
 # Install dependencies
 RUN apt-get update \
@@ -15,11 +14,12 @@ WORKDIR /home/bety
 
 # install gems (allowing for caching)
 COPY /Gemfile* /home/bety/
-RUN gem install bundler && \
-    bundle install --without javascript_testing --path vendor/bundle
+RUN gem install bundler \
+    && bundle install --with docker --without "test development production debug javascript_testing"
+
 
 # port that is exposed (standard ruby port)
-EXPOSE 3000
+EXPOSE 8000
 
 # copy rest of the files
 COPY / /home/bety
@@ -41,11 +41,17 @@ ARG BETY_GIT_DATE="unknown"
 ENV LOCAL_SERVER=99 \
     REMOTE_SERVERS="0 1 2 5" \
     RAILS_ENV="production" \
+    RAILS_RELATIVE_URL_ROOT="" \
+    UNICORN_WORKER_PROCESSES="3" \
+    UNICORN_PORT="8000" \
     BETY_GIT_TAGS=${BETY_GIT_TAGS} \
     BETY_GIT_BRANCH=${BETY_GIT_BRANCH} \
     BETY_GIT_CHECKSUM=${BETY_GIT_CHECKSUM} \
     BETY_GIT_DATE=${BETY_GIT_DATE}
 
+# expose public files
+VOLUME ["/home/bety/public"]
+
 # default command to run bety web-app
 ENTRYPOINT ["/home/bety/docker/entrypoint.sh"]
-CMD ["server"]
+CMD ["unicorn"]
diff --git a/Gemfile b/Gemfile
index 5286132ba..64d06704f 100644
--- a/Gemfile
+++ b/Gemfile
@@ -82,6 +82,10 @@ group :production do
   gem "passenger"
 end
 
+group :docker do
+  gem 'unicorn'
+end
+
 # API-related Gems:
 
 gem "rspec_api_documentation"
diff --git a/config.ru b/config.ru
index 52aeeab9d..6e715ca17 100644
--- a/config.ru
+++ b/config.ru
@@ -1,4 +1,7 @@
 # This file is used by Rack-based servers to start the application.
 
 require ::File.expand_path('../config/environment',  __FILE__)
-run BetyRails3::Application
+
+map (ENV['RAILS_RELATIVE_URL_ROOT'] || "") + "/" do
+    run BetyRails3::Application
+end
diff --git a/config/unicorn.rb b/config/unicorn.rb
new file mode 100644
index 000000000..a19c1d143
--- /dev/null
+++ b/config/unicorn.rb
@@ -0,0 +1,97 @@
+# Sample verbose configuration file for Unicorn (not Rack)
+#
+# This configuration file documents many features of Unicorn
+# that may not be needed for some applications. See
+# http://unicorn.bogomips.org/examples/unicorn.conf.minimal.rb
+# for a much simpler configuration file.
+#
+# See http://unicorn.bogomips.org/Unicorn/Configurator.html for complete
+# documentation.
+
+# Go with at least 1 per CPU core, a higher amount will usually help for fast
+# responses such as reading from a cache.
+worker_processes ENV['UNICORN_WORKER_PROCESSES'].to_i
+
+# Help ensure your application will always spawn in the symlinked
+# "current" directory that Capistrano sets up.
+#working_directory "/home/bety" # available in 0.94.0+
+
+# feel free to point this anywhere accessible on the filesystem
+#pid "/home/bety/tmp/pids/unicorn.pid"
+
+# Listen on both a Unix domain socket and a TCP port.
+# If you are load-balancing multiple Unicorn masters, lower the backlog
+# setting to e.g. 64 for faster failover.
+#listen "/home/git/gitlab/tmp/sockets/gitlab.socket", :backlog => 1024
+#listen "127.0.0.1:8080", :tcp_nopush => true
+listen "0.0.0.0:" + ENV['UNICORN_PORT']
+
+# nuke workers after 30 seconds instead of 60 seconds (the default)
+timeout 30
+
+# By default, the Unicorn logger will write to stderr.
+# Additionally, some applications/frameworks log to stderr or stdout,
+# so prevent them from going to /dev/null when daemonized here:
+#stderr_path "/home/bety/log/unicorn.stderr.log"
+#stdout_path "/home/bety/log/unicorn.stdout.log"
+
+# combine Ruby 2.0.0dev or REE with "preload_app true" for memory savings
+# http://rubyenterpriseedition.com/faq.html#adapt_apps_for_cow
+preload_app true
+GC.respond_to?(:copy_on_write_friendly=) and
+  GC.copy_on_write_friendly = true
+
+# Enable this flag to have unicorn test client connections by writing the
+# beginning of the HTTP headers before calling the application.  This
+# prevents calling the application for connections that have disconnected
+# while queued.  This is only guaranteed to detect clients on the same
+# host unicorn runs on, and unlikely to detect disconnects even on a
+# fast LAN.
+check_client_connection false
+
+before_fork do |server, worker|
+  # the following is highly recommended for Rails + "preload_app true"
+  # as there's no need for the master process to hold a connection
+  defined?(ActiveRecord::Base) and
+    ActiveRecord::Base.connection.disconnect!
+
+  # The following is only recommended for memory/DB-constrained
+  # installations.  It is not needed if your system can house
+  # twice as many worker_processes as you have configured.
+  #
+  # This allows a new master process to incrementally
+  # phase out the old master process with SIGTTOU to avoid a
+  # thundering herd (especially in the "preload_app false" case)
+  # when doing a transparent upgrade.  The last worker spawned
+  # will then kill off the old master process with a SIGQUIT.
+  old_pid = "#{server.config[:pid]}.oldbin"
+  if old_pid != server.pid
+    begin
+      sig = (worker.nr + 1) >= server.worker_processes ? :QUIT : :TTOU
+      Process.kill(sig, File.read(old_pid).to_i)
+    rescue Errno::ENOENT, Errno::ESRCH
+    end
+  end
+  #
+  # Throttle the master from forking too quickly by sleeping.  Due
+  # to the implementation of standard Unix signal handlers, this
+  # helps (but does not completely) prevent identical, repeated signals
+  # from being lost when the receiving process is busy.
+  # sleep 1
+end
+
+after_fork do |server, worker|
+  # per-process listener ports for debugging/admin/migrations
+  # addr = "127.0.0.1:#{9293 + worker.nr}"
+  # server.listen(addr, :tries => -1, :delay => 5, :tcp_nopush => true)
+
+  # the following is *required* for Rails + "preload_app true",
+  defined?(ActiveRecord::Base) and
+    ActiveRecord::Base.establish_connection
+
+  # if preload_app is true, then you may also want to check and
+  # restart any other shared sockets/descriptors such as Memcached,
+  # and Redis.  TokyoCabinet file handles are safe to reuse
+  # between any number of forked children (assuming your kernel
+  # correctly implements pread()/pwrite() system calls)
+end
diff --git a/docker/entrypoint.sh b/docker/entrypoint.sh
index 83ba8859e..7161d14f1 100755
--- a/docker/entrypoint.sh
+++ b/docker/entrypoint.sh
@@ -46,9 +46,14 @@ case $1 in
         ;;
     "server" )
         wait_for_postgres
-        echo "Start running BETY"
+        echo "Start running BETY (rails server)"
         exec rails s
         ;;
+    "unicorn" )
+        wait_for_postgres
+        echo "Start running BETY (unicorn)"
+        exec bundle exec unicorn -c config/unicorn.rb
+        ;;
     "help" )
         echo "initialize : create a new database and initialize with data from server 0"
         echo "sync       : synchronize database with remote servers ${REMOTE_SERVERS}"

From e7d40ca69f6c0b31e2dec79a1c3ffcb9d51cd322 Mon Sep 17 00:00:00 2001
From: Scott Rohde <srohde@igb.illinois.edu>
Date: Thu, 8 Feb 2018 15:04:49 -0600
Subject: [PATCH 06/44] Wrote replacement for obsolete Prototype method
 "observe_field", and added machinery to make it work for the case of species
 search.

---
 app/controllers/species_controller.rb   | 23 +++++------------------
 app/helpers/application_helper.rb       | 20 ++++++++++++++++++++
 app/views/species/species_search.js.erb | 17 +++++++++++++++++
 3 files changed, 42 insertions(+), 18 deletions(-)
 create mode 100644 app/views/species/species_search.js.erb

diff --git a/app/controllers/species_controller.rb b/app/controllers/species_controller.rb
index 03a624afb..deae39c13 100644
--- a/app/controllers/species_controller.rb
+++ b/app/controllers/species_controller.rb
@@ -53,27 +53,14 @@ def species_search
                               {:query => @query + "%", :query2 => "%" + @query + "%"}).limit(100).order("scientificname")
       @species.uniq!
     else
-      @species = []
+      @species = Specie.none
     end
 
-    render :update do |page|
-      if params[:cont] == "species"
-        page.replace_html "search_results", :partial => 'search', :object => @species
-      else
-        if @species.empty?
-          page.replace_html "#{params[:cont]}_specie_id", "<option value=''>There are no species that match your query.</option>"
-        else
-          page.replace_html "#{params[:cont]}_specie_id", options_from_collection_for_select(@species, :id, :select_default)
-        end
-      end
-      if params[:symbol].length > 3
-        page.replace_html "results", "<h3>Search results for #{sanitize(@query)}</h3>"
-      else
-        page.replace_html "results", "<h3>Search must be longer then 3 characters</h3>"
-      end
+    respond_to do |format|
+      format.js {
+        render layout: false
+      }
     end
-
-#    render :partial => 'species/species_search'
   end
 
 
diff --git a/app/helpers/application_helper.rb b/app/helpers/application_helper.rb
index 8eb186b50..12a9e9999 100644
--- a/app/helpers/application_helper.rb
+++ b/app/helpers/application_helper.rb
@@ -155,3 +155,23 @@ def commit_date
   e = ENV['BETY_GIT_DATE']
   e.nil? || e.empty? ? `git log --pretty=format:"%ad" -1` : e
 end
+
+# Replacement for the Prototype method of this name.
+def observe_field(element_id, **options)
+  raw(
+    %Q{<script>
+           jQuery(document).ready(function() {
+               jQuery("##{element_id.to_s}").bind("keyup", function() {
+                   var queryString = #{options[:with]}
+                   jQuery.post("#{url_for(options[:url])}" + '?' + queryString)
+               })
+           })
+       </script>}
+    ).html_safe
+end
+
+# Dummy method to replace Prototype method of this name.  Needs to be fleshed
+# out.
+def submit_to_remote(a, b, c)
+  'Create'
+end
diff --git a/app/views/species/species_search.js.erb b/app/views/species/species_search.js.erb
new file mode 100644
index 000000000..6655a518b
--- /dev/null
+++ b/app/views/species/species_search.js.erb
@@ -0,0 +1,17 @@
+<% options = escape_javascript options_from_collection_for_select(@species, :id, :select_default) %>
+
+<% if params[:cont] == "species" %>
+  jQuery('#search_results').html(<%= @species %>)
+<% else %>
+  <% if @species.empty? == true %>
+    jQuery("<%= "#" + params[:cont] + "_specie_id" %>").html("<option value=''>There are no species that match your query.</option>")
+  <% else %>
+    jQuery("<%= "#" + params[:cont] + "_specie_id" %>").html('<%= options %>')
+  <% end %>
+<% end %>
+<% if params[:symbol].length > 3 %>
+    jQuery("#results").html("<h3>Search results for <%= sanitize(@query) %></h3>")
+<% else %>
+    jQuery("#results").html("<h3>Search must be longer then 3 characters</h3>")
+<% end %>
+

From 95bf0a697ed0d99eb6e800a8d0f4db604f0cb0d6 Mon Sep 17 00:00:00 2001
From: Scott Rohde <srohde@igb.illinois.edu>
Date: Fri, 9 Feb 2018 11:00:09 -0600
Subject: [PATCH 07/44] Updated capybara to fix problems mentioned here:
 https://github.com/teamcapybara/capybara/issues/1592

---
 Gemfile      |  4 ++--
 Gemfile.lock | 11 ++++++-----
 2 files changed, 8 insertions(+), 7 deletions(-)

diff --git a/Gemfile b/Gemfile
index 742fa6901..7f686af6a 100644
--- a/Gemfile
+++ b/Gemfile
@@ -58,7 +58,7 @@ end
 group :test do
   # phasing out webrat:    
   # gem "webrat", "0.7.1"
-  gem "capybara"
+  gem "capybara", "~> 2.8"
   gem "database_cleaner"
   gem "rails-controller-testing" # TO-DO: rewrite the specs that rely on this
 end
@@ -69,7 +69,7 @@ end
 #     bundle install --without javascript_testing
 #
 group :javascript_testing do
-  gem "capybara-webkit", "1.7.1"
+  gem "capybara-webkit", "~>1.7"
 end
 
 # This group is used by RSpec if the environment variable RAILS_DEBUG is set to
diff --git a/Gemfile.lock b/Gemfile.lock
index ac61c05f8..fff127821 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -56,14 +56,15 @@ GEM
     bootstrap-will_paginate (1.0.0)
       will_paginate
     builder (3.2.3)
-    capybara (2.5.0)
+    capybara (2.13.0)
+      addressable
       mime-types (>= 1.16)
       nokogiri (>= 1.3.3)
       rack (>= 1.0.0)
       rack-test (>= 0.5.4)
       xpath (~> 2.0)
-    capybara-webkit (1.7.1)
-      capybara (>= 2.3.0, < 2.6.0)
+    capybara-webkit (1.14.0)
+      capybara (>= 2.3.0, < 2.14.0)
       json
     childprocess (0.8.0)
       ffi (~> 1.0, >= 1.0.11)
@@ -216,8 +217,8 @@ DEPENDENCIES
   activerecord-session_store
   apipie-rails
   bootstrap-will_paginate
-  capybara
-  capybara-webkit (= 1.7.1)
+  capybara (~> 2.8)
+  capybara-webkit (~> 1.7)
   choice (= 0.1.6)
   comma (= 3.0.4)
   database_cleaner

From bf247994fb5805e4965d3f7354372f40bdf89172 Mon Sep 17 00:00:00 2001
From: Scott Rohde <srohde@igb.illinois.edu>
Date: Fri, 9 Feb 2018 13:35:30 -0600
Subject: [PATCH 08/44] Rewrite observe_field for the case where options[:url]
 contains a key for :id.

In this case url_for already contains part of the query string and we must
append the rest using "&" rather than "?".
---
 app/helpers/application_helper.rb | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/app/helpers/application_helper.rb b/app/helpers/application_helper.rb
index 12a9e9999..340f3d6a8 100644
--- a/app/helpers/application_helper.rb
+++ b/app/helpers/application_helper.rb
@@ -163,7 +163,8 @@ def observe_field(element_id, **options)
            jQuery(document).ready(function() {
                jQuery("##{element_id.to_s}").bind("keyup", function() {
                    var queryString = #{options[:with]}
-                   jQuery.post("#{url_for(options[:url])}" + '?' + queryString)
+                   var connector = "#{options[:url].has_key?(:id) ? '&' : '?'}"
+                   jQuery.post("#{url_for(options[:url])}" + connector + queryString)
                })
            })
        </script>}

From 61091b1490ed2b384c83f313d9e36b9501915dcc Mon Sep 17 00:00:00 2001
From: Scott Rohde <srohde@igb.illinois.edu>
Date: Fri, 9 Feb 2018 13:38:06 -0600
Subject: [PATCH 09/44] Rewrite Inputs controller to render a js.erb template
 rather than using "render :update". Added said js.erb template.

---
 app/controllers/inputs_controller.rb      | 8 +++++---
 app/views/inputs/edit_inputs_files.js.erb | 4 ++++
 2 files changed, 9 insertions(+), 3 deletions(-)
 create mode 100644 app/views/inputs/edit_inputs_files.js.erb

diff --git a/app/controllers/inputs_controller.rb b/app/controllers/inputs_controller.rb
index 2798af258..2f09f2cc4 100644
--- a/app/controllers/inputs_controller.rb
+++ b/app/controllers/inputs_controller.rb
@@ -69,9 +69,11 @@ def edit_inputs_files
       @files = DBFile.where(search_cond).select("id, file_name").page(params[:page])
     end
 
-    render :update do |page|
-      page.replace_html :files_index_table, :partial => "edit_inputs_files_table"
-      page.replace_html :files_search_term, search
+    respond_to do |format|
+      format.js {
+        @search = search
+        render layout: false
+      }
     end
   end
 
diff --git a/app/views/inputs/edit_inputs_files.js.erb b/app/views/inputs/edit_inputs_files.js.erb
new file mode 100644
index 000000000..83e30a74c
--- /dev/null
+++ b/app/views/inputs/edit_inputs_files.js.erb
@@ -0,0 +1,4 @@
+<% Rails.logger.debug "@files = #{@files.to_a}" %>
+jQuery('#files_index_table').html("<%= escape_javascript(render 'edit_inputs_files_table', files: @files, input: @input, searchparam: @searchparam) %>")
+
+jQuery('#files_search_term').html("<%= @search %>")

From d9aeea8d029ee98cbcf649b380c1fad99eb37781 Mon Sep 17 00:00:00 2001
From: Scott Rohde <srohde@igb.illinois.edu>
Date: Fri, 9 Feb 2018 16:05:11 -0600
Subject: [PATCH 10/44] Continue modifying controllers to get rid of the
 "render :update do |page|" idiom.

Added needed js.erb templates.

Rewrote observe_field method (in application_helper.rb) to be more resilient.
---
 app/controllers/inputs_controller.rb      |  3 +-
 app/controllers/models_controller.rb      |  8 +++--
 app/controllers/pfts_controller.rb        |  7 +++--
 app/helpers/application_helper.rb         | 36 ++++++++++++++++-------
 app/views/inputs/edit_inputs_files.js.erb |  2 +-
 app/views/models/edit_models_files.js.erb |  3 ++
 app/views/pfts/edit2_pfts_species.js.erb  |  3 ++
 7 files changed, 42 insertions(+), 20 deletions(-)
 create mode 100644 app/views/models/edit_models_files.js.erb
 create mode 100644 app/views/pfts/edit2_pfts_species.js.erb

diff --git a/app/controllers/inputs_controller.rb b/app/controllers/inputs_controller.rb
index 2f09f2cc4..e40fc6c63 100644
--- a/app/controllers/inputs_controller.rb
+++ b/app/controllers/inputs_controller.rb
@@ -71,8 +71,7 @@ def edit_inputs_files
 
     respond_to do |format|
       format.js {
-        @search = search
-        render layout: false
+        render layout: false, locals: { search: search }
       }
     end
   end
diff --git a/app/controllers/models_controller.rb b/app/controllers/models_controller.rb
index 48bea5e8a..3528f57e0 100644
--- a/app/controllers/models_controller.rb
+++ b/app/controllers/models_controller.rb
@@ -52,9 +52,11 @@ def edit_models_files
       @files = DBFile.where(search_cond).select("id,file_name").page(params[:page])
     end
 
-    render :update do |page|
-      page.replace_html :files_index_table, :partial => "edit_models_files_table"
-      page.replace_html :files_search_term, search
+
+    respond_to do |format|
+      format.js {
+        render layout: false, locals: { search: search }
+      }
     end
   end
 
diff --git a/app/controllers/pfts_controller.rb b/app/controllers/pfts_controller.rb
index 6ac964bd3..c2d874ea9 100644
--- a/app/controllers/pfts_controller.rb
+++ b/app/controllers/pfts_controller.rb
@@ -96,9 +96,10 @@ def edit2_pfts_species
       @species = Specie.where(search_cond).select("id, scientificname").page(params[:page])
     end
 
-    render :update do |page|
-      page.replace_html :index_table, :partial => "edit2_pfts_species_table"
-      page.replace_html :search_term, search
+    respond_to do |format|
+      format.js {
+        render layout: false, locals: { search: search }
+      }
     end
   end
 
diff --git a/app/helpers/application_helper.rb b/app/helpers/application_helper.rb
index 340f3d6a8..ee0012d6f 100644
--- a/app/helpers/application_helper.rb
+++ b/app/helpers/application_helper.rb
@@ -158,17 +158,31 @@ def commit_date
 
 # Replacement for the Prototype method of this name.
 def observe_field(element_id, **options)
-  raw(
-    %Q{<script>
-           jQuery(document).ready(function() {
-               jQuery("##{element_id.to_s}").bind("keyup", function() {
-                   var queryString = #{options[:with]}
-                   var connector = "#{options[:url].has_key?(:id) ? '&' : '?'}"
-                   jQuery.post("#{url_for(options[:url])}" + connector + queryString)
-               })
-           })
-       </script>}
-    ).html_safe
+  # We assume options has either the key :url or the key :function (but not
+  # both).
+  if options.has_key? :url
+    url = url_for(options[:url])
+    connector = url.match(/\?/) ? '&' : '?'
+    raw(
+      %Q{<script>
+             jQuery(document).ready(function() {
+                 jQuery("##{element_id.to_s}").bind("keyup", function() {
+                     jQuery.post("#{url}" + "#{connector}" + #{options[:with]})
+                 })
+             })
+         </script>}
+      ).html_safe
+  else
+    raw(
+      %Q{<script>
+             jQuery(document).ready(function() {
+                 jQuery("##{element_id.to_s}").bind("keyup", function() {
+                     #{options[:function]}
+                 })
+             })
+         </script>}
+      ).html_safe
+  end
 end
 
 # Dummy method to replace Prototype method of this name.  Needs to be fleshed
diff --git a/app/views/inputs/edit_inputs_files.js.erb b/app/views/inputs/edit_inputs_files.js.erb
index 83e30a74c..a870ce0c8 100644
--- a/app/views/inputs/edit_inputs_files.js.erb
+++ b/app/views/inputs/edit_inputs_files.js.erb
@@ -1,4 +1,4 @@
 <% Rails.logger.debug "@files = #{@files.to_a}" %>
 jQuery('#files_index_table').html("<%= escape_javascript(render 'edit_inputs_files_table', files: @files, input: @input, searchparam: @searchparam) %>")
 
-jQuery('#files_search_term').html("<%= @search %>")
+jQuery('#files_search_term').html("<%= search %>")
diff --git a/app/views/models/edit_models_files.js.erb b/app/views/models/edit_models_files.js.erb
new file mode 100644
index 000000000..1ccf1d780
--- /dev/null
+++ b/app/views/models/edit_models_files.js.erb
@@ -0,0 +1,3 @@
+jQuery('#files_index_table').html("<%= escape_javascript(render 'edit_models_files_table', files: @files, model: @model, searchparam: @searchparam) %>")
+
+jQuery('#files_search_term').html("<%= search %>")
diff --git a/app/views/pfts/edit2_pfts_species.js.erb b/app/views/pfts/edit2_pfts_species.js.erb
new file mode 100644
index 000000000..8eb447348
--- /dev/null
+++ b/app/views/pfts/edit2_pfts_species.js.erb
@@ -0,0 +1,3 @@
+jQuery('#index_table').html("<%= escape_javascript(render 'edit2_pfts_species_table', species: @species, pft: @pft, search: @search) %>")
+
+jQuery('#search_term').html("<%= search %>")

From 9cecbdda5bfa366942f45b4affb689854a817971 Mon Sep 17 00:00:00 2001
From: Scott Rohde <srohde@igb.illinois.edu>
Date: Mon, 12 Feb 2018 15:53:24 -0600
Subject: [PATCH 11/44] Make expectation to find the word 'planting' in the
 page more specific: It should be not just in the page, but in the list of
 managements relationships.

---
 spec/features/treatment_integration_spec.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/spec/features/treatment_integration_spec.rb b/spec/features/treatment_integration_spec.rb
index 01ab0f585..d5dc634d1 100644
--- a/spec/features/treatment_integration_spec.rb
+++ b/spec/features/treatment_integration_spec.rb
@@ -58,7 +58,7 @@
         click_link 'View Related Managements'
         page.select 'planting', from: 'management_id'
         click_button 'Select'
-        expect(page).to have_content 'planting'
+        expect(page.find('table table')).to have_content 'planting'
 
       # now do clean-up:
       page.find(:xpath, ".//table/tbody/tr[preceding-sibling::tr/th/text() = 'Type'][contains(td[last()], 'planting')]/td/a[text() = 'X']").click

From 9544998f6ce39961b7f42c3f532abefab563148c Mon Sep 17 00:00:00 2001
From: Scott Rohde <srohde@igb.illinois.edu>
Date: Wed, 14 Feb 2018 16:27:23 -0600
Subject: [PATCH 12/44] Continue modifying controllers to get rid of the
 "render :update do |page|" idiom; added needed js.erb templates.

Miscellaneous other minor changes.
---
 app/controllers/sitegroups_controller.rb      |  7 ++-
 app/controllers/traits_controller.rb          |  7 +--
 app/controllers/treatments_controller.rb      | 60 +++++++++----------
 app/helpers/application_helper.rb             |  6 --
 app/views/inputs/edit_inputs_files.js.erb     |  1 -
 .../sitegroups/edit_sitegroups_sites.js.erb   |  3 +
 app/views/species/species_search.js.erb       |  1 +
 app/views/traits/unlink_covariate.js.erb      |  1 +
 app/views/treatments/_alert.html.erb          |  8 +++
 app/views/treatments/_new_management.html.erb |  4 +-
 .../treatments/create_new_management.js.erb   | 15 +++++
 app/views/treatments/edit.html.erb            |  2 +-
 .../edit_managements_treatments.js.erb        |  1 +
 spec/features/site_integration_spec.rb        |  2 +-
 14 files changed, 67 insertions(+), 51 deletions(-)
 create mode 100644 app/views/sitegroups/edit_sitegroups_sites.js.erb
 create mode 100644 app/views/traits/unlink_covariate.js.erb
 create mode 100644 app/views/treatments/_alert.html.erb
 create mode 100644 app/views/treatments/create_new_management.js.erb
 create mode 100644 app/views/treatments/edit_managements_treatments.js.erb

diff --git a/app/controllers/sitegroups_controller.rb b/app/controllers/sitegroups_controller.rb
index 55ecf4666..722adb6eb 100644
--- a/app/controllers/sitegroups_controller.rb
+++ b/app/controllers/sitegroups_controller.rb
@@ -52,9 +52,10 @@ def edit_sitegroups_sites
       @sites = Site.where(search_cond).paginate :page => params[:page]
     end
 
-    render :update do |page|
-      page.replace_html :sites_index_table, :partial => "edit_sitegroups_sites_table"
-      page.replace_html :sites_search_term, search
+    respond_to do |format|
+      format.js {
+        render layout: false, locals: { search: search }
+      }
     end
   end
 
diff --git a/app/controllers/traits_controller.rb b/app/controllers/traits_controller.rb
index 6b873e369..5de806007 100644
--- a/app/controllers/traits_controller.rb
+++ b/app/controllers/traits_controller.rb
@@ -254,11 +254,10 @@ def unlink_covariate
     @trait = Trait.all_limited(current_user).find(params[:id])
     Covariate.find(params[:covariate]).destroy
     respond_to do |format|
-      format.html {
-        render :action =>"edit" do |page|
-          page.replace_html "edit_covariates_traits", :partial =>"edit_covariates_traits"
-        end
+      format.js {
+        render layout: false
       }
+      format.html { head :ok }
       format.xml  { head :ok }
       format.csv  { head :ok }
     end
diff --git a/app/controllers/treatments_controller.rb b/app/controllers/treatments_controller.rb
index b9aac1311..75674870b 100644
--- a/app/controllers/treatments_controller.rb
+++ b/app/controllers/treatments_controller.rb
@@ -50,24 +50,17 @@ def create_new_management
 
     @management = Management.new(params[:management])
 
-    render :update do |page|
-      if @management.save
-        @treatment.managements << @management
-        flash[:notice] = "Management was successfully created"
-        page.replace_html 'edit_managements_treatments', :partial => 'edit_managements_treatments'
-
-        # After we've added the newly-created management to the collection, we
-        # have to pass an unsaved copy of it to the 'new_management' partial so the
-        # form it contains doesn't try to to a PUT instead of a POST:
-        @management = @management.dup
-
-        page.replace_html 'new_management', :partial => 'new_management'
-        page.call 'showHide', 'new_management'
-      else
-        flash[:notice] = "Management was not created"
-        page.replace_html 'edit_managements_treatments', :partial => 'edit_managements_treatments'
-        page.replace_html 'new_management', :partial => 'new_management'
-      end
+    if @management.save
+      @treatment.managements << @management
+      flash.now[:notice] = "Management was successfully created"
+    else
+      flash.now[:error] = "Management was not created"
+    end
+
+    respond_to do |format|
+      format.js {
+        render layout: false, locals: { flash: flash }
+      }
     end
    end
 
@@ -75,12 +68,12 @@ def rem_managements_treatments
     @treatment = Treatment.find(params[:id])
     @management = Management.find(params[:management])
 
-    render :update do |page|
-      if @management.treatments.delete(@treatment)
-        page.replace_html 'edit_managements_treatments', :partial => 'edit_managements_treatments'
-      else
-        page.replace_html 'edit_managements_treatments', :partial => 'edit_managements_treatments'
-      end
+    @management.treatments.delete(@treatment)
+
+    respond_to do |format|
+      format.js {
+        render "edit_managements_treatments", layout: false
+      }
     end
   end
 
@@ -88,17 +81,18 @@ def edit_managements_treatments
 
     @treatment = Treatment.find(params[:id])
 
-    render :update do |page|
-      if !params[:management].nil?
-        params[:management][:id].each do |c|
-          next if c.empty?
-          @treatment.managements << Management.find(c)
-        end
-        page.replace_html 'edit_managements_treatments', :partial => 'edit_managements_treatments'
-      else
-        page.replace_html 'edit_managements_treatments', :partial => 'edit_managements_treatments'
+    if !params[:management].nil?
+      params[:management][:id].each do |c|
+        next if c.empty?
+        @treatment.managements << Management.find(c)
       end
     end
+
+    respond_to do |format|
+      format.js {
+        render layout: false
+      }
+    end
   end
 
   def flag_control
diff --git a/app/helpers/application_helper.rb b/app/helpers/application_helper.rb
index ee0012d6f..132d37bef 100644
--- a/app/helpers/application_helper.rb
+++ b/app/helpers/application_helper.rb
@@ -184,9 +184,3 @@ def observe_field(element_id, **options)
       ).html_safe
   end
 end
-
-# Dummy method to replace Prototype method of this name.  Needs to be fleshed
-# out.
-def submit_to_remote(a, b, c)
-  'Create'
-end
diff --git a/app/views/inputs/edit_inputs_files.js.erb b/app/views/inputs/edit_inputs_files.js.erb
index a870ce0c8..f52c48d5a 100644
--- a/app/views/inputs/edit_inputs_files.js.erb
+++ b/app/views/inputs/edit_inputs_files.js.erb
@@ -1,4 +1,3 @@
-<% Rails.logger.debug "@files = #{@files.to_a}" %>
 jQuery('#files_index_table').html("<%= escape_javascript(render 'edit_inputs_files_table', files: @files, input: @input, searchparam: @searchparam) %>")
 
 jQuery('#files_search_term').html("<%= search %>")
diff --git a/app/views/sitegroups/edit_sitegroups_sites.js.erb b/app/views/sitegroups/edit_sitegroups_sites.js.erb
new file mode 100644
index 000000000..eedf99105
--- /dev/null
+++ b/app/views/sitegroups/edit_sitegroups_sites.js.erb
@@ -0,0 +1,3 @@
+jQuery('#sites_index_table').html("<%= escape_javascript(render 'edit_sitegroups_sites_table', sitegroup: @sitegroup, sites: @sites, searchparam: @searchparam) %>")
+
+jQuery('#search_term').html("<%= search %>")
diff --git a/app/views/species/species_search.js.erb b/app/views/species/species_search.js.erb
index 6655a518b..88c0c5b79 100644
--- a/app/views/species/species_search.js.erb
+++ b/app/views/species/species_search.js.erb
@@ -1,6 +1,7 @@
 <% options = escape_javascript options_from_collection_for_select(@species, :id, :select_default) %>
 
 <% if params[:cont] == "species" %>
+  // This branch may be obsolete.
   jQuery('#search_results').html(<%= @species %>)
 <% else %>
   <% if @species.empty? == true %>
diff --git a/app/views/traits/unlink_covariate.js.erb b/app/views/traits/unlink_covariate.js.erb
new file mode 100644
index 000000000..f14cf7488
--- /dev/null
+++ b/app/views/traits/unlink_covariate.js.erb
@@ -0,0 +1 @@
+jQuery('#edit_covariates_traits').html("<%= escape_javascript(render 'edit_covariates_traits', trait: @trait) %>")
diff --git a/app/views/treatments/_alert.html.erb b/app/views/treatments/_alert.html.erb
new file mode 100644
index 000000000..177dd0907
--- /dev/null
+++ b/app/views/treatments/_alert.html.erb
@@ -0,0 +1,8 @@
+<% flash.each do |key, value| %>
+  <%= content_tag(:div, class: "alert alert-#{key} fade in centered") do %>
+    <div style="width:850px; margin:auto">
+      <button class="close" data-dismiss="alert">×</button>
+      <%= value %>
+    </div>
+  <% end %>
+<% end %>
diff --git a/app/views/treatments/_new_management.html.erb b/app/views/treatments/_new_management.html.erb
index cb34df395..f8140e648 100644
--- a/app/views/treatments/_new_management.html.erb
+++ b/app/views/treatments/_new_management.html.erb
@@ -1,6 +1,6 @@
 <h1>New management</h1>
 
-<%= form_for(@management) do |f| %>
+<%= form_for @management, :url => create_new_management_treatments_path, :remote => true do |f| %>
   <%= f.error_messages %>
 
 <table>
@@ -41,7 +41,7 @@
   </p>
   <p>
     <%= f.hidden_field :id, :value => @treatment.id %>
-    <%= submit_to_remote f, 'Create', :url => { :action => "create_new_management" } %>
+    <%= button_tag 'Create', :type => 'submit' %>
   </p>
     </td>
   </tr>
diff --git a/app/views/treatments/create_new_management.js.erb b/app/views/treatments/create_new_management.js.erb
new file mode 100644
index 000000000..8616301ed
--- /dev/null
+++ b/app/views/treatments/create_new_management.js.erb
@@ -0,0 +1,15 @@
+jQuery('#edit_managements_treatments').html("<%= escape_javascript(render 'edit_managements_treatments', management: @management, treatment: @treatment) %>")
+
+<% if @management.persisted? %>
+  <% @management = @management.dup %>
+  jQuery('#new_management').slideUp(800);
+<% end %>
+
+jQuery('#new_management').html("<%= escape_javascript(render 'new_management', management: @management, treatment: @treatment) %>");
+
+jQuery('div.alert').detach();
+jQuery('div.nav').after("<%= escape_javascript(render 'alert', flash: flash) %>")
+
+jQuery('button.close').on('click', function(){
+  jQuery(this).closest('div.alert').hide();
+})
diff --git a/app/views/treatments/edit.html.erb b/app/views/treatments/edit.html.erb
index fd6f19d21..12d515bc5 100644
--- a/app/views/treatments/edit.html.erb
+++ b/app/views/treatments/edit.html.erb
@@ -11,7 +11,7 @@
         <%= render 'edit_managements_treatments' %>
       </div>
       <hr />
-      <a style="text-decoration: none" href="#" onclick="showHide('new_management')" id="show_new_management">[+] Create New Management</a>
+      <a style="text-decoration: none" href="#" onclick="jQuery('#new_management').slideToggle(800)" id="show_new_management">[+] Create New Management</a>
       <br/>
       <div id="new_management" class="hidden notvisible">
         <%= render 'new_management' %>
diff --git a/app/views/treatments/edit_managements_treatments.js.erb b/app/views/treatments/edit_managements_treatments.js.erb
new file mode 100644
index 000000000..6f4b2c69a
--- /dev/null
+++ b/app/views/treatments/edit_managements_treatments.js.erb
@@ -0,0 +1 @@
+jQuery('#edit_managements_treatments').html("<%= escape_javascript(render 'edit_managements_treatments', management: @management, treatment: @treatment) %>")
diff --git a/spec/features/site_integration_spec.rb b/spec/features/site_integration_spec.rb
index fa956ace4..cd488431d 100644
--- a/spec/features/site_integration_spec.rb
+++ b/spec/features/site_integration_spec.rb
@@ -56,7 +56,7 @@
       it 'show allow adding new related citations', js: true do
         click_link 'View Related Citations'
         fill_in 'search_citations', with: 'Wood'
-        sleep 1
+        sleep 2 # 1 often isn't enough
         click_link '+'
         click_button 'Update'
         # reopen related citations listing

From 74de6fccfafd4d9fd22c7cbd6fb9845c760d808f Mon Sep 17 00:00:00 2001
From: Scott Rohde <srohde@igb.illinois.edu>
Date: Thu, 15 Feb 2018 13:51:35 -0600
Subject: [PATCH 13/44] In POST and PUT calls, parameters keys with empty
 hashes as values get silently deleted, causing some tests to fail.  Revise
 these calls accordingly.

---
 spec/controllers/treatments_controller_spec.rb | 16 +++++++++-------
 1 file changed, 9 insertions(+), 7 deletions(-)

diff --git a/spec/controllers/treatments_controller_spec.rb b/spec/controllers/treatments_controller_spec.rb
index bf857c510..fce08d517 100644
--- a/spec/controllers/treatments_controller_spec.rb
+++ b/spec/controllers/treatments_controller_spec.rb
@@ -24,6 +24,8 @@
   # adjust the attributes here as well.
   let(:valid_attributes) { { name: "bogus" } }
 
+  let(:invalid_attribute_set) { { name: nil } }
+
   # This should return the minimal set of values that should be in the session
   # in order to pass any filters (e.g. authentication) defined in
   # TreatmentsController. Be sure to keep this updated too.
@@ -35,10 +37,10 @@
   }
 
   describe "GET index" do
-    it "assigns all treatments as @treatments" do
-      treatment = Treatment.first
+    it "assigns all treatments associated with the session citation as @treatments" do
+      treatments = Citation.find(valid_session[:citation]).treatments
       get :index, {}, valid_session
-      expect(assigns(:treatments)).to eq([treatment])
+      expect(assigns(:treatments)).to eq(treatments)
     end
   end
 
@@ -89,14 +91,14 @@
       it "assigns a newly created but unsaved treatment as @treatment" do
         # Trigger the behavior that occurs when invalid params are submitted
         allow_any_instance_of(Treatment).to receive(:save).and_return(false)
-        post :create, {:treatment => {  }}, valid_session
+        post :create, {}, valid_session
         expect(assigns(:treatment)).to be_a_new(Treatment)
       end
 
       it "re-renders the 'new' template" do
         # Trigger the behavior that occurs when invalid params are submitted
         allow_any_instance_of(Treatment).to receive(:save).and_return(false)
-        post :create, {:treatment => {  }}, valid_session
+        post :create, {}, valid_session
         expect(response).to render_template("new")
       end
     end
@@ -132,7 +134,7 @@
         treatment = Treatment.create! valid_attributes
         # Trigger the behavior that occurs when invalid params are submitted
         allow_any_instance_of(Treatment).to receive(:save).and_return(false)
-        put :update, {:id => treatment.to_param, :treatment => {  }}, valid_session
+        put :update, {:id => treatment.to_param, :treatment => invalid_attribute_set}, valid_session
         expect(assigns(:treatment)).to eq(treatment)
       end
 
@@ -140,7 +142,7 @@
         treatment = Treatment.create! valid_attributes
         # Trigger the behavior that occurs when invalid params are submitted
         allow_any_instance_of(Treatment).to receive(:save).and_return(false)
-        put :update, {:id => treatment.to_param, :treatment => {  }}, valid_session
+        put :update, {:id => treatment.to_param, :treatment => invalid_attribute_set}, valid_session
         expect(response).to render_template("edit")
       end
     end

From 9c97c3583ac863beff27ac62187a077da96371cd Mon Sep 17 00:00:00 2001
From: Scott Rohde <srohde@igb.illinois.edu>
Date: Thu, 15 Feb 2018 16:29:53 -0600
Subject: [PATCH 14/44] Fixed format variable editing.

---
 app/controllers/formats_controller.rb | 27 +++++++++++++++------------
 app/models/formats_variable.rb        |  2 ++
 config/routes.rb                      |  2 +-
 3 files changed, 18 insertions(+), 13 deletions(-)

diff --git a/app/controllers/formats_controller.rb b/app/controllers/formats_controller.rb
index 8a6a3b2fc..2ea39d971 100644
--- a/app/controllers/formats_controller.rb
+++ b/app/controllers/formats_controller.rb
@@ -4,15 +4,14 @@ class FormatsController < ApplicationController
   helper_method :sort_column, :sort_direction
 
   def rem_formats_variables
-    @formats_variable = FormatsVariable.find(params[:id])
-    @format = @formats_variable.format
+    formats_variable = FormatsVariable.find(params[:id])
+    @format = formats_variable.format
+    formats_variable.destroy
 
-    render :update do |page|
-      if @formats_variable.destroy
-        page.replace_html 'edit_formats_variables', :partial => 'edit_formats_variables'
-      else
-        page.replace_html 'edit_formats_variables', :partial => 'edit_formats_variables'
-      end
+    respond_to do |format|
+      format.js {
+        render "edit_formats_variables", layout: false
+      }
     end
   end
 
@@ -23,8 +22,10 @@ def add_formats_variables
     formats_variable.variable = Variable.find(params[:variable_id])
     formats_variable.save
 
-    render :update do |page|
-      page.replace_html 'edit_formats_variables', :partial => 'edit_formats_variables'
+    respond_to do |format|
+      format.js {
+        render "edit_formats_variables", layout: false
+      }
     end
   end
 
@@ -33,8 +34,10 @@ def edit_formats_variables
     @format = formats_variable.format
     formats_variable.update_attributes(params[:formats_variable])
 
-    render :update do |page|
-      page.replace_html 'edit_formats_variables', :partial => 'edit_formats_variables'
+    respond_to do |format|
+      format.js {
+        render layout: false
+      }
     end
   end
 
diff --git a/app/models/formats_variable.rb b/app/models/formats_variable.rb
index 3974378ee..2f2dbe399 100644
--- a/app/models/formats_variable.rb
+++ b/app/models/formats_variable.rb
@@ -1,4 +1,6 @@
 class FormatsVariable < ActiveRecord::Base
+  attr_protected []
+
   belongs_to :format
   belongs_to :variable
 end
diff --git a/config/routes.rb b/config/routes.rb
index c32fe4531..321556927 100644
--- a/config/routes.rb
+++ b/config/routes.rb
@@ -86,7 +86,7 @@
   resources :formats do
     post :add_formats_variables, on: :collection
   end
-  get 'formats/edit_formats_variables'
+  post 'formats/edit_formats_variables'
   get '/formats/rem_formats_variables(/:id)' => 'formats#rem_formats_variables'
 
   resources :likelihoods

From 92814e60dc3100c412f01fcbce2b45222fc5c39c Mon Sep 17 00:00:00 2001
From: Scott Rohde <srohde@igb.illinois.edu>
Date: Thu, 15 Feb 2018 16:51:52 -0600
Subject: [PATCH 15/44] Fix editing of modeltype formats.

---
 app/controllers/modeltypes_controller.rb | 24 ++++++++++++++----------
 app/models/modeltypes_format.rb          |  2 ++
 2 files changed, 16 insertions(+), 10 deletions(-)

diff --git a/app/controllers/modeltypes_controller.rb b/app/controllers/modeltypes_controller.rb
index 2c4ae3d11..01154957e 100644
--- a/app/controllers/modeltypes_controller.rb
+++ b/app/controllers/modeltypes_controller.rb
@@ -7,12 +7,12 @@ def remove_modeltypes_format
     @modeltypes_format = ModeltypesFormat.find(params[:id])
     @modeltype = @modeltypes_format.modeltype
 
-    render :update do |page|
-      if @modeltypes_format.destroy
-        page.replace_html 'edit_formats', :partial => 'edit_formats'
-      else
-        page.replace_html 'edit_formats', :partial => 'edit_formats'
-      end
+    @modeltypes_format.destroy
+
+    respond_to do |format|
+      format.js {
+        render "edit_modeltypes_format", layout: false
+      }
     end
   end
 
@@ -23,8 +23,10 @@ def add_modeltypes_format
     @modeltypes_format.format = Format.find(params[:format_id])
     @modeltypes_format.save
 
-    render :update do |page|
-      page.replace_html 'edit_formats', :partial => 'edit_formats'
+    respond_to do |format|
+      format.js {
+        render "edit_modeltypes_format", layout: false
+      }
     end
   end
 
@@ -33,8 +35,10 @@ def edit_modeltypes_format
     @modeltype = @modeltypes_format.modeltype
     @modeltypes_format.update_attributes(params[:modeltypes_format])
 
-    render :update do |page|
-      page.replace_html 'edit_formats', :partial => 'edit_formats'
+    respond_to do |format|
+      format.js {
+        render layout: false
+      }
     end
   end
 
diff --git a/app/models/modeltypes_format.rb b/app/models/modeltypes_format.rb
index a3166b714..a78a8ba2c 100644
--- a/app/models/modeltypes_format.rb
+++ b/app/models/modeltypes_format.rb
@@ -1,4 +1,6 @@
 class ModeltypesFormat < ActiveRecord::Base
+  attr_protected []
+
   validates :tag,
       presence: { message: "tag can't be blank" },
       format: { with: /\A[a-z]+\z/,

From 5003f6dc16be89497adb29581000f3a6a2cab441 Mon Sep 17 00:00:00 2001
From: Scott Rohde <srohde@igb.illinois.edu>
Date: Fri, 16 Feb 2018 09:57:05 -0600
Subject: [PATCH 16/44] Remove Ruby versions that don't support Rails 5.

---
 .travis.yml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index baaad9d05..1b206e858 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -7,8 +7,6 @@ sudo: false
 # versions of ruby to use
 # see the list at http://rubies.travis-ci.org/
 rvm:
-  - 2.1.5
-  - 2.1.8
   - 2.2.4
   - 2.3.0
 

From 233c69283683e252679d96b183809acbab34e954 Mon Sep 17 00:00:00 2001
From: Scott Rohde <srohde@igb.illinois.edu>
Date: Tue, 20 Feb 2018 15:37:47 -0600
Subject: [PATCH 17/44] Several changes to replace the "render :update"
 construct with .js.erb templates and associated machinery.

---
 app/controllers/sites_controller.rb           |  9 ++-
 app/controllers/traits_controller.rb          | 80 ++++++++++++-------
 app/controllers/yields_controller.rb          | 47 +++++++----
 app/helpers/application_helper.rb             | 50 +++++++++++-
 .../formats/edit_formats_variables.js.erb     |  1 +
 .../modeltypes/edit_modeltypes_format.js.erb  |  1 +
 app/views/sites/linked.js.erb                 |  7 ++
 app/views/traits/_index_table.html.erb        |  6 +-
 app/views/traits/access_level.js.erb          |  7 ++
 app/views/traits/checked.js.erb               |  1 +
 app/views/traits/trait_search.js.erb          |  2 +
 app/views/yields/_index_table.html.erb        |  6 +-
 app/views/yields/access_level.js.erb          |  7 ++
 app/views/yields/checked.js.erb               |  1 +
 14 files changed, 170 insertions(+), 55 deletions(-)
 create mode 100644 app/views/formats/edit_formats_variables.js.erb
 create mode 100644 app/views/modeltypes/edit_modeltypes_format.js.erb
 create mode 100644 app/views/sites/linked.js.erb
 create mode 100644 app/views/traits/access_level.js.erb
 create mode 100644 app/views/traits/checked.js.erb
 create mode 100644 app/views/traits/trait_search.js.erb
 create mode 100644 app/views/yields/access_level.js.erb
 create mode 100644 app/views/yields/checked.js.erb

diff --git a/app/controllers/sites_controller.rb b/app/controllers/sites_controller.rb
index 782316158..6eee0ac2b 100644
--- a/app/controllers/sites_controller.rb
+++ b/app/controllers/sites_controller.rb
@@ -15,13 +15,16 @@ def linked
 
     if exists
       @citation.sites.delete(@site)
+      @linking = false
     else
       @citation.sites<<@site
+      @linking = true
     end
 
-    render :update do |page|
-      page.replace_html "site-#{ @site.id }", ""
-      page.replace_html "linked", :partial => 'linked'
+    respond_to do |format|
+      format.js {
+        render layout: false
+      }
     end
   end
 
diff --git a/app/controllers/traits_controller.rb b/app/controllers/traits_controller.rb
index 5de806007..989c0068e 100644
--- a/app/controllers/traits_controller.rb
+++ b/app/controllers/traits_controller.rb
@@ -11,6 +11,7 @@ def trait_search
 
       @trait = Trait.all_limited(current_user).
         includes([:specie,:variable,:cultivar,:treatment,:citation]).
+        references([:specie,:variable,:treatment,:citation]).
         where(%q{   species.scientificname LIKE :query
                  OR species.genus LIKE :query
                  OR species."AcceptedSymbol" LIKE :query
@@ -24,52 +25,71 @@ def trait_search
       @trait = nil
     end
 
-
-    render :update do |page|
-      if params[:symbol].length > 3
-        if @trait.length == 100
-          page.replace_html "results", "<h3>Search results for #{@query}. More then 100 results, please narrow your search.</h3>"
-        else
-          page.replace_html "results", "<h3>Search results for #{@query}</h3>"
-        end
-      else
-        page.replace_html "results", "<h3>Search must be longer then 3 characters</h3>"
-      end
-      if @trait.nil?
-        page.replace_html "#{params[:cont]}_trait_id", "<option value=''>There are no traits that match your query.</option>"
+    if params[:symbol].length > 3
+      if @trait.length == 100
+        @message = "<h3>Search results for #{@query}. More then 100 results, please narrow your search.</h3>"
       else
-        page.replace_html "#{params[:cont]}_trait_id", options_from_collection_for_select(@trait, :id, :select_default)
+        @message = "<h3>Search results for #{@query}</h3>"
       end
+    else
+      @message = "<h3>Search must be longer then 3 characters</h3>"
     end
 
+    if @trait.nil?
+      @options = "<option value=''>There are no traits that match your query.</option>"
+    else
+      @options = ActionController::Base.helpers.options_from_collection_for_select(@trait, :id, :select_default)
+    end
+
+    respond_to do |format|
+      format.js {
+        render layout: false
+      }
+    end
   end
 
   def access_level
 
     t = Trait.all_limited(current_user).find(params[:id])
-
+    t.current_user = current_user
     t.access_level = params[:trait][:access_level] if t
 
-    render :update do |page|
-      if t and t.save
-        page['access_level-'+t.id.to_s].visual_effect :pulsate
-      else
-        page['access_level-'+t.id.to_s].visual_effect :shake
-      end
+    @element_id = "access_level-#{t.id}"
+
+    if t && t.save
+      @saved = true
+    else
+      @saved = false
+    end
+
+    respond_to do |format|
+      format.js {
+        render layout: false
+      }
     end
   end
 
   def checked
-    t = Trait.all_limited(current_user).find(params[:id])
-    t.current_user = current_user
-    t.checked = params[:trait][:checked] if t
+    id = params[:id]
+    t = Trait.all_limited(current_user).find_by_id(id)
 
-    render :update do |page|
-      if t and t.save
-        page.replace_html 'checked_notify-'+t.id.to_s, "<br />Updated to #{t.checked}"
-      else
-        page.replace_html 'checked_notify-'+t.id.to_s, "<br />Something went wrong, not updated!"
-      end
+    if t
+      t.current_user = current_user
+      t.checked = params[:trait][:checked]
+    end
+
+    @element_id = "checked_notify-#{id}"
+
+    if t && t.save
+      @message = "<br />Updated to #{t.checked}"
+    else
+      @message = "<br />Something went wrong, not updated!"
+    end
+
+    respond_to do |format|
+      format.js {
+        render layout: false
+      }
     end
   end
 
diff --git a/app/controllers/yields_controller.rb b/app/controllers/yields_controller.rb
index 1aae1a9d5..8d58b42de 100644
--- a/app/controllers/yields_controller.rb
+++ b/app/controllers/yields_controller.rb
@@ -5,31 +5,46 @@ class YieldsController < ApplicationController
   require 'csv'
 
   def checked
-    y = Yield.all_limited(current_user).find(params[:id])
-    
-    y.checked = params[:y][:checked]
+    id = params[:id]
+    y = Yield.all_limited(current_user).find(id)
 
-    render :update do |page|
-      if y and y.save
-        page.replace_html 'checked_notify-'+y.id.to_s, "<br />Updated to #{y.checked}"
-      else 
-        page.replace_html 'checked_notify-'+y.id.to_s, "<br />Something went wrong, not updated!"
-      end
+    if y
+      y.checked = params[:y][:checked]
+    end
+
+    @element_id = "checked_notify-#{id}"
+    binding.pry
+    if y && y.save
+      @message = "<br />Updated to #{y.checked}"
+    else
+      @message = "<br />Something went wrong, not updated!"
+    end
+
+    respond_to do |format|
+      format.js {
+        render layout: false
+      }
     end
   end
 
   def access_level
 
     y = Yield.all_limited(current_user).find(params[:id])
-
     y.access_level = params[:yield][:access_level] if y
     
-    render :update do |page|
-      if y and y.save
-        page['access_level-'+y.id.to_s].visual_effect :pulsate
-      else 
-        page['access_level-'+y.id.to_s].visual_effect :shake
-      end
+
+    @element_id = "access_level-#{y.id}"
+
+    if y && y.save
+      @saved = true
+    else
+      @saved = false
+    end
+
+    respond_to do |format|
+      format.js {
+        render layout: false
+      }
     end
   end
 
diff --git a/app/helpers/application_helper.rb b/app/helpers/application_helper.rb
index 132d37bef..abfeb4330 100644
--- a/app/helpers/application_helper.rb
+++ b/app/helpers/application_helper.rb
@@ -163,11 +163,57 @@ def observe_field(element_id, **options)
   if options.has_key? :url
     url = url_for(options[:url])
     connector = url.match(/\?/) ? '&' : '?'
+    confirmation = options[:confirmation] || "true"
+    observed_event = options[:event_name] || "keyup"
     raw(
       %Q{<script>
+             var data_access_level = #{current_user.access_level};
              jQuery(document).ready(function() {
-                 jQuery("##{element_id.to_s}").bind("keyup", function() {
-                     jQuery.post("#{url}" + "#{connector}" + #{options[:with]})
+                 jQuery("##{element_id.to_s}").bind("focus", function() {
+                     previous = this.value;
+                 }).bind("#{observed_event}", function(event) {
+                     var newvalue = this.value;
+                     jQuery.ajax({
+                         type: "POST",
+                         url: "#{url}" + "#{connector}" + #{options[:with]},
+                         beforeSend: function() {
+                             var returnValue;
+                             if ("##{element_id.to_s}".search("access_level-") == 1) {
+                                 // We are dealing with an element having an id of the form "access_level-...":
+                                 if (data_access_level > newvalue) {
+                                     var confirmation_message = "Really " +
+                                         "change the access level of this " +
+                                         "trait to " + newvalue + "?  " +
+                                         "You will lose access to it if you " +
+                                         "do so.";
+                                     var answer = confirm(confirmation_message);
+                                     if (answer == false) {
+                                         jQuery("##{element_id.to_s}").val(previous);
+                                         jQuery("##{element_id.to_s}").addClass('alert-error', 500);
+                                         jQuery("##{element_id.to_s}").removeClass('alert-error', 500);
+                                     }
+                                     returnValue = answer;
+                                 }
+                                 else {
+                                     returnValue = true;
+                                 }
+                             }
+                             else {
+                                 // This is not an element that changes the
+                                 // access level.  Just allow it to be changed.
+                                 returnValue = true;
+                             }
+                             previous = jQuery("##{element_id.to_s}").val();
+                             return returnValue;
+
+                         },
+                         success: function() {
+                             if ("##{element_id.to_s}".search("access_level-") == 1 &&
+                                 data_access_level > newvalue) {
+                                 jQuery("##{element_id}").closest('tr').fadeOut(1000, function() { jQuery(this).remove(); });
+                             }
+                         }
+                     });
                  })
              })
          </script>}
diff --git a/app/views/formats/edit_formats_variables.js.erb b/app/views/formats/edit_formats_variables.js.erb
new file mode 100644
index 000000000..2a9651e4d
--- /dev/null
+++ b/app/views/formats/edit_formats_variables.js.erb
@@ -0,0 +1 @@
+jQuery('#edit_formats_variables').html("<%= escape_javascript(render 'edit_formats_variables', format: @format) %>")
diff --git a/app/views/modeltypes/edit_modeltypes_format.js.erb b/app/views/modeltypes/edit_modeltypes_format.js.erb
new file mode 100644
index 000000000..90af12094
--- /dev/null
+++ b/app/views/modeltypes/edit_modeltypes_format.js.erb
@@ -0,0 +1 @@
+jQuery("#edit_formats").html("<%= escape_javascript(render 'edit_formats', modeltype: @modeltype, modeltypes_format: @modeltypes_format) %>")
diff --git a/app/views/sites/linked.js.erb b/app/views/sites/linked.js.erb
new file mode 100644
index 000000000..8fd35b40b
--- /dev/null
+++ b/app/views/sites/linked.js.erb
@@ -0,0 +1,7 @@
+jQuery("#site-<%= @site.id %>").remove()
+<% if @linking %>
+  jQuery("#linked").html("<%= escape_javascript(render "linked", citation: @citation) %>")
+<% end %>
+// (If unlinking, removing the site from the "linked sites" list is probably
+// sufficient even though this means we won't see the newly-unlinked sites in
+// the non-associated sites list right away.)
diff --git a/app/views/traits/_index_table.html.erb b/app/views/traits/_index_table.html.erb
index 61caeb48a..704705588 100644
--- a/app/views/traits/_index_table.html.erb
+++ b/app/views/traits/_index_table.html.erb
@@ -80,9 +80,11 @@
    <%= observe_field("access_level-" + trait.id.to_s,
                   :frequency => 1,
                   :with => "'id=' + #{trait.id} + '&trait[access_level]=' + Form.Element.getValue('access_level-#{trait.id.to_s}')",
-                  :url => { :action => :access_level }) %>
+                  :url => { :action => :access_level },
+                  :event_name => "change") %>
    <%= observe_field("checked-" + trait.id.to_s,
                   :frequency => 1,
                   :with => "'id=' + #{trait.id} + '&trait[checked]=' + Form.Element.getValue('checked-#{trait.id.to_s}')",
-                  :url => { :action => :checked }) %>
+                  :url => { :action => :checked },
+                  :event_name => "change") %>
 <% end %>
diff --git a/app/views/traits/access_level.js.erb b/app/views/traits/access_level.js.erb
new file mode 100644
index 000000000..6cda1274b
--- /dev/null
+++ b/app/views/traits/access_level.js.erb
@@ -0,0 +1,7 @@
+<% if @saved %>
+  jQuery("#<%= @element_id %>").addClass('alert-success', 500)
+  jQuery("#<%= @element_id %>").removeClass('alert-success', 500)
+<% else %>
+  jQuery("#<%= @element_id %>").addClass('alert-error', 500)
+  jQuery("#<%= @element_id %>").removeClass('alert-error', 500)
+<% end %>
diff --git a/app/views/traits/checked.js.erb b/app/views/traits/checked.js.erb
new file mode 100644
index 000000000..96ef48ba7
--- /dev/null
+++ b/app/views/traits/checked.js.erb
@@ -0,0 +1 @@
+jQuery("#<%= @element_id %>").html("<%= raw @message %>")
diff --git a/app/views/traits/trait_search.js.erb b/app/views/traits/trait_search.js.erb
new file mode 100644
index 000000000..4155f5f88
--- /dev/null
+++ b/app/views/traits/trait_search.js.erb
@@ -0,0 +1,2 @@
+jQuery("#results").html("<%= raw @message %>")
+jQuery("#<%= "#{params[:cont]}_trait_id" %>").html("<%= escape_javascript(@options) %>")
diff --git a/app/views/yields/_index_table.html.erb b/app/views/yields/_index_table.html.erb
index 4a004ca80..aefdfd0e1 100644
--- a/app/views/yields/_index_table.html.erb
+++ b/app/views/yields/_index_table.html.erb
@@ -93,11 +93,13 @@
    <%= observe_field("access_level-" + y.id.to_s,
                   :frequency => 1,
                   :with => "'id=' + #{y.id} + '&yield[access_level]=' + Form.Element.getValue('access_level-#{y.id.to_s}')",
-                  :url => { :action => :access_level }) %>
+                  :url => { :action => :access_level },
+                  :event_name => "change") %>
      <%= observe_field("checked-" + y.id.to_s,
                   :frequency => 1,
                   :with => "'id=' + #{y.id} + '&y[checked]=' + Form.Element.getValue('checked-#{y.id.to_s}')",
-                  :url => { :action => :checked }) %>
+                  :url => { :action => :checked },
+                  :event_name => "change") %>
 <% end %>
 
 
diff --git a/app/views/yields/access_level.js.erb b/app/views/yields/access_level.js.erb
new file mode 100644
index 000000000..6cda1274b
--- /dev/null
+++ b/app/views/yields/access_level.js.erb
@@ -0,0 +1,7 @@
+<% if @saved %>
+  jQuery("#<%= @element_id %>").addClass('alert-success', 500)
+  jQuery("#<%= @element_id %>").removeClass('alert-success', 500)
+<% else %>
+  jQuery("#<%= @element_id %>").addClass('alert-error', 500)
+  jQuery("#<%= @element_id %>").removeClass('alert-error', 500)
+<% end %>
diff --git a/app/views/yields/checked.js.erb b/app/views/yields/checked.js.erb
new file mode 100644
index 000000000..96ef48ba7
--- /dev/null
+++ b/app/views/yields/checked.js.erb
@@ -0,0 +1 @@
+jQuery("#<%= @element_id %>").html("<%= raw @message %>")

From 4a5adf8acd0e87ee83cd1884c68e7b2898ea9414 Mon Sep 17 00:00:00 2001
From: Scott Rohde <srohde@igb.illinois.edu>
Date: Tue, 20 Feb 2018 16:10:26 -0600
Subject: [PATCH 18/44] Modify controllers to replace deprecated
 "before_filter" and "after_filter" with "before_action" and "after_action".

---
 app/controllers/api/base_controller.rb               |  2 +-
 app/controllers/api/v1/base_controller.rb            |  4 ++--
 app/controllers/bulk_upload_controller.rb            | 10 +++++-----
 app/controllers/citations_controller.rb              |  2 +-
 app/controllers/citations_sites_controller.rb        |  2 +-
 app/controllers/citations_treatments_controller.rb   |  2 +-
 app/controllers/covariates_controller.rb             |  2 +-
 app/controllers/cultivars_controller.rb              |  2 +-
 app/controllers/dbfiles_controller.rb                |  2 +-
 app/controllers/ensembles_controller.rb              |  2 +-
 app/controllers/entities_controller.rb               |  2 +-
 app/controllers/experiments_controller.rb            |  2 +-
 app/controllers/formats_controller.rb                |  2 +-
 app/controllers/inputs_controller.rb                 |  2 +-
 app/controllers/inputs_runs_controller.rb            |  2 +-
 app/controllers/likelihoods_controller.rb            |  2 +-
 app/controllers/machines_controller.rb               |  2 +-
 app/controllers/managements_controller.rb            |  2 +-
 app/controllers/managements_treatments_controller.rb |  2 +-
 app/controllers/methods_controller.rb                |  2 +-
 app/controllers/models_controller.rb                 |  2 +-
 app/controllers/modeltypes_controller.rb             |  2 +-
 app/controllers/pfts_controller.rb                   |  2 +-
 app/controllers/pfts_priors_controller.rb            |  2 +-
 app/controllers/pfts_species_controller.rb           |  2 +-
 app/controllers/posteriors_controller.rb             |  2 +-
 app/controllers/priors_controller.rb                 |  2 +-
 app/controllers/runs_controller.rb                   |  2 +-
 app/controllers/sitegroups_controller.rb             |  2 +-
 app/controllers/sites_controller.rb                  |  2 +-
 app/controllers/species_controller.rb                |  2 +-
 app/controllers/traits_controller.rb                 |  2 +-
 app/controllers/treatments_controller.rb             |  2 +-
 app/controllers/users_controller.rb                  |  4 ++--
 app/controllers/variables_controller.rb              |  2 +-
 app/controllers/workflows_controller.rb              |  2 +-
 app/controllers/yields_controller.rb                 |  2 +-
 app/controllers/yieldsviews_controller.rb            |  2 +-
 spec/controllers/bulk_upload_controller_spec.rb      |  2 +-
 39 files changed, 45 insertions(+), 45 deletions(-)

diff --git a/app/controllers/api/base_controller.rb b/app/controllers/api/base_controller.rb
index 06dcbf205..05d5f247c 100644
--- a/app/controllers/api/base_controller.rb
+++ b/app/controllers/api/base_controller.rb
@@ -7,7 +7,7 @@ class Api::BaseController < ActionController::Base
   protect_from_forgery with: :null_session
 
   #  before_action :destroy_session <-- Rails 4
-  before_filter :destroy_session
+  before_action :destroy_session
 
   def destroy_session
     request.session_options[:skip] = true
diff --git a/app/controllers/api/v1/base_controller.rb b/app/controllers/api/v1/base_controller.rb
index 2a88c72ec..a417fae24 100644
--- a/app/controllers/api/v1/base_controller.rb
+++ b/app/controllers/api/v1/base_controller.rb
@@ -3,8 +3,8 @@
 class Api::V1::BaseController < Api::BaseController
   include ApiAuthenticationSystem
 
-  before_filter :set_content_type # IMPORTANT: Run this filter first!
-  before_filter :login_required
+  before_action :set_content_type # IMPORTANT: Run this filter first!
+  before_action :login_required
 
   NO_CONSTRAINT = lambda { |value| true }
 
diff --git a/app/controllers/bulk_upload_controller.rb b/app/controllers/bulk_upload_controller.rb
index 1486a103e..dccdc915f 100644
--- a/app/controllers/bulk_upload_controller.rb
+++ b/app/controllers/bulk_upload_controller.rb
@@ -38,12 +38,12 @@
 # of the session variable.
 class BulkUploadController < ApplicationController
 
-  before_filter :login_required
-  before_filter :record_stage
-  before_filter :clear_session_data, only: :start_upload
-  before_filter :valid_file_required, only: [ :choose_global_data_values, :confirm_data, :insert_data ]
+  before_action :login_required
+  before_action :record_stage
+  before_action :clear_session_data, only: :start_upload
+  before_action :valid_file_required, only: [ :choose_global_data_values, :confirm_data, :insert_data ]
 
-  after_filter :record_bulk_upload_citation
+  after_action :record_bulk_upload_citation
 
   private
 
diff --git a/app/controllers/citations_controller.rb b/app/controllers/citations_controller.rb
index 92a64470c..a38eadf58 100644
--- a/app/controllers/citations_controller.rb
+++ b/app/controllers/citations_controller.rb
@@ -1,6 +1,6 @@
 class CitationsController < ApplicationController
 
-  before_filter :login_required 
+  before_action :login_required
   helper_method :sort_column, :sort_direction
 
   require 'csv'
diff --git a/app/controllers/citations_sites_controller.rb b/app/controllers/citations_sites_controller.rb
index da9bd4e3b..9d442b342 100644
--- a/app/controllers/citations_sites_controller.rb
+++ b/app/controllers/citations_sites_controller.rb
@@ -1,5 +1,5 @@
 class CitationsSitesController < ApplicationController
-  before_filter :login_required, :except => [ :show ]
+  before_action :login_required, :except => [ :show ]
 
   require 'csv'
 
diff --git a/app/controllers/citations_treatments_controller.rb b/app/controllers/citations_treatments_controller.rb
index f0ddd02df..9f1b48c2b 100644
--- a/app/controllers/citations_treatments_controller.rb
+++ b/app/controllers/citations_treatments_controller.rb
@@ -1,5 +1,5 @@
 class CitationsTreatmentsController < ApplicationController
-  before_filter :login_required, :except => [ :show ]
+  before_action :login_required, :except => [ :show ]
 
   require 'csv'
 
diff --git a/app/controllers/covariates_controller.rb b/app/controllers/covariates_controller.rb
index 4a160add1..7ef6845ec 100644
--- a/app/controllers/covariates_controller.rb
+++ b/app/controllers/covariates_controller.rb
@@ -1,5 +1,5 @@
 class CovariatesController < ApplicationController
-  before_filter :login_required
+  before_action :login_required
   helper_method :sort_column, :sort_direction
 
   # GET /covariates
diff --git a/app/controllers/cultivars_controller.rb b/app/controllers/cultivars_controller.rb
index ec3aa5654..f8b4f28c8 100644
--- a/app/controllers/cultivars_controller.rb
+++ b/app/controllers/cultivars_controller.rb
@@ -1,5 +1,5 @@
 class CultivarsController < ApplicationController
-  before_filter :login_required, :except => [ :show ]
+  before_action :login_required, :except => [ :show ]
   helper_method :sort_column, :sort_direction
 
   require 'csv'
diff --git a/app/controllers/dbfiles_controller.rb b/app/controllers/dbfiles_controller.rb
index 14a74ab83..e462b4423 100644
--- a/app/controllers/dbfiles_controller.rb
+++ b/app/controllers/dbfiles_controller.rb
@@ -1,6 +1,6 @@
 class DbfilesController < ApplicationController
 
-  before_filter :login_required 
+  before_action :login_required
   helper_method :sort_column, :sort_direction
 
   require 'csv'
diff --git a/app/controllers/ensembles_controller.rb b/app/controllers/ensembles_controller.rb
index e956a1090..96f27175f 100644
--- a/app/controllers/ensembles_controller.rb
+++ b/app/controllers/ensembles_controller.rb
@@ -1,6 +1,6 @@
 class EnsemblesController < ApplicationController
 
-  before_filter :login_required 
+  before_action :login_required
   helper_method :sort_column, :sort_direction
 
   # GET /ensembles
diff --git a/app/controllers/entities_controller.rb b/app/controllers/entities_controller.rb
index a147fef19..6486079bd 100644
--- a/app/controllers/entities_controller.rb
+++ b/app/controllers/entities_controller.rb
@@ -1,7 +1,7 @@
 class EntitiesController < ApplicationController
   require 'will_paginate/array' 
 
-  before_filter :login_required
+  before_action :login_required
 
   # GET /entitys
   # GET /entitys.xml
diff --git a/app/controllers/experiments_controller.rb b/app/controllers/experiments_controller.rb
index ca7817515..c63a63392 100644
--- a/app/controllers/experiments_controller.rb
+++ b/app/controllers/experiments_controller.rb
@@ -1,6 +1,6 @@
 class ExperimentsController < ApplicationController
 
-  before_filter :login_required 
+  before_action :login_required
   helper_method :sort_column, :sort_direction
 
   # GET /experiments
diff --git a/app/controllers/formats_controller.rb b/app/controllers/formats_controller.rb
index 2ea39d971..edfe78dad 100644
--- a/app/controllers/formats_controller.rb
+++ b/app/controllers/formats_controller.rb
@@ -1,6 +1,6 @@
 class FormatsController < ApplicationController
 
-  before_filter :login_required 
+  before_action :login_required
   helper_method :sort_column, :sort_direction
 
   def rem_formats_variables
diff --git a/app/controllers/inputs_controller.rb b/app/controllers/inputs_controller.rb
index e40fc6c63..5b5688bed 100644
--- a/app/controllers/inputs_controller.rb
+++ b/app/controllers/inputs_controller.rb
@@ -1,6 +1,6 @@
 class InputsController < ApplicationController
 
-  before_filter :login_required
+  before_action :login_required
   helper_method :sort_direction, :sort_column
 
   # general autocompletion
diff --git a/app/controllers/inputs_runs_controller.rb b/app/controllers/inputs_runs_controller.rb
index 6c244eb2d..5bb2237cc 100644
--- a/app/controllers/inputs_runs_controller.rb
+++ b/app/controllers/inputs_runs_controller.rb
@@ -1,5 +1,5 @@
 class InputsRunsController < ApplicationController
-  before_filter :login_required, :except => [ :show ]
+  before_action :login_required, :except => [ :show ]
 
   require 'csv'
 
diff --git a/app/controllers/likelihoods_controller.rb b/app/controllers/likelihoods_controller.rb
index d0133eab6..f412ac12c 100644
--- a/app/controllers/likelihoods_controller.rb
+++ b/app/controllers/likelihoods_controller.rb
@@ -1,6 +1,6 @@
 class LikelihoodsController < ApplicationController
 
-  before_filter :login_required 
+  before_action :login_required
   helper_method :sort_column, :sort_direction
 
   # GET /likelihoods
diff --git a/app/controllers/machines_controller.rb b/app/controllers/machines_controller.rb
index 0f7dae1b1..ad125b4a0 100644
--- a/app/controllers/machines_controller.rb
+++ b/app/controllers/machines_controller.rb
@@ -1,6 +1,6 @@
 class MachinesController < ApplicationController
 
-  before_filter :login_required 
+  before_action :login_required
   helper_method :sort_column, :sort_direction
 
   # GET /machines
diff --git a/app/controllers/managements_controller.rb b/app/controllers/managements_controller.rb
index 43df41b40..596a3a15c 100644
--- a/app/controllers/managements_controller.rb
+++ b/app/controllers/managements_controller.rb
@@ -1,5 +1,5 @@
 class ManagementsController < ApplicationController
-  before_filter :login_required
+  before_action :login_required
   helper_method :sort_column, :sort_direction
 
   require 'csv'
diff --git a/app/controllers/managements_treatments_controller.rb b/app/controllers/managements_treatments_controller.rb
index b53abdd58..d6d609694 100644
--- a/app/controllers/managements_treatments_controller.rb
+++ b/app/controllers/managements_treatments_controller.rb
@@ -1,5 +1,5 @@
 class ManagementsTreatmentsController < ApplicationController
-  before_filter :login_required, :except => [ :show ]
+  before_action :login_required, :except => [ :show ]
 
   require 'csv'
 
diff --git a/app/controllers/methods_controller.rb b/app/controllers/methods_controller.rb
index a875aff48..d8f43e4ce 100644
--- a/app/controllers/methods_controller.rb
+++ b/app/controllers/methods_controller.rb
@@ -1,6 +1,6 @@
 class MethodsController < ApplicationController
 
-  before_filter :login_required 
+  before_action :login_required
   helper_method :sort_column, :sort_direction
 
   # GET /methods
diff --git a/app/controllers/models_controller.rb b/app/controllers/models_controller.rb
index 3528f57e0..c81ca9d24 100644
--- a/app/controllers/models_controller.rb
+++ b/app/controllers/models_controller.rb
@@ -1,6 +1,6 @@
 class ModelsController < ApplicationController
 
-  before_filter :login_required 
+  before_action :login_required
   helper_method :sort_column, :sort_direction
 
   def edit_models_files
diff --git a/app/controllers/modeltypes_controller.rb b/app/controllers/modeltypes_controller.rb
index 01154957e..9ce1962c6 100644
--- a/app/controllers/modeltypes_controller.rb
+++ b/app/controllers/modeltypes_controller.rb
@@ -1,6 +1,6 @@
 class ModeltypesController < ApplicationController
 
-  before_filter :login_required 
+  before_action :login_required
   helper_method :sort_column, :sort_direction
 
   def remove_modeltypes_format
diff --git a/app/controllers/pfts_controller.rb b/app/controllers/pfts_controller.rb
index c2d874ea9..cbea9d48a 100644
--- a/app/controllers/pfts_controller.rb
+++ b/app/controllers/pfts_controller.rb
@@ -1,5 +1,5 @@
 class PftsController < ApplicationController
-  before_filter :login_required
+  before_action :login_required
   helper_method :sort_column, :sort_direction
 
   require 'csv'
diff --git a/app/controllers/pfts_priors_controller.rb b/app/controllers/pfts_priors_controller.rb
index a03570bb0..58b2d19b1 100644
--- a/app/controllers/pfts_priors_controller.rb
+++ b/app/controllers/pfts_priors_controller.rb
@@ -1,5 +1,5 @@
 class PftsPriorsController < ApplicationController
-  before_filter :login_required, :except => [ :show ]
+  before_action :login_required, :except => [ :show ]
 
   require 'csv'
 
diff --git a/app/controllers/pfts_species_controller.rb b/app/controllers/pfts_species_controller.rb
index 2cfacc78b..5361a64f5 100644
--- a/app/controllers/pfts_species_controller.rb
+++ b/app/controllers/pfts_species_controller.rb
@@ -1,5 +1,5 @@
 class PftsSpeciesController < ApplicationController
-  before_filter :login_required, :except => [ :show ]
+  before_action :login_required, :except => [ :show ]
 
   require 'csv'
 
diff --git a/app/controllers/posteriors_controller.rb b/app/controllers/posteriors_controller.rb
index 96559de37..78fec86c2 100644
--- a/app/controllers/posteriors_controller.rb
+++ b/app/controllers/posteriors_controller.rb
@@ -1,6 +1,6 @@
 class PosteriorsController < ApplicationController
 
-  before_filter :login_required 
+  before_action :login_required
   helper_method :sort_column, :sort_direction
 
   # GET /posteriors
diff --git a/app/controllers/priors_controller.rb b/app/controllers/priors_controller.rb
index e09c67ec1..02408d3d4 100644
--- a/app/controllers/priors_controller.rb
+++ b/app/controllers/priors_controller.rb
@@ -1,5 +1,5 @@
 class PriorsController < ApplicationController
-  before_filter :login_required
+  before_action :login_required
   helper_method :sort_column, :sort_direction
 
   require 'csv'
diff --git a/app/controllers/runs_controller.rb b/app/controllers/runs_controller.rb
index be5425bbf..d11e54441 100644
--- a/app/controllers/runs_controller.rb
+++ b/app/controllers/runs_controller.rb
@@ -1,6 +1,6 @@
 class RunsController < ApplicationController
 
-  before_filter :login_required 
+  before_action :login_required
   helper_method :sort_column, :sort_direction
 
   # GET /runs
diff --git a/app/controllers/sitegroups_controller.rb b/app/controllers/sitegroups_controller.rb
index 722adb6eb..1b69108f6 100644
--- a/app/controllers/sitegroups_controller.rb
+++ b/app/controllers/sitegroups_controller.rb
@@ -1,6 +1,6 @@
 class SitegroupsController < ApplicationController
 
-  before_filter :login_required 
+  before_action :login_required
   helper_method :sort_column, :sort_direction
 
   def edit_sitegroups_sites
diff --git a/app/controllers/sites_controller.rb b/app/controllers/sites_controller.rb
index 6eee0ac2b..38902d794 100644
--- a/app/controllers/sites_controller.rb
+++ b/app/controllers/sites_controller.rb
@@ -1,5 +1,5 @@
 class SitesController < ApplicationController
-  before_filter :login_required, :except => [ :show ]
+  before_action :login_required, :except => [ :show ]
   helper_method :sort_column, :sort_direction
 
   layout 'application', :except => [ :map ]
diff --git a/app/controllers/species_controller.rb b/app/controllers/species_controller.rb
index deae39c13..2abf199a2 100644
--- a/app/controllers/species_controller.rb
+++ b/app/controllers/species_controller.rb
@@ -2,7 +2,7 @@
 # RAILS3 added above encoding (actually this is needed with Ruby 1.9.2)
 
 class SpeciesController < ApplicationController
-  before_filter :login_required, :except => [ :show ]
+  before_action :login_required, :except => [ :show ]
   helper_method :sort_column, :sort_direction
 
   require 'csv'
diff --git a/app/controllers/traits_controller.rb b/app/controllers/traits_controller.rb
index 989c0068e..fce784b5c 100644
--- a/app/controllers/traits_controller.rb
+++ b/app/controllers/traits_controller.rb
@@ -1,5 +1,5 @@
 class TraitsController < ApplicationController
-  before_filter :login_required, :except => [ :show ]
+  before_action :login_required, :except => [ :show ]
   helper_method :sort_column, :sort_direction
 
   require 'csv'
diff --git a/app/controllers/treatments_controller.rb b/app/controllers/treatments_controller.rb
index 75674870b..69521907a 100644
--- a/app/controllers/treatments_controller.rb
+++ b/app/controllers/treatments_controller.rb
@@ -1,7 +1,7 @@
 require 'will_paginate/array'
 
 class TreatmentsController < ApplicationController
-  before_filter :login_required, :except => [ :show ]
+  before_action :login_required, :except => [ :show ]
 
   helper_method :sort_column, :sort_direction
 
diff --git a/app/controllers/users_controller.rb b/app/controllers/users_controller.rb
index 1759f0241..c00cd3876 100644
--- a/app/controllers/users_controller.rb
+++ b/app/controllers/users_controller.rb
@@ -1,7 +1,7 @@
 class UsersController < ApplicationController
 
-  before_filter :login_required, :except => [:create,:new]
-  #before_filter :login_required
+  before_action :login_required, :except => [:create,:new]
+
   helper_method :sort_column, :sort_direction
 
   def index
diff --git a/app/controllers/variables_controller.rb b/app/controllers/variables_controller.rb
index 2e7510635..b02db28c9 100644
--- a/app/controllers/variables_controller.rb
+++ b/app/controllers/variables_controller.rb
@@ -1,5 +1,5 @@
 class VariablesController < ApplicationController
-  before_filter :login_required
+  before_action :login_required
   helper_method :sort_column, :sort_direction
 
   require 'csv'
diff --git a/app/controllers/workflows_controller.rb b/app/controllers/workflows_controller.rb
index f87094c37..900ab9c0e 100644
--- a/app/controllers/workflows_controller.rb
+++ b/app/controllers/workflows_controller.rb
@@ -1,5 +1,5 @@
 class WorkflowsController < ApplicationController
-  before_filter :login_required, :except => [ :show ]
+  before_action :login_required, :except => [ :show ]
   helper_method :sort_column, :sort_direction
 
   require 'csv'
diff --git a/app/controllers/yields_controller.rb b/app/controllers/yields_controller.rb
index 8d58b42de..4d08e5641 100644
--- a/app/controllers/yields_controller.rb
+++ b/app/controllers/yields_controller.rb
@@ -1,5 +1,5 @@
 class YieldsController < ApplicationController
-  before_filter :login_required, :except => [ :show ]
+  before_action :login_required, :except => [ :show ]
   helper_method :sort_column, :sort_direction
 
   require 'csv'
diff --git a/app/controllers/yieldsviews_controller.rb b/app/controllers/yieldsviews_controller.rb
index 99ee39737..b03d920a9 100644
--- a/app/controllers/yieldsviews_controller.rb
+++ b/app/controllers/yieldsviews_controller.rb
@@ -1,5 +1,5 @@
 class YieldsviewsController < ApplicationController
-  before_filter :login_required
+  before_action :login_required
 
   require 'csv'
 
diff --git a/spec/controllers/bulk_upload_controller_spec.rb b/spec/controllers/bulk_upload_controller_spec.rb
index e033ec77f..697882b2d 100644
--- a/spec/controllers/bulk_upload_controller_spec.rb
+++ b/spec/controllers/bulk_upload_controller_spec.rb
@@ -3,7 +3,7 @@
 
   class BulkUploadController
     # override the login requirement for testing:
-    before_filter :login_required, only: []
+    before_action :login_required, only: []
   end
 
   describe "display csv file" do

From c0794c9af8c6096cecefa07fe63788954cd9e32f Mon Sep 17 00:00:00 2001
From: Scott Rohde <srohde@igb.illinois.edu>
Date: Wed, 21 Feb 2018 15:55:08 -0600
Subject: [PATCH 19/44] Changes to get rid of most deprecation warnings seen
 when running RSpec.

---
 app/controllers/api/base_controller.rb        |  2 +-
 app/controllers/species_controller.rb         |  2 +-
 app/controllers/traits_controller.rb          |  2 +-
 app/views/traits/_new_covariate.html.erb      |  2 +-
 config/application.rb                         |  3 --
 config/routes.rb                              | 12 ++++---
 spec/api/trait_insertion_api_spec.rb          | 16 ++++-----
 .../bulk_upload_controller_spec.rb            | 28 +++++++--------
 spec/controllers/traits_controller_spec.rb    | 18 +++++-----
 .../controllers/treatments_controller_spec.rb | 34 +++++++++----------
 .../bulk_upload_integration_2_spec.rb         |  2 +-
 11 files changed, 61 insertions(+), 60 deletions(-)

diff --git a/app/controllers/api/base_controller.rb b/app/controllers/api/base_controller.rb
index 05d5f247c..3a4b95af6 100644
--- a/app/controllers/api/base_controller.rb
+++ b/app/controllers/api/base_controller.rb
@@ -129,7 +129,7 @@ def fuzzy_match_restrictions(model_or_relation, where_params)
     # remove these from where_params
     where_params.delete_if { |k, v| fuzzy_params.has_key?(k) }
 
-    kv_pairs = fuzzy_params.to_a
+    kv_pairs = fuzzy_params.to_unsafe_h.to_a
     
     where_clause_array = kv_pairs.map { |kv| "#{kv[0]}::text ~* ?" }
     where_clause = where_clause_array.join(" AND ")
diff --git a/app/controllers/species_controller.rb b/app/controllers/species_controller.rb
index 2abf199a2..3a616c5e2 100644
--- a/app/controllers/species_controller.rb
+++ b/app/controllers/species_controller.rb
@@ -51,7 +51,7 @@ def species_search
       @species = Specie.where('LOWER(scientificname) LIKE LOWER(:query) OR LOWER(genus) LIKE LOWER(:query) OR LOWER("AcceptedSymbol") LIKE LOWER(:query) OR LOWER(commonname) LIKE LOWER(:query)' +
                               ' OR LOWER(scientificname) LIKE LOWER(:query2) OR LOWER(genus) LIKE LOWER(:query2) OR LOWER("AcceptedSymbol") LIKE LOWER(:query2) OR LOWER(commonname) LIKE LOWER(:query2)', 
                               {:query => @query + "%", :query2 => "%" + @query + "%"}).limit(100).order("scientificname")
-      @species.uniq!
+      @species.distinct!
     else
       @species = Specie.none
     end
diff --git a/app/controllers/traits_controller.rb b/app/controllers/traits_controller.rb
index fce784b5c..9e72fc604 100644
--- a/app/controllers/traits_controller.rb
+++ b/app/controllers/traits_controller.rb
@@ -229,7 +229,7 @@ def update
               # these "saved" covariates are rolled back if any save errors occur
               saved_covariates << @covariate
             else
-              @trait.errors.add(:covariates, (@covariate.errors.get(:level))[0])
+              @trait.errors.add(:covariates, (@covariate.errors[:level])[0])
             end
           end
         end
diff --git a/app/views/traits/_new_covariate.html.erb b/app/views/traits/_new_covariate.html.erb
index 9d266d16e..458f2517e 100644
--- a/app/views/traits/_new_covariate.html.erb
+++ b/app/views/traits/_new_covariate.html.erb
@@ -1,6 +1,6 @@
 <div class="row">
   <% if covariate.errors.size >0 %>
-    <%= content_tag(:div, "<b>Error</b> : #{(covariate.errors.get(:level))[0]}".html_safe) %>
+    <%= content_tag(:div, "<b>Error</b> : #{(covariate.errors[:level])[0]}".html_safe) %>
   <% end %>
   <div class="three columns alpha">
     <%= label_tag :variable_id %>
diff --git a/config/application.rb b/config/application.rb
index 572a1da6b..3b9e24684 100644
--- a/config/application.rb
+++ b/config/application.rb
@@ -74,8 +74,5 @@ class Application < Rails::Application
 #    config.action_view.javascript_expansions[:defaults] = ['prototype', 'effects']
     # Enable the asset pipeline
     # config.assets.enabled = true
-
-    # Do not swallow errors in after_commit/after_rollback callbacks.
-    config.active_record.raise_in_transactional_callbacks = true
   end
 end
diff --git a/config/routes.rb b/config/routes.rb
index 321556927..532477a10 100644
--- a/config/routes.rb
+++ b/config/routes.rb
@@ -59,11 +59,15 @@
   # Note: This route will make all actions in every controller accessible via GET requests.
   # match ':controller(/:action(/:id(.:format)))'
 
-  # route for autocompletion actions used by the bulk upload wizard:
-  get ':controller/bu_autocomplete', action: 'bu_autocomplete'
+  # routes for autocompletion actions used by the bulk upload wizard:
+  %w{citations cultivars sites species treatments}.each do |controller|
+    get "#{controller}/bu_autocomplete", controller: controller
+  end
 
-  # route for other autocompletion actions:
-  get ':controller/autocomplete', action: 'autocomplete'
+  # routes for other autocompletion actions:
+  %w{citations mimetypes inputs sites variables}.each do |controller|
+    get "#{controller}/autocomplete", controller: controller
+  end
 
   resources :yieldsviews, :only => [:show]
   resources :workflows
diff --git a/spec/api/trait_insertion_api_spec.rb b/spec/api/trait_insertion_api_spec.rb
index cc14432b2..88855ee7c 100644
--- a/spec/api/trait_insertion_api_spec.rb
+++ b/spec/api/trait_insertion_api_spec.rb
@@ -24,7 +24,7 @@
 
         aggregate_failures "Insertion works correctly" do
           expect {
-            post "#{path}?key=3333333333333333333333333333333333333333", valid_data_doc
+            post "#{path}?key=3333333333333333333333333333333333333333", params: valid_data_doc
           }.to change { Trait.count }.by(num_new_traits)
             .and change { Entity.count }.by(num_new_entities)
             .and change { Covariate.count }.by(num_new_covariates)
@@ -51,7 +51,7 @@
 
         aggregate_failures "Insertion fails without proper authorization" do
           expect {
-            post "#{path}?key=4444444444444444444444444444444444444444", valid_data_doc
+            post "#{path}?key=4444444444444444444444444444444444444444", params: valid_data_doc
           }.to change { Trait.count }.by(0)
             .and change { Entity.count }.by(0)
             .and change { Covariate.count }.by(0)
@@ -75,7 +75,7 @@
     include_examples "format", "spec/fixtures/files/api/v1/valid-test-data.json", "JSON", "", "application/json"
 
     specify "Sending a malformed JSON document should return a Bad Request status" do
-      post "/api/v1/traits?key=3333333333333333333333333333333333333333", "{ no-closing-brace "
+      post "/api/v1/traits?key=3333333333333333333333333333333333333333", params: "{ no-closing-brace "
       aggregate_failures do
         expect(response.status).to eq 400
         expect(response.content_type).to eq "application/json"
@@ -93,7 +93,7 @@
     include_examples "format", "spec/fixtures/files/api/v1/valid-test-data.xml", "XML", ".xml", "application/xml"
 
     specify "Sending a malformed XML document should return a Bad Request status" do
-      post "/api/v1/traits.xml?key=3333333333333333333333333333333333333333", "<no-closing-tag>"
+      post "/api/v1/traits.xml?key=3333333333333333333333333333333333333333", params: "<no-closing-tag>"
       aggregate_failures do
         expect(response.status).to eq 400
         expect(response.content_type).to eq "application/xml"
@@ -106,7 +106,7 @@
     end
 
     specify "Sending an invalid XML document should return a Bad Request status" do
-      post "/api/v1/traits.xml?key=3333333333333333333333333333333333333333", "<xml-doc-not-conforming-to-schema/>"
+      post "/api/v1/traits.xml?key=3333333333333333333333333333333333333333", params: "<xml-doc-not-conforming-to-schema/>"
       aggregate_failures do
         expect(response.status).to eq 400
         expect(response.content_type).to eq "application/xml"
@@ -128,7 +128,7 @@
 
       expect {
         post "/api/v1/traits.csv?key=3333333333333333333333333333333333333333",
-          File.open(Rails.root.join "spec/fixtures/files/api/v1/missing-meta-data.csv").read
+          params: File.open(Rails.root.join "spec/fixtures/files/api/v1/missing-meta-data.csv").read
       }.not_to change { Trait.count }
 
     end
@@ -137,7 +137,7 @@
 
       expect {
         post "/api/v1/traits.csv?key=3333333333333333333333333333333333333333",
-          File.open(Rails.root.join "spec/fixtures/files/api/v1/missing-meta-data.csv").read
+          params: File.open(Rails.root.join "spec/fixtures/files/api/v1/missing-meta-data.csv").read
       }.not_to change { Entity.count }
 
     end
@@ -146,7 +146,7 @@
 
       expect {
         post "/api/v1/traits.csv?key=3333333333333333333333333333333333333333",
-          File.open(Rails.root.join "spec/fixtures/files/api/v1/out-of-range-data.csv").read
+          params: File.open(Rails.root.join "spec/fixtures/files/api/v1/out-of-range-data.csv").read
       }.not_to change { Entity.count }
 
     end
diff --git a/spec/controllers/bulk_upload_controller_spec.rb b/spec/controllers/bulk_upload_controller_spec.rb
index 697882b2d..2dc77c361 100644
--- a/spec/controllers/bulk_upload_controller_spec.rb
+++ b/spec/controllers/bulk_upload_controller_spec.rb
@@ -16,7 +16,7 @@ class BulkUploadController
 
       it "should display an error when no file has been uploaded" do
 
-        post 'display_csv_file', { 'new upload' => true }
+        post 'display_csv_file', params: { 'new upload' => true }
         assert_equal("No file chosen", flash[:error] )
         assert_operator(200, :!=, response.status) # Since this is a redirect, we should get 302; this test is somewhat redundant in view of the next.
         assert_redirected_to '/bulk_upload/start_upload', "Failed to redirect when no file chosen"
@@ -25,7 +25,7 @@ class BulkUploadController
       it "should create a data set when a well-formed CSV file is uploaded" do
 
         @file = fixture_file_upload("/files/bulk_upload/sample_yields.csv", "text/csv")
-        post 'display_csv_file', { 'new upload' => true, "CSV file" => @file }
+        post 'display_csv_file', params: { 'new upload' => true, "CSV file" => @file }
         assert(!assigns(:data_set).nil?)
         assert_instance_of BulkUploadDataSet, assigns(:data_set), "Failed to return dataset instance"
       end
@@ -35,7 +35,7 @@ class BulkUploadController
 
         @file = fixture_file_upload("/files/bulk_upload/sample_yields.csv", "text/csv")
         session[:csvpath] = @file.path
-        post 'display_csv_file', { 'new upload' => false }
+        post 'display_csv_file', params: { 'new upload' => false }
         assert(!assigns(:data_set).nil?)
         assert_instance_of BulkUploadDataSet, assigns(:data_set), "Failed to return dataset instance"
       end
@@ -45,7 +45,7 @@ class BulkUploadController
         @file = fixture_file_upload("/files/bulk_upload/sample_yields.csv", "text/csv")
         session[:csvpath] = @file.path
         get 'start_upload'
-        post 'display_csv_file', { 'CSV file' => nil }
+        post 'display_csv_file', params: { 'CSV file' => nil }
         assert_equal("No file chosen", flash[:error])
         assert_operator(200, :!=, response.status)
         assert_redirected_to '/bulk_upload/start_upload', "Failed to redirect when no file chosen"
@@ -66,14 +66,14 @@ class BulkUploadController
         it "should remove a linked citation when a file is uploaded that includes citation information" do
 
           session[:citation] = 1
-          post 'display_csv_file', @form
+          post 'display_csv_file', params: @form
           assert_nil session[:citation], "Failed to remove citation from session"
           expect(flash[:warning]).to match(/^Removing/i)
         end
 
         it "should validate the file data" do
 
-          post 'display_csv_file', @form
+          post 'display_csv_file', params: @form
           @dataset = assigns(:data_set)
           @validated_data = @dataset.validated_data
           assert(!@validated_data.nil?, "Failed to validate rows")
@@ -95,7 +95,7 @@ class BulkUploadController
         ## some error at the data insertion step if they have a null or wrong citation...
         it "should not allow visiting the 'choose_global_data_values' page without having choosen a citation" do
 
-          post 'display_csv_file', @form
+          post 'display_csv_file', params: @form
           session[:citation] = nil
           get 'choose_global_data_values'
           assert_operator(200, :!=, response.status, "Failed to stop when no citation present")
@@ -105,7 +105,7 @@ class BulkUploadController
         it "should not allow visiting the 'choose_global_data_values' page when a citation inconsistent with the data set has been chosen" do
 
           session[:citation] = 4
-          post 'display_csv_file', @form
+          post 'display_csv_file', params: @form
           @dataset = assigns(:data_set)
           # Ensure the citation we set actually *is* inconsistent:
           assert(@dataset.validation_summary.has_key?("Site is inconsistent with citation") && 
@@ -123,7 +123,7 @@ class BulkUploadController
 
           @file = fixture_file_upload("/files/bulk_upload/invalid_file.csv", "text/csv")
           @form = { 'new upload' => true, "CSV file" => @file }
-          post 'display_csv_file', @form
+          post 'display_csv_file', params: @form
           assert(!flash[:error].nil?, "Failed to display error message")
           assert_redirected_to '/bulk_upload/start_upload', "Failed to redirect to start upload"
         end
@@ -139,7 +139,7 @@ class BulkUploadController
       get 'start_upload'
       @file = fixture_file_upload("/files/bulk_upload/sample_yields.csv", "text/csv")
       @form = { 'new upload' => true, "CSV file" => @file }
-      post 'display_csv_file', @form
+      post 'display_csv_file', params: @form
       get 'choose_global_data_values'
     end
 
@@ -156,11 +156,11 @@ class BulkUploadController
     before(:each) do
       get 'start_upload'
       @file = fixture_file_upload("/files/bulk_upload/rounding_demo.csv", "text/csv")
-      post 'display_csv_file', { 'new upload' => true, "CSV file" => @file }
+      post 'display_csv_file', params: { 'new upload' => true, "CSV file" => @file }
       get 'choose_global_data_values'
       @values ={ "global_values" => {}, "rounding" => { "yields" => "2" } }
       request.env["HTTP_REFERER"] = 'choose_global_data_values'
-      post 'confirm_data', @values
+      post 'confirm_data', params: @values
     end
 
     it "should return a new dataset" do
@@ -190,11 +190,11 @@ class BulkUploadController
     before(:each) do
       @count = Yield.count
       @file = fixture_file_upload("/files/bulk_upload/sample_yields.csv", "text/csv")
-      post 'display_csv_file', { 'new upload' => true, "CSV file" => @file }
+      post 'display_csv_file', params: { 'new upload' => true, "CSV file" => @file }
       get 'choose_global_data_values'
       @values ={ "global_values" => {}, "rounding" => { "yields" => "2" } }
       request.env["HTTP_REFERER"] = 'choose_global_data_values'
-      post 'confirm_data', @values
+      post 'confirm_data', params: @values
       session[:user_id] = 1 # needed for the insertion step
       post 'insert_data'
     end
diff --git a/spec/controllers/traits_controller_spec.rb b/spec/controllers/traits_controller_spec.rb
index 983cdd99e..3635d1aba 100644
--- a/spec/controllers/traits_controller_spec.rb
+++ b/spec/controllers/traits_controller_spec.rb
@@ -21,13 +21,13 @@
 	context'message on invalid input' do
     it 'should not return success message' do
 			trait = Trait.find_by_id('2')
-	    post :update,{:id =>trait.to_param,:trait => invalid_attr},session
+	    post :update, params: {:id =>trait.to_param, :trait => invalid_attr}, session: session
 	    assert_operator(flash[:notice], :!=, "Trait was successfully updated.")
 	  end
 
     it 'should return error message' do
 	    trait = Trait.find_by_id('2')
-	    post :update,{:id =>trait.to_param,:covariate => invalid_covariate},session
+	    post :update, params: {:id =>trait.to_param, :covariate => invalid_covariate}, session: session
 	    assert(!flash[:error].nil?)
 	  end
 	end
@@ -38,21 +38,21 @@
     end
 
     it 'should not modify attribute if covariate is invalid' do
-	    post :update,{:id =>@trait.to_param, :covariate => invalid_covariate, :trait =>valid_attr},session
+	    post :update, params: {:id => @trait.to_param, :covariate => invalid_covariate, :trait =>valid_attr}, session: session
       new_trait = Trait.find_by_id('2')
       assert_equal(@trait.mean, new_trait.mean)
     end
 
     it 'should not modify covariate list if attribute is invalid' do
       old_size = @trait.covariates.size
-	    post :update,{:id =>@trait.to_param, :covariate => valid_covariate, :trait => invalid_attr},session
+	    post :update, params: {:id => @trait.to_param, :covariate => valid_covariate, :trait => invalid_attr}, session: session
       new_trait = Trait.find_by_id('2')
       assert_equal(old_size, new_trait.covariates.size)
     end
 
     it 'should not modify covariate list if any covariate is invalid' do
       old_size = @trait.covariates.size
-	    post :update,{:id =>@trait.to_param, :covariate => mixed_covariate, :trait =>valid_attr},session
+	    post :update, params: {:id => @trait.to_param, :covariate => mixed_covariate, :trait =>valid_attr}, session: session
       new_trait = Trait.find_by_id('2')
       assert_equal(old_size, new_trait.covariates.size)
     end
@@ -65,22 +65,22 @@
     end
 
     it "should render edit action" do
-	    post :update,{:id =>@trait.to_param,:trait => invalid_attr},session
+	    post :update, params: {:id => @trait.to_param, :trait => invalid_attr}, session: session
 	    assert_template 'edit', "Failed to render edit action"
     end
 
     it "should display error messages" do
-	    post :update,{:id =>@trait.to_param,:trait => invalid_attr},session
+	    post :update, params: {:id => @trait.to_param, :trait => invalid_attr}, session: session
 	    expect(response.body).to have_content("2 errors")
     end
 
     it "should not change attribute inputs" do
-	    post :update,{:id =>@trait.to_param,:trait => invalid_attr},session
+	    post :update, params: {:id => @trait.to_param, :trait => invalid_attr}, session: session
       expect(response.body).to have_selector("input#trait_mean[value = '#{invalid_attr[:mean]}']")
     end
 
     it "should not change covariate inputs" do
-	    post :update,{:id =>@trait.to_param,:trait => invalid_attr, :covariate =>invalid_covariate},session
+	    post :update, params: {:id => @trait.to_param, :trait => invalid_attr, :covariate =>invalid_covariate}, session: session
 	    expect(response.body).to have_xpath(".//select[@id='covariate__variable_id']/option[@value='404' and @selected='selected']")
     end
   end
diff --git a/spec/controllers/treatments_controller_spec.rb b/spec/controllers/treatments_controller_spec.rb
index fce08d517..15bcdeb60 100644
--- a/spec/controllers/treatments_controller_spec.rb
+++ b/spec/controllers/treatments_controller_spec.rb
@@ -39,7 +39,7 @@
   describe "GET index" do
     it "assigns all treatments associated with the session citation as @treatments" do
       treatments = Citation.find(valid_session[:citation]).treatments
-      get :index, {}, valid_session
+      get :index, params: {}, session: valid_session
       expect(assigns(:treatments)).to eq(treatments)
     end
   end
@@ -47,14 +47,14 @@
   describe "GET show" do
     it "assigns the requested treatment as @treatment" do
       treatment = Treatment.create! valid_attributes
-      get :show, {:id => treatment.to_param}, valid_session
+      get :show, params: {:id => treatment.to_param}, session: valid_session
       expect(assigns(:treatment)).to eq(treatment)
     end
   end
 
   describe "GET new" do
     it "assigns a new treatment as @treatment" do
-      get :new, {}, valid_session
+      get :new, params: {}, session: valid_session
       expect(assigns(:treatment)).to be_a_new(Treatment)
     end
   end
@@ -62,7 +62,7 @@
   describe "GET edit" do
     it "assigns the requested treatment as @treatment" do
       treatment = Treatment.create! valid_attributes
-      get :edit, {:id => treatment.to_param}, valid_session
+      get :edit, params: {:id => treatment.to_param}, session: valid_session
       expect(assigns(:treatment)).to eq(treatment)
     end
   end
@@ -71,18 +71,18 @@
     describe "with valid params" do
       it "creates a new Treatment" do
         expect {
-          post :create, {:treatment => valid_attributes}, valid_session
+          post :create, params: {:treatment => valid_attributes}, session: valid_session
         }.to change(Treatment, :count).by(1)
       end
 
       it "assigns a newly created treatment as @treatment" do
-        post :create, {:treatment => valid_attributes}, valid_session
+        post :create, params: {:treatment => valid_attributes}, session: valid_session
         expect(assigns(:treatment)).to be_a(Treatment)
         expect(assigns(:treatment)).to be_persisted
       end
 
       it "redirects to the treatment index page" do
-        post :create, {:treatment => valid_attributes}, valid_session
+        post :create, params: {:treatment => valid_attributes}, session: valid_session
         expect(response).to redirect_to(action: :index)
       end
     end
@@ -91,14 +91,14 @@
       it "assigns a newly created but unsaved treatment as @treatment" do
         # Trigger the behavior that occurs when invalid params are submitted
         allow_any_instance_of(Treatment).to receive(:save).and_return(false)
-        post :create, {}, valid_session
+        post :create, params: {}, session: valid_session
         expect(assigns(:treatment)).to be_a_new(Treatment)
       end
 
       it "re-renders the 'new' template" do
         # Trigger the behavior that occurs when invalid params are submitted
         allow_any_instance_of(Treatment).to receive(:save).and_return(false)
-        post :create, {}, valid_session
+        post :create, params: {}, session: valid_session
         expect(response).to render_template("new")
       end
     end
@@ -112,19 +112,19 @@
         # specifies that the Treatment created on the previous line
         # receives the :update_attributes message with whatever params are
         # submitted in the request.
-        expect_any_instance_of(Treatment).to receive(:update_attributes).with({ "these" => "params" })
-        put :update, {:id => treatment.to_param, :treatment => { "these" => "params" }}, valid_session
+        expect_any_instance_of(Treatment).to receive(:update_attributes).with(ActionController::Parameters.new({ "these" => "params" }))
+        put :update, params: {:id => treatment.to_param, :treatment => { "these" => "params" }}, session: valid_session
       end
 
       it "assigns the requested treatment as @treatment" do
         treatment = Treatment.create! valid_attributes
-        put :update, {:id => treatment.to_param, :treatment => valid_attributes}, valid_session
+        put :update, params: {:id => treatment.to_param, :treatment => valid_attributes}, session: valid_session
         expect(assigns(:treatment)).to eq(treatment)
       end
 
       it "redirects to the treatment index page" do
         treatment = Treatment.create! valid_attributes
-        put :update, {:id => treatment.to_param, :treatment => valid_attributes}, valid_session
+        put :update, params: {:id => treatment.to_param, :treatment => valid_attributes}, session: valid_session
         expect(response).to redirect_to(treatments_path)
       end
     end
@@ -134,7 +134,7 @@
         treatment = Treatment.create! valid_attributes
         # Trigger the behavior that occurs when invalid params are submitted
         allow_any_instance_of(Treatment).to receive(:save).and_return(false)
-        put :update, {:id => treatment.to_param, :treatment => invalid_attribute_set}, valid_session
+        put :update, params: {:id => treatment.to_param, :treatment => invalid_attribute_set}, session: valid_session
         expect(assigns(:treatment)).to eq(treatment)
       end
 
@@ -142,7 +142,7 @@
         treatment = Treatment.create! valid_attributes
         # Trigger the behavior that occurs when invalid params are submitted
         allow_any_instance_of(Treatment).to receive(:save).and_return(false)
-        put :update, {:id => treatment.to_param, :treatment => invalid_attribute_set}, valid_session
+        put :update, params: {:id => treatment.to_param, :treatment => invalid_attribute_set}, session: valid_session
         expect(response).to render_template("edit")
       end
     end
@@ -152,13 +152,13 @@
     it "destroys the requested treatment" do
       treatment = Treatment.create! valid_attributes
       expect {
-        delete :destroy, {:id => treatment.to_param}, valid_session
+        delete :destroy, params: {:id => treatment.to_param}, session: valid_session
       }.to change(Treatment, :count).by(-1)
     end
 
     it "redirects to the treatments list" do
       treatment = Treatment.create! valid_attributes
-      delete :destroy, {:id => treatment.to_param}, valid_session
+      delete :destroy, params: {:id => treatment.to_param}, session: valid_session
       expect(response).to redirect_to(treatments_path)
     end
   end
diff --git a/spec/features/bulk_upload_integration_2_spec.rb b/spec/features/bulk_upload_integration_2_spec.rb
index b0567359e..b8b8613b5 100644
--- a/spec/features/bulk_upload_integration_2_spec.rb
+++ b/spec/features/bulk_upload_integration_2_spec.rb
@@ -447,7 +447,7 @@
                      : 30 # than for WebKit
         begin
           # Wrap while loops in timeout in case some deletion fails
-          timeout time_limit do
+          Timeout.timeout time_limit do
 
             # Remove covariates before traits because they refer to traits:
             visit '/covariates'

From 1ef1a19fda74b9e6314526b9923da64a7b17f078 Mon Sep 17 00:00:00 2001
From: Scott Rohde <srohde@igb.illinois.edu>
Date: Fri, 23 Feb 2018 10:19:44 -0600
Subject: [PATCH 20/44] Modified comments only.

---
 config/routes.rb | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/config/routes.rb b/config/routes.rb
index 532477a10..b67cccb57 100644
--- a/config/routes.rb
+++ b/config/routes.rb
@@ -1,4 +1,5 @@
 Rails.application.routes.draw do
+  # For details on the DSL available within this file, see http://guides.rubyonrails.org/routing.html
   apipie
   # The priority is based upon order of creation: first created -> highest priority.
   # See how all your routes lay out with "rake routes".
@@ -55,10 +56,6 @@
   #     resources :products
   #   end
 
-  # This is a legacy wild controller route that's not recommended for RESTful applications.
-  # Note: This route will make all actions in every controller accessible via GET requests.
-  # match ':controller(/:action(/:id(.:format)))'
-
   # routes for autocompletion actions used by the bulk upload wizard:
   %w{citations cultivars sites species treatments}.each do |controller|
     get "#{controller}/bu_autocomplete", controller: controller

From 34bf012459715691255404f422a416021ee0c4be Mon Sep 17 00:00:00 2001
From: Scott Rohde <srohde@igb.illinois.edu>
Date: Mon, 26 Feb 2018 11:59:01 -0600
Subject: [PATCH 21/44] Moved assets in public/images, public/javascripts, and
 public/stylesheets into the app/assets directory.

---
 {public => app/assets}/images/.gitignore            |   0
 {public => app/assets}/images/4.jpg                 | Bin
 {public => app/assets}/images/EBI-Logo.jpg          | Bin
 {public => app/assets}/images/Sorting icons.psd     | Bin
 {public => app/assets}/images/arrow-gr.png          | Bin
 {public => app/assets}/images/back_disabled.png     | Bin
 {public => app/assets}/images/back_enabled.png      | Bin
 .../assets}/images/back_enabled_hover.png           | Bin
 {public => app/assets}/images/bety-db.png           | Bin
 {public => app/assets}/images/bg-grain-grey.jpg     | Bin
 {public => app/assets}/images/bg-nav-item.png       | Bin
 {public => app/assets}/images/bg-nav.jpg            | Bin
 {public => app/assets}/images/blu-circle_maps.png   | Bin
 {public => app/assets}/images/blueball.gif          | Bin
 {public => app/assets}/images/blueball.png          | Bin
 {public => app/assets}/images/ch_beg_r.gif          | Bin
 {public => app/assets}/images/ch_beg_r.png          | Bin
 {public => app/assets}/images/ch_begin.gif          | Bin
 {public => app/assets}/images/ch_begin.png          | Bin
 {public => app/assets}/images/ch_del_r.gif          | Bin
 {public => app/assets}/images/ch_del_r.png          | Bin
 {public => app/assets}/images/ch_delet.gif          | Bin
 {public => app/assets}/images/ch_delet.png          | Bin
 {public => app/assets}/images/ch_end.gif            | Bin
 {public => app/assets}/images/ch_end.png            | Bin
 {public => app/assets}/images/ch_end_r.gif          | Bin
 {public => app/assets}/images/ch_end_r.png          | Bin
 {public => app/assets}/images/check.gif             | Bin
 {public => app/assets}/images/citations_new.png     | Bin
 {public => app/assets}/images/contents.gif          | Bin
 {public => app/assets}/images/contents.png          | Bin
 {public => app/assets}/images/crossref.gif          | Bin
 {public => app/assets}/images/crossref.png          | Bin
 .../assets}/images/custom/arpa-e-logo.png           | Bin
 {public => app/assets}/images/custom/doe-logo.png   | Bin
 .../assets}/images/custom/mac_sorghum.jpg           | Bin
 .../assets}/images/custom/terraref-logo.png         | Bin
 {public => app/assets}/images/database_stats.png    | Bin
 {public => app/assets}/images/db_header.png         | Bin
 {public => app/assets}/images/down_arrow.gif        | Bin
 {public => app/assets}/images/drop-over.png         | Bin
 {public => app/assets}/images/drop.png              | Bin
 {public => app/assets}/images/drop2.png             | Bin
 {public => app/assets}/images/eye.png               | Bin
 {public => app/assets}/images/favicon.ico           | Bin
 {public => app/assets}/images/feedback-tab.png      | Bin
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diff --git a/public/stylesheets/themes/alert.css b/app/assets/stylesheets/themes/alert.css
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diff --git a/public/stylesheets/themes/alphacube.css b/app/assets/stylesheets/themes/alphacube.css
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diff --git a/public/stylesheets/themes/default/clear.gif b/app/assets/stylesheets/themes/default/clear.gif
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diff --git a/public/stylesheets/themes/iefix/blank.gif b/app/assets/stylesheets/themes/iefix/blank.gif
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diff --git a/public/stylesheets/windows_js_1.3/documentation/themes/spread/button-max-focus.gif b/app/assets/stylesheets/windows_js_1.3/documentation/themes/spread/button-max-focus.gif
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rename from public/stylesheets/windows_js_1.3/documentation/themes/spread/button-max-focus.gif
rename to app/assets/stylesheets/windows_js_1.3/documentation/themes/spread/button-max-focus.gif
diff --git a/public/stylesheets/windows_js_1.3/documentation/themes/spread/button-min-focus.gif b/app/assets/stylesheets/windows_js_1.3/documentation/themes/spread/button-min-focus.gif
similarity index 100%
rename from public/stylesheets/windows_js_1.3/documentation/themes/spread/button-min-focus.gif
rename to app/assets/stylesheets/windows_js_1.3/documentation/themes/spread/button-min-focus.gif
diff --git a/public/stylesheets/windows_js_1.3/documentation/themes/spread/frame-left.gif b/app/assets/stylesheets/windows_js_1.3/documentation/themes/spread/frame-left.gif
similarity index 100%
rename from public/stylesheets/windows_js_1.3/documentation/themes/spread/frame-left.gif
rename to app/assets/stylesheets/windows_js_1.3/documentation/themes/spread/frame-left.gif
diff --git a/public/stylesheets/windows_js_1.3/documentation/themes/spread/frame-right.gif b/app/assets/stylesheets/windows_js_1.3/documentation/themes/spread/frame-right.gif
similarity index 100%
rename from public/stylesheets/windows_js_1.3/documentation/themes/spread/frame-right.gif
rename to app/assets/stylesheets/windows_js_1.3/documentation/themes/spread/frame-right.gif
diff --git a/public/stylesheets/windows_js_1.3/documentation/themes/spread/left-top.gif b/app/assets/stylesheets/windows_js_1.3/documentation/themes/spread/left-top.gif
similarity index 100%
rename from public/stylesheets/windows_js_1.3/documentation/themes/spread/left-top.gif
rename to app/assets/stylesheets/windows_js_1.3/documentation/themes/spread/left-top.gif
diff --git a/public/stylesheets/windows_js_1.3/documentation/themes/spread/right-top.gif b/app/assets/stylesheets/windows_js_1.3/documentation/themes/spread/right-top.gif
similarity index 100%
rename from public/stylesheets/windows_js_1.3/documentation/themes/spread/right-top.gif
rename to app/assets/stylesheets/windows_js_1.3/documentation/themes/spread/right-top.gif
diff --git a/public/stylesheets/windows_js_1.3/documentation/themes/spread/top-middle.gif b/app/assets/stylesheets/windows_js_1.3/documentation/themes/spread/top-middle.gif
similarity index 100%
rename from public/stylesheets/windows_js_1.3/documentation/themes/spread/top-middle.gif
rename to app/assets/stylesheets/windows_js_1.3/documentation/themes/spread/top-middle.gif
diff --git a/public/stylesheets/windows_js_1.3/helper/prototype_window_class_helper.rb b/app/assets/stylesheets/windows_js_1.3/helper/prototype_window_class_helper.rb
similarity index 100%
rename from public/stylesheets/windows_js_1.3/helper/prototype_window_class_helper.rb
rename to app/assets/stylesheets/windows_js_1.3/helper/prototype_window_class_helper.rb
diff --git a/public/stylesheets/windows_js_1.3/javascripts/debug.js b/app/assets/stylesheets/windows_js_1.3/javascripts/debug.js
similarity index 100%
rename from public/stylesheets/windows_js_1.3/javascripts/debug.js
rename to app/assets/stylesheets/windows_js_1.3/javascripts/debug.js
diff --git a/public/stylesheets/windows_js_1.3/javascripts/effects.js b/app/assets/stylesheets/windows_js_1.3/javascripts/effects.js
similarity index 100%
rename from public/stylesheets/windows_js_1.3/javascripts/effects.js
rename to app/assets/stylesheets/windows_js_1.3/javascripts/effects.js
diff --git a/public/stylesheets/windows_js_1.3/javascripts/extended_debug.js b/app/assets/stylesheets/windows_js_1.3/javascripts/extended_debug.js
similarity index 100%
rename from public/stylesheets/windows_js_1.3/javascripts/extended_debug.js
rename to app/assets/stylesheets/windows_js_1.3/javascripts/extended_debug.js
diff --git a/public/stylesheets/windows_js_1.3/javascripts/prototype.js b/app/assets/stylesheets/windows_js_1.3/javascripts/prototype.js
similarity index 100%
rename from public/stylesheets/windows_js_1.3/javascripts/prototype.js
rename to app/assets/stylesheets/windows_js_1.3/javascripts/prototype.js
diff --git a/public/stylesheets/windows_js_1.3/javascripts/tooltip.js b/app/assets/stylesheets/windows_js_1.3/javascripts/tooltip.js
similarity index 100%
rename from public/stylesheets/windows_js_1.3/javascripts/tooltip.js
rename to app/assets/stylesheets/windows_js_1.3/javascripts/tooltip.js
diff --git a/public/stylesheets/windows_js_1.3/javascripts/window_effects.js b/app/assets/stylesheets/windows_js_1.3/javascripts/window_effects.js
similarity index 100%
rename from public/stylesheets/windows_js_1.3/javascripts/window_effects.js
rename to app/assets/stylesheets/windows_js_1.3/javascripts/window_effects.js
diff --git a/public/stylesheets/windows_js_1.3/javascripts/window_ext.js b/app/assets/stylesheets/windows_js_1.3/javascripts/window_ext.js
similarity index 100%
rename from public/stylesheets/windows_js_1.3/javascripts/window_ext.js
rename to app/assets/stylesheets/windows_js_1.3/javascripts/window_ext.js
diff --git a/public/stylesheets/windows_js_1.3/samples/constraint.html b/app/assets/stylesheets/windows_js_1.3/samples/constraint.html
similarity index 100%
rename from public/stylesheets/windows_js_1.3/samples/constraint.html
rename to app/assets/stylesheets/windows_js_1.3/samples/constraint.html
diff --git a/public/stylesheets/windows_js_1.3/samples/dialog.html b/app/assets/stylesheets/windows_js_1.3/samples/dialog.html
similarity index 100%
rename from public/stylesheets/windows_js_1.3/samples/dialog.html
rename to app/assets/stylesheets/windows_js_1.3/samples/dialog.html
diff --git a/public/stylesheets/windows_js_1.3/samples/dialog_ajax.html b/app/assets/stylesheets/windows_js_1.3/samples/dialog_ajax.html
similarity index 100%
rename from public/stylesheets/windows_js_1.3/samples/dialog_ajax.html
rename to app/assets/stylesheets/windows_js_1.3/samples/dialog_ajax.html
diff --git a/public/stylesheets/windows_js_1.3/samples/inframe.html b/app/assets/stylesheets/windows_js_1.3/samples/inframe.html
similarity index 100%
rename from public/stylesheets/windows_js_1.3/samples/inframe.html
rename to app/assets/stylesheets/windows_js_1.3/samples/inframe.html
diff --git a/public/stylesheets/windows_js_1.3/samples/inset.html b/app/assets/stylesheets/windows_js_1.3/samples/inset.html
similarity index 100%
rename from public/stylesheets/windows_js_1.3/samples/inset.html
rename to app/assets/stylesheets/windows_js_1.3/samples/inset.html
diff --git a/public/stylesheets/windows_js_1.3/samples/multi_modal.html b/app/assets/stylesheets/windows_js_1.3/samples/multi_modal.html
similarity index 100%
rename from public/stylesheets/windows_js_1.3/samples/multi_modal.html
rename to app/assets/stylesheets/windows_js_1.3/samples/multi_modal.html
diff --git a/public/stylesheets/windows_js_1.3/samples/oldFirstSampleCode.html b/app/assets/stylesheets/windows_js_1.3/samples/oldFirstSampleCode.html
similarity index 100%
rename from public/stylesheets/windows_js_1.3/samples/oldFirstSampleCode.html
rename to app/assets/stylesheets/windows_js_1.3/samples/oldFirstSampleCode.html
diff --git a/public/stylesheets/windows_js_1.3/samples/openInside.html b/app/assets/stylesheets/windows_js_1.3/samples/openInside.html
similarity index 100%
rename from public/stylesheets/windows_js_1.3/samples/openInside.html
rename to app/assets/stylesheets/windows_js_1.3/samples/openInside.html
diff --git a/public/stylesheets/windows_js_1.3/samples/parent.html b/app/assets/stylesheets/windows_js_1.3/samples/parent.html
similarity index 100%
rename from public/stylesheets/windows_js_1.3/samples/parent.html
rename to app/assets/stylesheets/windows_js_1.3/samples/parent.html
diff --git a/public/stylesheets/windows_js_1.3/samples/popup_open.html b/app/assets/stylesheets/windows_js_1.3/samples/popup_open.html
similarity index 100%
rename from public/stylesheets/windows_js_1.3/samples/popup_open.html
rename to app/assets/stylesheets/windows_js_1.3/samples/popup_open.html
diff --git a/public/stylesheets/windows_js_1.3/samples/rico/index.html b/app/assets/stylesheets/windows_js_1.3/samples/rico/index.html
similarity index 100%
rename from public/stylesheets/windows_js_1.3/samples/rico/index.html
rename to app/assets/stylesheets/windows_js_1.3/samples/rico/index.html
diff --git a/public/stylesheets/windows_js_1.3/samples/rico/properties_1.gif b/app/assets/stylesheets/windows_js_1.3/samples/rico/properties_1.gif
similarity index 100%
rename from public/stylesheets/windows_js_1.3/samples/rico/properties_1.gif
rename to app/assets/stylesheets/windows_js_1.3/samples/rico/properties_1.gif
diff --git a/public/stylesheets/windows_js_1.3/samples/rico/rico.css b/app/assets/stylesheets/windows_js_1.3/samples/rico/rico.css
similarity index 100%
rename from public/stylesheets/windows_js_1.3/samples/rico/rico.css
rename to app/assets/stylesheets/windows_js_1.3/samples/rico/rico.css
diff --git a/public/stylesheets/windows_js_1.3/samples/rico/rico_change.js b/app/assets/stylesheets/windows_js_1.3/samples/rico/rico_change.js
similarity index 100%
rename from public/stylesheets/windows_js_1.3/samples/rico/rico_change.js
rename to app/assets/stylesheets/windows_js_1.3/samples/rico/rico_change.js
diff --git a/public/stylesheets/windows_js_1.3/samples/tooltips/tooltip.html b/app/assets/stylesheets/windows_js_1.3/samples/tooltips/tooltip.html
similarity index 100%
rename from public/stylesheets/windows_js_1.3/samples/tooltips/tooltip.html
rename to app/assets/stylesheets/windows_js_1.3/samples/tooltips/tooltip.html
diff --git a/public/stylesheets/windows_js_1.3/samples/tooltips/tooltip_ajax.html b/app/assets/stylesheets/windows_js_1.3/samples/tooltips/tooltip_ajax.html
similarity index 100%
rename from public/stylesheets/windows_js_1.3/samples/tooltips/tooltip_ajax.html
rename to app/assets/stylesheets/windows_js_1.3/samples/tooltips/tooltip_ajax.html
diff --git a/public/stylesheets/windows_js_1.3/samples/tooltips/tooltip_url.html b/app/assets/stylesheets/windows_js_1.3/samples/tooltips/tooltip_url.html
similarity index 100%
rename from public/stylesheets/windows_js_1.3/samples/tooltips/tooltip_url.html
rename to app/assets/stylesheets/windows_js_1.3/samples/tooltips/tooltip_url.html
diff --git a/public/stylesheets/windows_js_1.3/samples/window_key.html b/app/assets/stylesheets/windows_js_1.3/samples/window_key.html
similarity index 100%
rename from public/stylesheets/windows_js_1.3/samples/window_key.html
rename to app/assets/stylesheets/windows_js_1.3/samples/window_key.html
diff --git a/public/stylesheets/windows_js_1.3/samples/window_key_url_content.html b/app/assets/stylesheets/windows_js_1.3/samples/window_key_url_content.html
similarity index 100%
rename from public/stylesheets/windows_js_1.3/samples/window_key_url_content.html
rename to app/assets/stylesheets/windows_js_1.3/samples/window_key_url_content.html
diff --git a/public/stylesheets/windows_js_1.3/samples/window_store.html b/app/assets/stylesheets/windows_js_1.3/samples/window_store.html
similarity index 100%
rename from public/stylesheets/windows_js_1.3/samples/window_store.html
rename to app/assets/stylesheets/windows_js_1.3/samples/window_store.html

From 78fe1e36f906af54783b99cdd59c8908171a1b12 Mon Sep 17 00:00:00 2001
From: Scott Rohde <srohde@igb.illinois.edu>
Date: Tue, 27 Feb 2018 16:07:22 -0600
Subject: [PATCH 22/44] Renamed some stylesheets to ERB templates.

---
 app/assets/stylesheets/{base.css => base.css.erb}         | 0
 app/assets/stylesheets/{dropdown.css => dropdown.css.erb} | 0
 app/assets/stylesheets/{layout.css => layout.css.erb}     | 0
 app/assets/stylesheets/{tables.css => tables.css.erb}     | 0
 4 files changed, 0 insertions(+), 0 deletions(-)
 rename app/assets/stylesheets/{base.css => base.css.erb} (100%)
 rename app/assets/stylesheets/{dropdown.css => dropdown.css.erb} (100%)
 rename app/assets/stylesheets/{layout.css => layout.css.erb} (100%)
 rename app/assets/stylesheets/{tables.css => tables.css.erb} (100%)

diff --git a/app/assets/stylesheets/base.css b/app/assets/stylesheets/base.css.erb
similarity index 100%
rename from app/assets/stylesheets/base.css
rename to app/assets/stylesheets/base.css.erb
diff --git a/app/assets/stylesheets/dropdown.css b/app/assets/stylesheets/dropdown.css.erb
similarity index 100%
rename from app/assets/stylesheets/dropdown.css
rename to app/assets/stylesheets/dropdown.css.erb
diff --git a/app/assets/stylesheets/layout.css b/app/assets/stylesheets/layout.css.erb
similarity index 100%
rename from app/assets/stylesheets/layout.css
rename to app/assets/stylesheets/layout.css.erb
diff --git a/app/assets/stylesheets/tables.css b/app/assets/stylesheets/tables.css.erb
similarity index 100%
rename from app/assets/stylesheets/tables.css
rename to app/assets/stylesheets/tables.css.erb

From 134455b6739014492ba4d275bb5ab1113331b85e Mon Sep 17 00:00:00 2001
From: Scott Rohde <srohde@igb.illinois.edu>
Date: Tue, 27 Feb 2018 17:42:00 -0600
Subject: [PATCH 23/44] Several changes to facilitate use of the asset
 pipeline:

Gemfile, Gemfile.lock:

Added Gems "sass-rails", "coffee-rails", and "uglifier".  Added "jquery-rails",
commented-out for now.  Regenerated lock file.

application.js:

Added require directives, using the application.html.erb layout as a model.

application.css:

Created, and added require directives, using the application.html.erb layout as
a model.

base.css.erb, dropdown.css.erb, layout.css.erb, tables.css.erb:

Use the "asset_path" helper when setting URLs for background images.

scaffold.css:

Fix syntax error in rule for "div#banner a.logo" selector.

application.html.erb:

Changed charset from iso-8859-1 to utf-8 (long overdue!).

Added directives to include manifest files application.js and application.css.

Commented out all all javascript_include_tag and stylesheet_link_tag directives
except those included conditionally now that we use manifest files (but keep the
commented-out lines for now for documentation).

config/initializers/assets.rb:

Set the version.
Added needed files to the precompile set.
---
 Gemfile                                 |  8 ++-
 Gemfile.lock                            | 28 +++++++++++
 app/assets/javascripts/application.js   | 24 +++++++++
 app/assets/stylesheets/application.css  | 25 ++++++++++
 app/assets/stylesheets/base.css.erb     |  4 +-
 app/assets/stylesheets/dropdown.css.erb | 18 +++----
 app/assets/stylesheets/layout.css.erb   | 21 ++++----
 app/assets/stylesheets/scaffold.css     |  2 +-
 app/assets/stylesheets/tables.css.erb   | 22 ++++-----
 app/views/layouts/application.html.erb  | 66 ++++++++++++++-----------
 config/initializers/assets.rb           | 10 +++-
 11 files changed, 160 insertions(+), 68 deletions(-)
 create mode 100644 app/assets/stylesheets/application.css

diff --git a/Gemfile b/Gemfile
index 7f686af6a..82e9d773e 100644
--- a/Gemfile
+++ b/Gemfile
@@ -26,9 +26,13 @@ gem 'yajl-ruby', '~> 1.3.1'
 gem 'rubyzip', '~> 1.2.1'
 gem 'activerecord-session_store' # no longer part of Rails proper
 gem 'protected_attributes_continued' # Use this until and unless we start using Strong Parameters.
+gem 'sass-rails'
+gem 'coffee-rails'
+gem 'uglifier'
 
-# to-do: remove prototype dependencies so we no longer need this gem
-#gem 'prototype_legacy_helper', '0.0.0', :git => 'git://github.com/rails/prototype_legacy_helper.git'
+
+# to-do: Use this Gem instead of adding the library to the assets directory.
+## gem 'jquery-rails'
 
 gem 'memoist'
 
diff --git a/Gemfile.lock b/Gemfile.lock
index fff127821..a8f1c3439 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -70,6 +70,13 @@ GEM
       ffi (~> 1.0, >= 1.0.11)
     choice (0.1.6)
     coderay (1.1.2)
+    coffee-rails (4.2.2)
+      coffee-script (>= 2.2.0)
+      railties (>= 4.0.0)
+    coffee-script (2.4.1)
+      coffee-script-source
+      execjs
+    coffee-script-source (1.12.2)
     comma (3.0.4)
     concurrent-ruby (1.0.5)
     crass (1.0.3)
@@ -77,6 +84,7 @@ GEM
     diff-lcs (1.3)
     dynamic_form (1.1.4)
     erubis (2.7.0)
+    execjs (2.7.0)
     ffi (1.9.18)
     globalid (0.4.1)
       activesupport (>= 4.2.0)
@@ -150,6 +158,9 @@ GEM
       rake (>= 0.8.7)
       thor (>= 0.18.1, < 2.0)
     rake (12.3.0)
+    rb-fsevent (0.10.2)
+    rb-inotify (0.9.10)
+      ffi (>= 0.5.0, < 2)
     recaptcha (0.3.4)
     rgeo (0.5.0)
     rgeo-activerecord (5.0.1)
@@ -184,6 +195,17 @@ GEM
     rubyzip (1.2.1)
     safe_attributes (1.0.10)
       activerecord (>= 3.0.0)
+    sass (3.5.5)
+      sass-listen (~> 4.0.0)
+    sass-listen (4.0.0)
+      rb-fsevent (~> 0.9, >= 0.9.4)
+      rb-inotify (~> 0.9, >= 0.9.7)
+    sass-rails (5.0.7)
+      railties (>= 4.0.0, < 6)
+      sass (~> 3.1)
+      sprockets (>= 2.8, < 4.0)
+      sprockets-rails (>= 2.0, < 4.0)
+      tilt (>= 1.1, < 3)
     seer (0.10.0)
     selenium-webdriver (3.8.0)
       childprocess (~> 0.5)
@@ -197,9 +219,12 @@ GEM
       sprockets (>= 3.0.0)
     thor (0.20.0)
     thread_safe (0.3.6)
+    tilt (2.0.8)
     trollop (2.1.2)
     tzinfo (1.2.4)
       thread_safe (~> 0.1)
+    uglifier (4.1.6)
+      execjs (>= 0.3.0, < 3)
     websocket-driver (0.6.5)
       websocket-extensions (>= 0.1.0)
     websocket-extensions (0.1.3)
@@ -220,6 +245,7 @@ DEPENDENCIES
   capybara (~> 2.8)
   capybara-webkit (~> 1.7)
   choice (= 0.1.6)
+  coffee-rails
   comma (= 3.0.4)
   database_cleaner
   dynamic_form
@@ -246,10 +272,12 @@ DEPENDENCIES
   ruby-graphviz (= 1.0.8)
   rubyzip (~> 1.2.1)
   safe_attributes
+  sass-rails
   seer (= 0.10.0)
   selenium-webdriver
   trollop
   tzinfo
+  uglifier
   will_paginate
   yajl-ruby (~> 1.3.1)
   yard
diff --git a/app/assets/javascripts/application.js b/app/assets/javascripts/application.js
index 767991890..2f194e17f 100644
--- a/app/assets/javascripts/application.js
+++ b/app/assets/javascripts/application.js
@@ -1,4 +1,28 @@
 // Place your application-specific JavaScript functions and classes here
 // This file is automatically included by javascript_include_tag :defaults
 
+//= require lazy/jquery-1.11.0
+//= require libs/jquery-ui-1.10.4.custom/js/jquery-ui-1.10.4.custom
+//= require libs/jquery-migrate-1.2.1
 
+//= require lazy/jquery-1.7.2
+//= require lazy/jquery-ui-1.10.4.min
+
+//= require libs/jquery-1.6.2.min
+
+//= require prototype
+//= require effects
+//= require bootstrap
+//= require controls
+//= require dragdrop
+//= require min
+//= require plugins
+//= require rails
+//= require script
+//= require window
+
+//= require libs/respond.min.js
+//= require libs/modernizr-2.0.6.min
+
+//= require lazy/simple_search
+//= require lazy/application
diff --git a/app/assets/stylesheets/application.css b/app/assets/stylesheets/application.css
new file mode 100644
index 000000000..fc0b14604
--- /dev/null
+++ b/app/assets/stylesheets/application.css
@@ -0,0 +1,25 @@
+/*
+ * This is a manifest file that'll be compiled into application.css, which will include all the files
+ * listed below.
+ *
+ * Any CSS and SCSS file within this directory, lib/assets/stylesheets, or any plugin's
+ * vendor/assets/stylesheets directory can be referenced here using a relative path.
+ *
+ * You're free to add application-wide styles to this file and they'll appear at the bottom of the
+ * compiled file so the styles you add here take precedence over styles defined in any other CSS/SCSS
+ * files in this directory. Styles in this file should be added after the last require_* statement.
+ * It is generally better to create a new file per style scope.
+ *
+ * =require jquery-ui-1.10.4.min
+ * =require themes/default
+ * =require themes/alphacube
+ * =require scaffold
+ * =require base
+ * =require grid
+ * =require layout
+ * =require dropdown
+ * =require tables
+ * =require demo
+ * =require jquery-ui-1.10.4.custom/css/ui-lightness/jquery-ui-1.10.4.custom.css
+ * =require_self
+ */
diff --git a/app/assets/stylesheets/base.css.erb b/app/assets/stylesheets/base.css.erb
index bb007ce18..7e3cc9bb5 100755
--- a/app/assets/stylesheets/base.css.erb
+++ b/app/assets/stylesheets/base.css.erb
@@ -1698,7 +1698,7 @@ table th[class*="span"],
 	*margin-right: .3em;
 	line-height: 14px;
 	vertical-align: text-top;
-	background-image: url("../images/glyphicons-halflings.png");
+	background-image: url(<%= asset_path("glyphicons-halflings.png") %>);
 	background-position: 14px 14px;
 	background-repeat: no-repeat;
 }
@@ -1718,7 +1718,7 @@ table th[class*="span"],
 .dropdown-menu > .active > a > [class*=" icon-"],
 .dropdown-submenu:hover > a > [class^="icon-"],
 .dropdown-submenu:hover > a > [class*=" icon-"] {
-	background-image: url("../images/glyphicons-halflings-white.png");
+	background-image: url(<%= asset_path("glyphicons-halflings-white.png") %>);
 }
 
 .icon-glass {
diff --git a/app/assets/stylesheets/dropdown.css.erb b/app/assets/stylesheets/dropdown.css.erb
index 7ec3e9b63..db7597988 100755
--- a/app/assets/stylesheets/dropdown.css.erb
+++ b/app/assets/stylesheets/dropdown.css.erb
@@ -148,7 +148,7 @@ ul.sf-menu li li li:hover ul, ul.sf-menu li li li.sfHover ul{
         width: 12.5%; /* this will need to be adjusted for your needs */
         height: 69px;
 		background-color: transparent;
-    	background-image: url('../images/nav-separator.png');
+    	background-image: url(<%= asset_path('nav-separator.png') %>);
 		background-position: 0 0;
 		background-repeat: repeat-y;
     }
@@ -169,7 +169,7 @@ ul.sf-menu li li li:hover ul, ul.sf-menu li li li.sfHover ul{
     /* new style for drop list items */
     .main-menu li li {
         background: #000;
-    	background-image: url('../images/nav-separator.png');
+    	background-image: url(<%= asset_path('nav-separator.png') %>);
         background-repeat: repeat-y;
         clear: left;
         width: 100%;
@@ -227,31 +227,31 @@ ul.sf-menu li li li:hover ul, ul.sf-menu li li li.sfHover ul{
 		font-size: 14px;
     }
 	.main-menu li.menu-home > a {
-		background: transparent url(../images/nav-icon-home.png) 10px 41px no-repeat;
+		background: transparent url(<%= asset_path("nav-icon-home.png") %>) 10px 41px no-repeat;
 		padding-left: 23px;
 	}
 	.main-menu li.menu-docs > a {
-		background: transparent url(../images/nav-icon-docs.png) 10px 41px no-repeat;
+		background: transparent url(<%= asset_path("nav-icon-docs.png") %>) 10px 41px no-repeat;
 		padding-left: 23px;
 	}
 	.main-menu li.menu-maps > a {
-		background: transparent url(../images/nav-icon-maps.png) 10px 41px no-repeat;
+		background: transparent url(<%= asset_path("nav-icon-maps.png") %>) 10px 41px no-repeat;
 		padding-left: 23px;
 	}
 	.main-menu li.menu-data > a {
-		background: transparent url(../images/nav-icon-data.png) 10px 41px no-repeat;
+		background: transparent url(<%= asset_path("nav-icon-data.png") %>) 10px 41px no-repeat;
 		padding-left: 23px;
 	}
 	.main-menu li.menu-new > a {
-		background: transparent url(../images/nav-icon-new.png) 10px 41px no-repeat;
+		background: transparent url(<%= asset_path("nav-icon-new.png") %>) 10px 41px no-repeat;
 		padding-left: 23px;
 	}
 	.main-menu li.menu-admin > a {
-		background: transparent url(../images/nav-icon-admin.png) 10px 41px no-repeat;
+		background: transparent url(<%= asset_path("nav-icon-admin.png") %>) 10px 41px no-repeat;
 		padding-left: 23px;
 	}
 	.main-menu li.menu-login > a {
-		background: transparent url(../images/nav-icon-logout.png) 100% 41px no-repeat;
+		background: transparent url(<%= asset_path("nav-icon-logout.png") %>) 100% 41px no-repeat;
 		width: 84%;
 		padding-right: 23px;
 	}
diff --git a/app/assets/stylesheets/layout.css.erb b/app/assets/stylesheets/layout.css.erb
index 4673a9591..5eeedd3dd 100755
--- a/app/assets/stylesheets/layout.css.erb
+++ b/app/assets/stylesheets/layout.css.erb
@@ -96,8 +96,7 @@ line-height:normal;
 		bottom: 0;
 		right: 0;
 		height: 80px;
-		width: 80px;
-		background: url(../../stylesheets/images/resize.png); }
+		width: 80px; }
 
 
 	img {
@@ -250,7 +249,7 @@ Bootstrap Styles
 }
 
 .header {
-	background: #dfdfdf url("../images/bg-grain-grey.jpg") top left repeat;
+	background: #dfdfdf url(<%= asset_path("bg-grain-grey.jpg") %>) top left repeat;
 	text-shadow: 0px 1px 1px rgba(255,255,255,1);
 }
 .header h1 {
@@ -273,7 +272,7 @@ Bootstrap Styles
 	width: 100px;
 	text-align: right;
 	display: inline-block;
-	background: url(../images/logo-ebi.png) top right no-repeat;
+	background: url(<%= asset_path("logo-ebi.png") %>) top right no-repeat;
 	padding-right: 45px;
 	height: 46px;
 	padding-top: 4px;
@@ -300,7 +299,7 @@ Bootstrap Styles
 	color: #444;
 }
 body > .nav {
-	background: #505050 url("../images/bg-nav.jpg") top left repeat-x;
+	background: #505050 url(<%= asset_path("bg-nav.jpg") %>) top left repeat-x;
 	color: #fff;
 	height: 75px;
 	padding-top: 6px;
@@ -383,7 +382,7 @@ body > .nav {
 }
 .sidenav .active .icon-chevron-right,
 .sidenav .active a:hover .icon-chevron-right {
-  background-image: url(../images/glyphicons-halflings-white.png);
+  background-image: url(<%= asset_path("glyphicons-halflings-white.png") %>);
   opacity: 1;
 }
 .sidenav.affix {
@@ -463,7 +462,7 @@ border-bottom-color: transparent;
 	padding-top: 40px;
 	line-height: 13px;
 	font-size: 11px;
-	background: url("../images/logo-ebi-footer.jpg") top center no-repeat;
+	background: url(<%= asset_path("logo-ebi-footer.jpg") %>) top center no-repeat;
 }
 .footer .six.columns.omega p:first-child {
 	margin-bottom: 10px;
@@ -612,22 +611,22 @@ border-bottom-color: transparent;
 		  overflow: hidden;
 	  }
 	  .footer .footnotes a.illinois {
-		  background: url(../images/logo-illinois.png) 0 0 no-repeat;
+		  background: url(<%= asset_path("logo-illinois.png") %>) 0 0 no-repeat;
 		  width: 246px;
 	  
 	  }
 	  .footer .footnotes a.berkeley {
-		  background: url(../images/logo-berkeley.png) 0 0 no-repeat;
+		  background: url(<%= asset_path("logo-berkeley.png") %>) 0 0 no-repeat;
 		  width: 145px;
 		  margin-left: 20%;
 	  }
 	  .footer .footnotes a.lbl {
-		  background: url(../images/logo-lbl.png) 0 0 no-repeat;
+		  background: url(<%= asset_path("logo-lbl.png") %>) 0 0 no-repeat;
 		  width: 232px;
 	  
 	  }
 	  .footer .footnotes a.bp {
-		  background: url(../images/logo-bp.png) 0 0 no-repeat;
+		  background: url(<%= asset_path("logo-bp.png") %>) 0 0 no-repeat;
 		  width: 54px;
 		  margin-right: 40%;
 	  }
diff --git a/app/assets/stylesheets/scaffold.css b/app/assets/stylesheets/scaffold.css
index d1bc40749..a649d0da2 100644
--- a/app/assets/stylesheets/scaffold.css
+++ b/app/assets/stylesheets/scaffold.css
@@ -225,7 +225,7 @@ div#banner a.logo {
   width: 213px;
   height: 109px;
   text-indent: -9999em;
- top left no-repeat;
+  background: top left no-repeat;
 }
 
 div#banner a.bety-db {
diff --git a/app/assets/stylesheets/tables.css.erb b/app/assets/stylesheets/tables.css.erb
index ddaaa2df5..20210e590 100755
--- a/app/assets/stylesheets/tables.css.erb
+++ b/app/assets/stylesheets/tables.css.erb
@@ -110,25 +110,25 @@ div.dataTables_filter label {
 }
 
 .paginate_disabled_previous {
-	background: url('../images/back_disabled.png') no-repeat top left;
+	background: url(<%= asset_path("back_disabled.png") %>) no-repeat top left;
 }
 
 .paginate_enabled_previous {
-	background: url('../images/back_enabled.png') no-repeat top left;
+	background: url(<%= asset_path("back_enabled.png") %>) no-repeat top left;
 }
 .paginate_enabled_previous:hover {
-	background: url('../images/back_enabled_hover.png') no-repeat top left;
+	background: url(<%= asset_path("back_enabled_hover.png") %>) no-repeat top left;
 }
 
 .paginate_disabled_next {
-	background: url('../images/forward_disabled.png') no-repeat top right;
+	background: url(<%= asset_path("forward_disabled.png") %>) no-repeat top right;
 }
 
 .paginate_enabled_next {
-	background: url('../images/forward_enabled.png') no-repeat top right;
+	background: url(<%= asset_path("forward_enabled.png") %>) no-repeat top right;
 }
 .paginate_enabled_next:hover {
-	background: url('../images/forward_enabled_hover.png') no-repeat top right;
+	background: url(<%= asset_path("forward_enabled_hover.png") %>) no-repeat top right;
 }
 
 
@@ -239,27 +239,27 @@ table.table thead .sorting_desc_disabled {
 	*cursor: hand;
 }
 table.table .sorting_asc {
-	background: url('../images/sort_asc.png') no-repeat center right;
+	background: url(<%= asset_path("sort_asc.png") %>) no-repeat center right;
 	
 	color: #007eac;
 }
 
 table.table .sorting_desc {
-	background: url('../images/sort_desc.png') no-repeat center right;
+	background: url(<%= asset_path("sort_desc.png") %>) no-repeat center right;
 	
 	color: #007eac;
 }
 
 table.table .sorting {
-	background: url('../images/sort_both.png') no-repeat center right;
+	background: url(<%= asset_path("sort_both.png") %>) no-repeat center right;
 }
 
 table.table .sorting_asc_disabled {
-	background: url('../images/sort_asc_disabled.png') no-repeat center right;
+	background: url(<%= asset_path("sort_asc_disabled.png") %>) no-repeat center right;
 }
 
 table.table .sorting_desc_disabled {
-	background: url('../images/sort_desc_disabled.png') no-repeat center right;
+	background: url(<%= asset_path("sort_desc_disabled.png") %>) no-repeat center right;
 }
  
 table.table thead th:active,
diff --git a/app/views/layouts/application.html.erb b/app/views/layouts/application.html.erb
index edf8e5b35..a7424ae0f 100644
--- a/app/views/layouts/application.html.erb
+++ b/app/views/layouts/application.html.erb
@@ -2,7 +2,7 @@
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 <html xmlns="http://www.w3.org/1999/xhtml">
 <head>
-  <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
+  <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
   <title><%= if @title then @title else "BETYdb: #{request.env['PATH_INFO']}" end %></title>
   <meta name="verify-v1" content="T7Z0mdC+KbUOu+J0CJ6oBySKYz1WUJQJLH0BOtUn1QA=" />
   <meta name="keywords" content="biofuel, biofuels, agriculture, pecan, pecanproject, miscanthus, switchgrass, willow, poplar, sugarcane, ecosystem, crop modeling" />
@@ -11,17 +11,23 @@
 
   <%= csrf_meta_tag %>
 
+  <% if params[:controller] == 'bulk_upload' %>
+    <%= stylesheet_link_tag 'bulk_upload', media: 'all', 'data-turbolinks-track': 'reload' %>
+  <% end %>
+  <%= stylesheet_link_tag 'application', media: 'all', 'data-turbolinks-track': 'reload' %>
+  <%= javascript_include_tag 'application', 'data-turbolinks-track': 'reload' %>
+
   <!-- to do: reconcile these two sets of includes: -->
 
   <!-- Set One -->
-  <%= javascript_include_tag 'lazy/jquery-1.11.0.js' %>
-  <%= javascript_include_tag 'libs/jquery-ui-1.10.4.custom/js/jquery-ui-1.10.4.custom.js' %>
-  <%= javascript_include_tag 'libs/jquery-migrate-1.2.1.js' %>
+  <%#= javascript_include_tag 'lazy/jquery-1.11.0.js' %>
+  <%#= javascript_include_tag 'libs/jquery-ui-1.10.4.custom/js/jquery-ui-1.10.4.custom.js' %>
+  <%#= javascript_include_tag 'libs/jquery-migrate-1.2.1.js' %>
 
   <!-- Set Two -->
-  <%= javascript_include_tag 'lazy/jquery-1.7.2.js' %>
-  <%= javascript_include_tag 'lazy/jquery-ui-1.10.4.min.js' %>
-  <%= stylesheet_link_tag "jquery-ui-1.10.4.min" %>
+  <%#= javascript_include_tag 'lazy/jquery-1.7.2.js' %>
+  <%#= javascript_include_tag 'lazy/jquery-ui-1.10.4.min.js' %>
+  <%#= stylesheet_link_tag "jquery-ui-1.10.4.min" %>
 
   <!--  It seems so far that everything works in 1.7.2.-->
 
@@ -31,26 +37,26 @@
 
   <!-- Since as of Rails 4, javascript_include_tag doesn't recognize the :all option, we have to do this: -->
   <% if Rails.env == "production" %>
-    <%= javascript_include_tag "cache/all" %>
+    <%#= javascript_include_tag "cache/all" %>
   <% else %>
-    <%= javascript_include_tag 'prototype.js' %>
-    <%= javascript_include_tag 'effects.js' %>
-    <%= javascript_include_tag 'bootstrap.js' %>
-    <%= javascript_include_tag 'controls.js' %>
-    <%= javascript_include_tag 'dragdrop.js' %>
-    <%= javascript_include_tag 'min.js' %>
-    <%= javascript_include_tag 'plugins.js' %>
-    <%= javascript_include_tag 'rails.js' %>
-    <%= javascript_include_tag 'script.js' %>
-    <%= javascript_include_tag 'window.js' %>
-    <%= javascript_include_tag 'application.js' %>
+    <%#= javascript_include_tag 'prototype.js' %>
+    <%#= javascript_include_tag 'effects.js' %>
+    <%#= javascript_include_tag 'bootstrap.js' %>
+    <%#= javascript_include_tag 'controls.js' %>
+    <%#= javascript_include_tag 'dragdrop.js' %>
+    <%#= javascript_include_tag 'min.js' %>
+    <%#= javascript_include_tag 'plugins.js' %>
+    <%#= javascript_include_tag 'rails.js' %>
+    <%#= javascript_include_tag 'script.js' %>
+    <%#= javascript_include_tag 'window.js' %>
+    <%#= javascript_include_tag 'application.js' %>
   <% end %>
 
   <!-- ############## BEGAN verifying all JS imports from here ############## -->
   <!--[if (lt IE 9) & (!IEMobile)]>
     <script src="js/libs/selectivizr-min.js"></script>
   <![endif]-->
-  <%= javascript_include_tag 'libs/respond.min.js', 'libs/modernizr-2.0.6.min.js' %>
+  <%#= javascript_include_tag 'libs/respond.min.js', 'libs/modernizr-2.0.6.min.js' %>
 
   <%= yield :autocomplete_javascript %>
 
@@ -70,8 +76,8 @@
   <!--  This disables the use of $ as the jQuery alias-->
   <script> jQuery.noConflict(); </script>
 
-  <%= javascript_include_tag 'lazy/simple_search.js' %>
-  <%= javascript_include_tag 'lazy/application.js' %>
+  <%#= javascript_include_tag 'lazy/simple_search.js' %>
+  <%#= javascript_include_tag 'lazy/application.js' %>
 
   <% if params[:controller] == 'sessions' %>
     <%= javascript_include_tag 'lazy/login' %>
@@ -84,8 +90,8 @@
   <% end %>
 
   <meta name="verify-v1" content="T7Z0mdC+KbUOu+J0CJ6oBySKYz1WUJQJLH0BOtUn1QA=" />
-  <%= stylesheet_link_tag 'themes/default' %>
-  <%= stylesheet_link_tag 'themes/alphacube' %>
+  <%#= stylesheet_link_tag 'themes/default' %>
+  <%#= stylesheet_link_tag 'themes/alphacube' %>
 
   <script type="text/javascript">
     var _gaq = _gaq || [];
@@ -101,16 +107,16 @@
 
   <!-- Maintain the order of the following CSS until we can gut the "scaffold" CSS -->
   <!-- Old CSS -->
-  <%= stylesheet_link_tag "scaffold" %>
+  <%#= stylesheet_link_tag "scaffold" %>
   <!-- Redesign CSS -->
   <%= yield :schemaCSS %>
-  <%= stylesheet_link_tag "base", "grid", "layout", "dropdown", "tables", "demo" %>
+  <%#= stylesheet_link_tag "base", "grid", "layout", "dropdown", "tables", "demo" %>
 
-  <% if params[:controller] == 'bulk_upload' %>
-    <%= stylesheet_link_tag "bulk_upload" %>
-  <% end %>
+  <%# if params[:controller] == 'bulk_upload' %>
+    <%#= stylesheet_link_tag "bulk_upload" %>
+  <%# end %>
 
-  <%= stylesheet_link_tag "jquery-ui-1.10.4.custom/css/ui-lightness/jquery-ui-1.10.4.custom.css" %>
+  <%#= stylesheet_link_tag "jquery-ui-1.10.4.custom/css/ui-lightness/jquery-ui-1.10.4.custom.css" %>
 
 </head>
 
diff --git a/config/initializers/assets.rb b/config/initializers/assets.rb
index ff2d2299a..8a1134cef 100644
--- a/config/initializers/assets.rb
+++ b/config/initializers/assets.rb
@@ -1,11 +1,17 @@
 # Be sure to restart your server when you modify this file.
 
 # Version of your assets, change this if you want to expire all your assets.
-# Rails.application.config.assets.version = '1.0'
+Rails.application.config.assets.version = '1.0'
 
 # Add additional assets to the asset load path
 # Rails.application.config.assets.paths << Emoji.images_path
 
 # Precompile additional assets.
 # application.js, application.css, and all non-JS/CSS in app/assets folder are already added.
-# Rails.application.config.assets.precompile += %w( search.js )
+Rails.application.config.assets.precompile += %w(
+  bulk_upload.css
+
+  lazy/login.js
+  lazy/map_search.js
+  lazy/feedback.js
+ )

From 367daab2acce3a478c47028ee7bc0c473b6860d2 Mon Sep 17 00:00:00 2001
From: Rob Kooper <kooper@illinois.edu>
Date: Wed, 28 Feb 2018 09:44:01 -0600
Subject: [PATCH 24/44] upgrade to latest bety

---
 Dockerfile           |  2 ++
 docker/entrypoint.sh | 22 ++++++++++++++++------
 2 files changed, 18 insertions(+), 6 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index f485e4ac1..792543fe8 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -23,6 +23,7 @@ EXPOSE 8000
 
 # copy rest of the files
 COPY / /home/bety
+COPY /public/javascripts/cache/all.js-sample /home/bety/public/javascripts/cache/all.js
 COPY /docker/database.yml /home/bety/config/database.yml
 
 # download dump.bety and load.bety scripts and configure app
@@ -42,6 +43,7 @@ ENV LOCAL_SERVER=99 \
     REMOTE_SERVERS="0 1 2 5" \
     RAILS_ENV="production" \
     RAILS_RELATIVE_URL_ROOT="" \
+    SECRET_KEY_BASE="ThisIsNotReallySuchAGreatSecret" \
     UNICORN_WORKER_PROCESSES="3" \
     UNICORN_PORT="8000" \
     BETY_GIT_TAGS=${BETY_GIT_TAGS} \
diff --git a/docker/entrypoint.sh b/docker/entrypoint.sh
index 7161d14f1..87c057957 100755
--- a/docker/entrypoint.sh
+++ b/docker/entrypoint.sh
@@ -20,11 +20,10 @@ function wait_for_postgres() {
 case $1 in
     "initialize" )
         wait_for_postgres
-        SERVER=$( echo ${REMOTE_SERVERS} | awk '{print $1}' )
-        echo "Create new database, initialized from server ${SERVER}"
+        echo "Create new database, initialized from all data."
         psql -h postgres -p 5432 -U postgres -c "CREATE ROLE bety WITH LOGIN CREATEDB NOSUPERUSER NOCREATEROLE PASSWORD 'bety'"
         psql -h postgres -p 5432 -U postgres -c "CREATE DATABASE bety WITH OWNER bety"
-        ./load.bety.sh -a "postgres" -d "bety" -p "-h postgres -p 5432" -o bety -c -u -g -m ${LOCAL_SERVER} -r ${SERVER}
+        ./load.bety.sh -a "postgres" -d "bety" -p "-h postgres -p 5432" -o bety -c -u -g -m ${LOCAL_SERVER} -r 0 -w https://ebi-forecast.igb.illinois.edu/pecan/dumpall/bety.tar.gz
         ;;
     "sync" )
         wait_for_postgres
@@ -41,7 +40,7 @@ case $1 in
         ;;
     "migrate" )
         wait_for_postgres
-        echo "Migrate databae."
+        echo "Migrate database."
         rake db:migrate SKIP_SCHEMASPY=YES
         ;;
     "server" )
@@ -54,13 +53,24 @@ case $1 in
         echo "Start running BETY (unicorn)"
         exec bundle exec unicorn -c config/unicorn.rb
         ;;
+    "autoserver" )
+        wait_for_postgres
+        echo "Migrate database."
+        rake db:migrate SKIP_SCHEMASPY=YES
+        echo "Start running BETY (unicorn)"
+        exec bundle exec unicorn -c config/unicorn.rb
+        ;;
     "help" )
-        echo "initialize : create a new database and initialize with data from server 0"
+        echo "initialize : create a new database and initialize with all data from server 0"
         echo "sync       : synchronize database with remote servers ${REMOTE_SERVERS}"
         echo "dump       : dumps local database"
         echo "migrate    : migrates the database to a new version of bety"
-        echo "server     : runs the server"
+        echo "server     : runs the server (using rails server)"
+        echo "unicorn    : runs the server (using unicorn)"
+        echo "autoserver : runs the server (using unicorn) after running a migrate"
         echo "help       : this text"
+        echo ""
+        echo "Default is to run bety using unicorn. no automatic migrations."
         ;;
     * )
         exec "$@"

From 56e790296df2b963e7c4aa050a9b90a2eaa7d83a Mon Sep 17 00:00:00 2001
From: Rob Kooper <kooper@illinois.edu>
Date: Thu, 1 Mar 2018 11:06:15 -0600
Subject: [PATCH 25/44] unicorn and dependencies in Gemfile.lock

---
 Gemfile.lock | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/Gemfile.lock b/Gemfile.lock
index 6f76d3a12..2fa67175d 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -74,6 +74,7 @@ GEM
     json (1.8.6)
     json-schema (2.8.0)
       addressable (>= 2.4)
+    kgio (2.11.2)
     mail (2.7.0)
       mini_mime (>= 0.1.1)
     memoist (0.16.0)
@@ -124,6 +125,7 @@ GEM
       activesupport (= 4.1.16)
       rake (>= 0.8.7)
       thor (>= 0.18.1, < 2.0)
+    raindrops (0.19.0)
     rake (12.3.0)
     recaptcha (0.3.4)
     rgeo (0.5.3)
@@ -175,6 +177,9 @@ GEM
     trollop (2.1.2)
     tzinfo (1.2.4)
       thread_safe (~> 0.1)
+    unicorn (5.4.0)
+      kgio (~> 2.6)
+      raindrops (~> 0.7)
     will_paginate (3.1.6)
     xpath (2.1.0)
       nokogiri (~> 1.3)
@@ -223,6 +228,10 @@ DEPENDENCIES
   selenium-webdriver
   trollop
   tzinfo
+  unicorn
   will_paginate
   yajl-ruby (~> 1.3.1)
   yard
+
+BUNDLED WITH
+   1.16.1

From d2403f7cf777a1fc9c06af0584cdae51e4f016b0 Mon Sep 17 00:00:00 2001
From: Scott Rohde <srohde@igb.illinois.edu>
Date: Thu, 1 Mar 2018 14:20:59 -0600
Subject: [PATCH 26/44] Updated Gemfile to use Rails 5.1.5.

Removed code in databases-hack.rake related to db:test:clone_structure, which
doesn't exist in Rails 5.1.
---
 Gemfile                       |   8 ++-
 Gemfile.lock                  | 113 ++++++++++++++++++----------------
 lib/tasks/databases-hack.rake |  19 ------
 3 files changed, 64 insertions(+), 76 deletions(-)

diff --git a/Gemfile b/Gemfile
index 7f686af6a..4e202ec66 100644
--- a/Gemfile
+++ b/Gemfile
@@ -1,9 +1,8 @@
 source "http://rubygems.org"
 
-gem "rails", "5.0.6"
+gem "rails", "5.1.5"
 # needed for rails 3.1 and above until we phase out prototype:
 ## gem 'prototype-rails', github: 'rails/prototype-rails', branch: '4.2' # see https://github.com/rails/prototype-rails/issues/37
-gem "query_reviewer", "0.1.6"
 gem "nokogiri"
 gem "narray", "0.6.0.4"
 gem "choice", "0.1.6"
@@ -53,7 +52,10 @@ group :development, :test do
   gem "yard"
 end
 
-
+group :development, :test do
+  gem "pry-rails"
+  gem "pry-byebug"
+end
 
 group :test do
   # phasing out webrat:    
diff --git a/Gemfile.lock b/Gemfile.lock
index fff127821..034267943 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -1,61 +1,61 @@
 GEM
   remote: http://rubygems.org/
   specs:
-    actioncable (5.0.6)
-      actionpack (= 5.0.6)
-      nio4r (>= 1.2, < 3.0)
+    actioncable (5.1.5)
+      actionpack (= 5.1.5)
+      nio4r (~> 2.0)
       websocket-driver (~> 0.6.1)
-    actionmailer (5.0.6)
-      actionpack (= 5.0.6)
-      actionview (= 5.0.6)
-      activejob (= 5.0.6)
+    actionmailer (5.1.5)
+      actionpack (= 5.1.5)
+      actionview (= 5.1.5)
+      activejob (= 5.1.5)
       mail (~> 2.5, >= 2.5.4)
       rails-dom-testing (~> 2.0)
-    actionpack (5.0.6)
-      actionview (= 5.0.6)
-      activesupport (= 5.0.6)
+    actionpack (5.1.5)
+      actionview (= 5.1.5)
+      activesupport (= 5.1.5)
       rack (~> 2.0)
-      rack-test (~> 0.6.3)
+      rack-test (>= 0.6.3)
       rails-dom-testing (~> 2.0)
       rails-html-sanitizer (~> 1.0, >= 1.0.2)
-    actionview (5.0.6)
-      activesupport (= 5.0.6)
+    actionview (5.1.5)
+      activesupport (= 5.1.5)
       builder (~> 3.1)
-      erubis (~> 2.7.0)
+      erubi (~> 1.4)
       rails-dom-testing (~> 2.0)
       rails-html-sanitizer (~> 1.0, >= 1.0.3)
-    activejob (5.0.6)
-      activesupport (= 5.0.6)
+    activejob (5.1.5)
+      activesupport (= 5.1.5)
       globalid (>= 0.3.6)
-    activemodel (5.0.6)
-      activesupport (= 5.0.6)
-    activerecord (5.0.6)
-      activemodel (= 5.0.6)
-      activesupport (= 5.0.6)
-      arel (~> 7.0)
-    activerecord-postgis-adapter (4.0.5)
-      activerecord (~> 5.0.0)
-      rgeo-activerecord (~> 5.0.0)
+    activemodel (5.1.5)
+      activesupport (= 5.1.5)
+    activerecord (5.1.5)
+      activemodel (= 5.1.5)
+      activesupport (= 5.1.5)
+      arel (~> 8.0)
+    activerecord-postgis-adapter (5.0.3)
+      activerecord (~> 5.1)
+      rgeo-activerecord (~> 5.1)
     activerecord-session_store (1.1.0)
       actionpack (>= 4.0, < 5.2)
       activerecord (>= 4.0, < 5.2)
       multi_json (~> 1.11, >= 1.11.2)
       rack (>= 1.5.2, < 3)
       railties (>= 4.0, < 5.2)
-    activesupport (5.0.6)
+    activesupport (5.1.5)
       concurrent-ruby (~> 1.0, >= 1.0.2)
       i18n (~> 0.7)
       minitest (~> 5.1)
       tzinfo (~> 1.1)
     addressable (2.5.2)
       public_suffix (>= 2.0.2, < 4.0)
-    apipie-rails (0.4.0)
-      json
-      rails (>= 4.0)
-    arel (7.1.4)
+    apipie-rails (0.5.6)
+      rails (>= 4.1)
+    arel (8.0.0)
     bootstrap-will_paginate (1.0.0)
       will_paginate
     builder (3.2.3)
+    byebug (10.0.0)
     capybara (2.13.0)
       addressable
       mime-types (>= 1.16)
@@ -76,16 +76,16 @@ GEM
     database_cleaner (1.6.2)
     diff-lcs (1.3)
     dynamic_form (1.1.4)
-    erubis (2.7.0)
+    erubi (1.7.0)
     ffi (1.9.18)
     globalid (0.4.1)
       activesupport (>= 4.2.0)
-    i18n (0.9.3)
+    i18n (0.9.5)
       concurrent-ruby (~> 1.0)
     json (2.1.0)
     json-schema (2.8.0)
       addressable (>= 2.4)
-    loofah (2.1.1)
+    loofah (2.2.0)
       crass (~> 1.0.2)
       nokogiri (>= 1.5.9)
     mail (2.7.0)
@@ -113,25 +113,29 @@ GEM
     pry (0.11.3)
       coderay (~> 1.1.0)
       method_source (~> 0.9.0)
+    pry-byebug (3.6.0)
+      byebug (~> 10.0)
+      pry (~> 0.10)
+    pry-rails (0.3.6)
+      pry (>= 0.10.4)
     public_suffix (3.0.1)
-    query_reviewer (0.1.6)
     rabl (0.13.1)
       activesupport (>= 2.3.14)
     rack (2.0.4)
-    rack-test (0.6.3)
-      rack (>= 1.0)
+    rack-test (0.8.3)
+      rack (>= 1.0, < 3)
     railroad (0.5.0)
-    rails (5.0.6)
-      actioncable (= 5.0.6)
-      actionmailer (= 5.0.6)
-      actionpack (= 5.0.6)
-      actionview (= 5.0.6)
-      activejob (= 5.0.6)
-      activemodel (= 5.0.6)
-      activerecord (= 5.0.6)
-      activesupport (= 5.0.6)
+    rails (5.1.5)
+      actioncable (= 5.1.5)
+      actionmailer (= 5.1.5)
+      actionpack (= 5.1.5)
+      actionview (= 5.1.5)
+      activejob (= 5.1.5)
+      activemodel (= 5.1.5)
+      activerecord (= 5.1.5)
+      activesupport (= 5.1.5)
       bundler (>= 1.3.0)
-      railties (= 5.0.6)
+      railties (= 5.1.5)
       sprockets-rails (>= 2.0.0)
     rails-controller-testing (1.0.2)
       actionpack (~> 5.x, >= 5.0.1)
@@ -143,17 +147,17 @@ GEM
     rails-html-sanitizer (1.0.3)
       loofah (~> 2.0)
     rails3-restful-authentication (3.0.1)
-    railties (5.0.6)
-      actionpack (= 5.0.6)
-      activesupport (= 5.0.6)
+    railties (5.1.5)
+      actionpack (= 5.1.5)
+      activesupport (= 5.1.5)
       method_source
       rake (>= 0.8.7)
       thor (>= 0.18.1, < 2.0)
     rake (12.3.0)
     recaptcha (0.3.4)
     rgeo (0.5.0)
-    rgeo-activerecord (5.0.1)
-      activerecord (~> 5.0.0)
+    rgeo-activerecord (5.1.1)
+      activerecord (~> 5.0)
       rgeo (~> 0.3)
     rspec (3.7.0)
       rspec-core (~> 3.7.0)
@@ -198,7 +202,7 @@ GEM
     thor (0.20.0)
     thread_safe (0.3.6)
     trollop (2.1.2)
-    tzinfo (1.2.4)
+    tzinfo (1.2.5)
       thread_safe (~> 0.1)
     websocket-driver (0.6.5)
       websocket-extensions (>= 0.1.0)
@@ -233,10 +237,11 @@ DEPENDENCIES
   pg
   protected_attributes_continued
   pry
-  query_reviewer (= 0.1.6)
+  pry-byebug
+  pry-rails
   rabl
   railroad (= 0.5.0)
-  rails (= 5.0.6)
+  rails (= 5.1.5)
   rails-controller-testing
   rails3-restful-authentication (~> 3.0.1)
   recaptcha (= 0.3.4)
diff --git a/lib/tasks/databases-hack.rake b/lib/tasks/databases-hack.rake
index 05c8219c8..16ef144ef 100644
--- a/lib/tasks/databases-hack.rake
+++ b/lib/tasks/databases-hack.rake
@@ -22,16 +22,6 @@
 end
 =end
 
-# gems/activerecord-3.2.21/lib/active_record/railties/databases.rake:521
-# defines db:test:clone_structure with prerequisites db:structure:dump
-# and db:test:load_structure and no actions.  The postgis adapter Gem
-# overrides this in
-# "gems/activerecord-postgis-adapter-0.6.6/lib/active_record/connection_adapters/postgis_adapter/rails3/databases.rake",
-# adding an action to set run the structure file directly.  This is
-# redundant, so we clear out that action.
-Rake::Task["db:test:clone_structure"].clear_actions
-
-
 # Add descriptions for test-database-related tasks:
 Rake::Task["db:test:load_structure"].add_description(<<DESC
 Loads the test database with database structure defined in the file "db/<RAILS_ENV>_structure.sql",
@@ -41,15 +31,6 @@ recreate it.
 DESC
 )
 
-Rake::Task["db:test:clone_structure"].add_description(<<DESC
-Clones the structure of the current environment and then loads it into the test database.
-It will first run db:test:purge to drop the test database (if it exists) and
-recreate it.  Then it creates (or recreates) the structure.sql file for the
-current environment ("db/<RAILS_ENV>_structure.sql") and loads it into the test
-database.
-DESC
-)
-
 namespace :db do
   namespace :fixtures do
     task :load => :block_for_non_test_env

From ada9195c4e4a51857ad80568d8c2aa5fac61e60a Mon Sep 17 00:00:00 2001
From: Scott Rohde <srohde@igb.illinois.edu>
Date: Fri, 2 Mar 2018 17:18:15 -0600
Subject: [PATCH 27/44] Several changes needed for the upgrade to Rails 5.1 to
 get RSpec tests to pass:

app/controllers/application_controller.rb,
app/controllers/dbfiles_controller.rb,
app/controllers/treatments_controller.rb:

  Replace obsolete "redirect_to :back" calls with "redirect_back(...)".

app/controllers/priors_controller.rb:

  Be smarter about setting the path when calling R.

app/models/bulk_upload_data_set.rb

  When @session["global_values"] is nil, return an empty
  ActionControllerParameters object instead of a Hash so that subsequent code can
  treat the returned object uniformly.  Call "#permit!" on global_values now that
  Rails enforces attribute protection in this new way.

test/fixtures/machines.yml

  Explicitly set the id to 1 since the DBFiles fixture expects there to be a
  machine with id 1.
---
 app/controllers/application_controller.rb |  5 ++---
 app/controllers/dbfiles_controller.rb     |  4 ++--
 app/controllers/priors_controller.rb      | 12 +++++++++---
 app/controllers/treatments_controller.rb  |  4 ++--
 app/models/bulk_upload_data_set.rb        |  7 +++++--
 test/fixtures/machines.yml                |  1 +
 6 files changed, 21 insertions(+), 12 deletions(-)

diff --git a/app/controllers/application_controller.rb b/app/controllers/application_controller.rb
index dfb418383..d65356476 100644
--- a/app/controllers/application_controller.rb
+++ b/app/controllers/application_controller.rb
@@ -24,8 +24,7 @@ class ApplicationController < ActionController::Base
       flash[:error] = e.message
     end
 
-
-    redirect_to :back
+    redirect_back(fallback_location: root_path)
   end
 
   # Be sure to include AuthenticationSystem in Application Controller instead
@@ -170,7 +169,7 @@ def handle_constraint_violations(e)
     logger.info(e)
     match = e.message.match /The value of .*? for .*? .*? must be between .*? and .*?\./
     flash[:error] = match && match[0] || e.message
-    redirect_to :back
+    redirect_back(fallback_location: root_path)
   end
 
   # Given a model class, a list of columns (attributes) of the model, and a
diff --git a/app/controllers/dbfiles_controller.rb b/app/controllers/dbfiles_controller.rb
index e462b4423..92f2c2983 100644
--- a/app/controllers/dbfiles_controller.rb
+++ b/app/controllers/dbfiles_controller.rb
@@ -34,12 +34,12 @@ def unlink
     respond_to do |format|
       if dbfile.save
         flash[:notice] = "File unlinked"
-        format.html { redirect_to :back }
+        format.html { redirect_back(fallback_location: root_path) }
         format.xml  { render :xml => 'File unlinked' }
         format.json  { render :json => 'File unlinked' }
       else
         flash[:notice] = "File not removed"
-        format.html {redirect_to :back }
+        format.html {redirect_back(fallback_location: root_path) }
         format.xml  { render :xml => 'File not removed' }
         format.json  { render :json => 'File not removed' }
       end
diff --git a/app/controllers/priors_controller.rb b/app/controllers/priors_controller.rb
index 02408d3d4..5da91b59a 100644
--- a/app/controllers/priors_controller.rb
+++ b/app/controllers/priors_controller.rb
@@ -107,9 +107,15 @@ def preview
         # On ebi-forecast, the version of R we want to use is in
         # /usr/local/R-3.1.0/bin, so put it first in the path so that that version
         # gets used if it exists:
-        ENV["PATH"] = "/usr/local/R-3.1.0/bin:/usr/bin:/usr/local/bin"                                                                                 
-        o, error_output, s = Open3.capture3("R", "--vanilla", "--args", imgfile, distname, aparam.to_s, bparam.to_s, n.to_s,                           
-                                            stdin_data: Rails.root.join('script/previewhelp.R').read)
+        path_additions = "/usr/local/R-3.1.0/bin:"
+
+        o, error_output, s = Open3.capture3(
+                           {"PATH" => path_additions + ENV["PATH"]},
+                           "R", "--vanilla", "--args", imgfile, distname,
+                           aparam.to_s, bparam.to_s, n.to_s,
+                           stdin_data: Rails.root.join('script/previewhelp.R').read
+                         )
+
       else
         error_output = sprintf("Invalid argument set:\n\timgfile = %s\n\tdistname = %s\n\taparam = %s\n\tbparam = %s\n\tn = %s\n", 
                                imgfile, distname, aparam, bparam, n)
diff --git a/app/controllers/treatments_controller.rb b/app/controllers/treatments_controller.rb
index 69521907a..1ff2b1a56 100644
--- a/app/controllers/treatments_controller.rb
+++ b/app/controllers/treatments_controller.rb
@@ -107,12 +107,12 @@ def flag_control
     respond_to do |format|
       if @treatment.save
         flash[:notice] = 'Treatment was successfully updated.'
-        format.html { redirect_to :back }
+        format.html { redirect_back(fallback_location: root_path) }
         format.xml  { head :ok }
         format.csv  { head :ok }
         format.json  { head :ok }
       else
-        format.html { redirect_to :back }
+        format.html { redirect_back(fallback_location: root_path) }
         format.xml  { render :xml => @treatment.errors, :status => :unprocessable_entity }
         format.csv  { render :csv => @treatment.errors, :status => :unprocessable_entity }
         format.json  { render :json => @treatment.errors, :status => :unprocessable_entity }
diff --git a/app/models/bulk_upload_data_set.rb b/app/models/bulk_upload_data_set.rb
index 05d4c046b..321de2e95 100644
--- a/app/models/bulk_upload_data_set.rb
+++ b/app/models/bulk_upload_data_set.rb
@@ -1833,7 +1833,7 @@ def get_insertion_data
     # Get interactively-specified values, or set to empty hash if nil; since we
     # are going to alter interactively_specified_values, we use clone to make a
     # copy so that the session value remains as is.
-    interactively_specified_values = @session["global_values"].clone rescue {}
+    interactively_specified_values = @session["global_values"].clone rescue ActionController::Parameters.new
 
     # TO DO: decide if this code serves any useful purpose:
     # Double-check that all form fields are were non-empty:
@@ -1891,7 +1891,10 @@ def get_insertion_data
       csv_row_as_hash.merge!(id_values)
 
       # Merge the global interactively-specified values into this row:
-      csv_row_as_hash.merge!(global_values)
+
+
+      # global_values.permit! if global_values.respond_to? :permit!
+      csv_row_as_hash.merge!(global_values.permit!)
 
       if csv_row_as_hash.has_key?("SE")
         # apply rounding to the standard error
diff --git a/test/fixtures/machines.yml b/test/fixtures/machines.yml
index 061f9c015..f70798465 100644
--- a/test/fixtures/machines.yml
+++ b/test/fixtures/machines.yml
@@ -1,4 +1,5 @@
 test_machine:
+  id: 1
   hostname: "ebi-cluster.igb.illinois.edu"
   created_at: "2012-04-26 13:07:08"
   updated_at: "2012-12-26 23:53:39"

From 76f10b71e64e7b3792f099f8c5562c60561fc201 Mon Sep 17 00:00:00 2001
From: Scott Rohde <srohde@igb.illinois.edu>
Date: Tue, 6 Mar 2018 13:27:21 -0600
Subject: [PATCH 28/44] In Gemfile.lock, replaced erubis with erubi so Rails
 doesn't give startup error.

---
 Gemfile.lock | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Gemfile.lock b/Gemfile.lock
index 3efa2a948..72857802e 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -83,7 +83,7 @@ GEM
     database_cleaner (1.6.2)
     diff-lcs (1.3)
     dynamic_form (1.1.4)
-    erubis (2.7.0)
+    erubi (1.7.0)
     execjs (2.7.0)
     ffi (1.9.18)
     globalid (0.4.1)

From 2916a0dd3e1c90c3b429732a0bef0013a731582c Mon Sep 17 00:00:00 2001
From: Scott Rohde <srohde@igb.illinois.edu>
Date: Tue, 6 Mar 2018 13:37:45 -0600
Subject: [PATCH 29/44] Added to assets.precompile list.

---
 config/initializers/assets.rb | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/config/initializers/assets.rb b/config/initializers/assets.rb
index 8a1134cef..9db54675a 100644
--- a/config/initializers/assets.rb
+++ b/config/initializers/assets.rb
@@ -14,4 +14,6 @@
   lazy/login.js
   lazy/map_search.js
   lazy/feedback.js
+  lazy/autocomplete.js
+  lazy/bulk_upload.js
  )

From 236f183b221d430e49ffac6892b735a7ce812554 Mon Sep 17 00:00:00 2001
From: Scott Rohde <srohde@igb.illinois.edu>
Date: Wed, 7 Mar 2018 16:16:07 -0600
Subject: [PATCH 30/44] Tweaked comment about merging global_values into
 csv_row Hash.

---
 app/models/bulk_upload_data_set.rb | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/app/models/bulk_upload_data_set.rb b/app/models/bulk_upload_data_set.rb
index 321de2e95..ff9f6287d 100644
--- a/app/models/bulk_upload_data_set.rb
+++ b/app/models/bulk_upload_data_set.rb
@@ -1891,9 +1891,7 @@ def get_insertion_data
       csv_row_as_hash.merge!(id_values)
 
       # Merge the global interactively-specified values into this row:
-
-
-      # global_values.permit! if global_values.respond_to? :permit!
+      # To-Do: Be more specific about which values to permit.
       csv_row_as_hash.merge!(global_values.permit!)
 
       if csv_row_as_hash.has_key?("SE")

From 072605082f00a604d26a160ab928d1f063d1160d Mon Sep 17 00:00:00 2001
From: Scott Rohde <srohde@igb.illinois.edu>
Date: Wed, 7 Mar 2018 15:58:02 -0600
Subject: [PATCH 31/44] Changed Gemfile and JavaScript manifest to use jquery
 and jquery-ui from Gems and to not use no-longer-needed JavaScript files.

Changed RSpec helper functions to track changes in jquery-ui.

Use assets in debug mode when in the test environment (for now).
---
 Gemfile                                |  5 ++---
 Gemfile.lock                           |  8 ++++++++
 app/assets/javascripts/application.js  | 26 ++++++++------------------
 app/views/layouts/application.html.erb |  2 +-
 config/environments/test.rb            |  2 ++
 spec/support/helpers.rb                |  4 ++--
 6 files changed, 23 insertions(+), 24 deletions(-)

diff --git a/Gemfile b/Gemfile
index eabff61d5..089ef36ea 100644
--- a/Gemfile
+++ b/Gemfile
@@ -29,9 +29,8 @@ gem 'sass-rails'
 gem 'coffee-rails'
 gem 'uglifier'
 
-
-# to-do: Use this Gem instead of adding the library to the assets directory.
-## gem 'jquery-rails'
+gem 'jquery-rails'
+gem 'jquery-ui-rails'
 
 gem 'memoist'
 
diff --git a/Gemfile.lock b/Gemfile.lock
index 72857802e..227d1e933 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -90,6 +90,12 @@ GEM
       activesupport (>= 4.2.0)
     i18n (0.9.5)
       concurrent-ruby (~> 1.0)
+    jquery-rails (4.3.1)
+      rails-dom-testing (>= 1, < 3)
+      railties (>= 4.2.0)
+      thor (>= 0.14, < 2.0)
+    jquery-ui-rails (6.0.1)
+      railties (>= 3.2.16)
     json (2.1.0)
     json-schema (2.8.0)
       addressable (>= 2.4)
@@ -253,6 +259,8 @@ DEPENDENCIES
   comma (= 3.0.4)
   database_cleaner
   dynamic_form
+  jquery-rails
+  jquery-ui-rails
   json
   json-schema
   memoist
diff --git a/app/assets/javascripts/application.js b/app/assets/javascripts/application.js
index 2f194e17f..53dd315c7 100644
--- a/app/assets/javascripts/application.js
+++ b/app/assets/javascripts/application.js
@@ -1,28 +1,18 @@
 // Place your application-specific JavaScript functions and classes here
 // This file is automatically included by javascript_include_tag :defaults
 
-//= require lazy/jquery-1.11.0
-//= require libs/jquery-ui-1.10.4.custom/js/jquery-ui-1.10.4.custom
-//= require libs/jquery-migrate-1.2.1
-
-//= require lazy/jquery-1.7.2
-//= require lazy/jquery-ui-1.10.4.min
-
-//= require libs/jquery-1.6.2.min
+//= require jquery
+//= require rails-ujs
+//= require jquery-ui
 
+// defines Form:
 //= require prototype
+
+// defines Effect
 //= require effects
-//= require bootstrap
-//= require controls
-//= require dragdrop
-//= require min
-//= require plugins
-//= require rails
-//= require script
-//= require window
 
-//= require libs/respond.min.js
-//= require libs/modernizr-2.0.6.min
+// defines showHide
+//= require min
 
 //= require lazy/simple_search
 //= require lazy/application
diff --git a/app/views/layouts/application.html.erb b/app/views/layouts/application.html.erb
index a7424ae0f..8b5a4e2cc 100644
--- a/app/views/layouts/application.html.erb
+++ b/app/views/layouts/application.html.erb
@@ -74,7 +74,7 @@
   <!-- ############## ENDED verifying all JS imports from here ############## -->
 
   <!--  This disables the use of $ as the jQuery alias-->
-  <script> jQuery.noConflict(); </script>
+
 
   <%#= javascript_include_tag 'lazy/simple_search.js' %>
   <%#= javascript_include_tag 'lazy/application.js' %>
diff --git a/config/environments/test.rb b/config/environments/test.rb
index ff7c69fda..a79ff9eb4 100644
--- a/config/environments/test.rb
+++ b/config/environments/test.rb
@@ -42,4 +42,6 @@
 
   # Raises error for missing translations
   # config.action_view.raise_on_missing_translations = true
+
+  config.assets.debug = true
 end
diff --git a/spec/support/helpers.rb b/spec/support/helpers.rb
index f744ba912..c477a54d3 100644
--- a/spec/support/helpers.rb
+++ b/spec/support/helpers.rb
@@ -41,7 +41,7 @@ def choose_citation_from_dropdown(author = 'Adler')
     sleep 1 # maybe not needed
     page.execute_script("jQuery('#autocomplete_citation').trigger('keydown', {keyCode: 40})")
     sleep 1 # necessary!
-    first("#ui-id-1 li.ui-menu-item a").click
+    first("#ui-id-1 li.ui-menu-item > *").click
     click_button "View Validation Results"
   end
 end
@@ -49,7 +49,7 @@ def choose_citation_from_dropdown(author = 'Adler')
 module AutocompletionHelper
   def fill_autocomplete(field_id, options = {})
     fill_in field_id, :with => options[:with]
-    selector = "ul.ui-autocomplete a:contains('#{options[:select]}')"
+    selector = "ul.ui-autocomplete div:contains('#{options[:select]}')"
 
     # RSpec doesn't seem to recognize the :contains syntax for selectors
     #page.should have_selector selector

From 2ad13946d77b3c8cf333e06dd433abafc9de3bcf Mon Sep 17 00:00:00 2001
From: Scott Rohde <srohde@igb.illinois.edu>
Date: Fri, 9 Mar 2018 10:48:52 -0600
Subject: [PATCH 32/44] Got RSpec tests to pass without putting the test
 environment in assets.debug mode by using JQuery noconflict call before
 loading Prototype, and by adding to assets.paths so that the
 jquery-ui-1.10.4.custom can find the image files it uses.

---
 app/assets/javascripts/application.js | 3 +++
 app/assets/javascripts/noconflict.js  | 1 +
 config/environments/test.rb           | 2 --
 config/initializers/assets.rb         | 4 ++++
 4 files changed, 8 insertions(+), 2 deletions(-)
 create mode 100644 app/assets/javascripts/noconflict.js

diff --git a/app/assets/javascripts/application.js b/app/assets/javascripts/application.js
index 53dd315c7..66d868d2d 100644
--- a/app/assets/javascripts/application.js
+++ b/app/assets/javascripts/application.js
@@ -5,6 +5,9 @@
 //= require rails-ujs
 //= require jquery-ui
 
+// Remove conflicting definition of $ before loading Prototype:
+//= require noconflict
+
 // defines Form:
 //= require prototype
 
diff --git a/app/assets/javascripts/noconflict.js b/app/assets/javascripts/noconflict.js
new file mode 100644
index 000000000..f4b1f44e8
--- /dev/null
+++ b/app/assets/javascripts/noconflict.js
@@ -0,0 +1 @@
+jQuery.noConflict();
diff --git a/config/environments/test.rb b/config/environments/test.rb
index a79ff9eb4..ff7c69fda 100644
--- a/config/environments/test.rb
+++ b/config/environments/test.rb
@@ -42,6 +42,4 @@
 
   # Raises error for missing translations
   # config.action_view.raise_on_missing_translations = true
-
-  config.assets.debug = true
 end
diff --git a/config/initializers/assets.rb b/config/initializers/assets.rb
index 9db54675a..f28b18bf9 100644
--- a/config/initializers/assets.rb
+++ b/config/initializers/assets.rb
@@ -17,3 +17,7 @@
   lazy/autocomplete.js
   lazy/bulk_upload.js
  )
+
+Rails.application.config.assets.paths <<
+  Rails.root.join("app", "assets", "stylesheets", "jquery-ui-1.10.4.custom",
+                  "css", "ui-lightness").to_s

From 4c3411edfff5abbece0bb482d621c501b1f86779 Mon Sep 17 00:00:00 2001
From: Scott Rohde <srohde@igb.illinois.edu>
Date: Thu, 19 Apr 2018 16:17:51 -0500
Subject: [PATCH 33/44] Modified some initializers to fix problems discovered
 during testing.

---
 config/initializers/apipie.rb | 2 ++
 config/initializers/assets.rb | 1 +
 2 files changed, 3 insertions(+)

diff --git a/config/initializers/apipie.rb b/config/initializers/apipie.rb
index 9f3dbac94..5b3b120d1 100644
--- a/config/initializers/apipie.rb
+++ b/config/initializers/apipie.rb
@@ -6,4 +6,6 @@
   # where is your API defined?
   config.api_controllers_matcher = "#{Rails.root}/app/controllers/api/v1/*.rb"
 
+  config.translate               = false
+  config.default_locale          = nil
 end
diff --git a/config/initializers/assets.rb b/config/initializers/assets.rb
index f28b18bf9..0098a0d6a 100644
--- a/config/initializers/assets.rb
+++ b/config/initializers/assets.rb
@@ -10,6 +10,7 @@
 # application.js, application.css, and all non-JS/CSS in app/assets folder are already added.
 Rails.application.config.assets.precompile += %w(
   bulk_upload.css
+  schemaSpy.css
 
   lazy/login.js
   lazy/map_search.js

From 06cce1d2fb50a3cc6ae00fa0c9ad574c764ad3ed Mon Sep 17 00:00:00 2001
From: Scott Rohde <srohde@igb.illinois.edu>
Date: Thu, 19 Apr 2018 16:28:11 -0500
Subject: [PATCH 34/44] Locked apipie-rails Gem at version 0.5.6 because 0.5.7
 doesn't seem to work.

Ran "bundle update" and updated Gemfile.lock from the resulting file.
---
 Gemfile      |  2 +-
 Gemfile.lock | 69 +++++++++++++++++++++++++---------------------------
 2 files changed, 34 insertions(+), 37 deletions(-)

diff --git a/Gemfile b/Gemfile
index 089ef36ea..70e638605 100644
--- a/Gemfile
+++ b/Gemfile
@@ -96,7 +96,7 @@ end
 gem "rspec_api_documentation"
 gem "json-schema" # needed by rspec_api_documentation
 
-gem "apipie-rails"
+gem "apipie-rails", "0.5.6"
 
 # Although it was previously noted that test-unit seems to be needed by
 # apipie-rails and prototype-rails, it interferes with routing specs, so we are
diff --git a/Gemfile.lock b/Gemfile.lock
index 227d1e933..19441ed85 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -36,12 +36,12 @@ GEM
     activerecord-postgis-adapter (5.0.3)
       activerecord (~> 5.1)
       rgeo-activerecord (~> 5.1)
-    activerecord-session_store (1.1.0)
-      actionpack (>= 4.0, < 5.2)
-      activerecord (>= 4.0, < 5.2)
+    activerecord-session_store (1.1.1)
+      actionpack (>= 4.0)
+      activerecord (>= 4.0)
       multi_json (~> 1.11, >= 1.11.2)
       rack (>= 1.5.2, < 3)
-      railties (>= 4.0, < 5.2)
+      railties (>= 4.0)
     activesupport (5.1.5)
       concurrent-ruby (~> 1.0, >= 1.0.2)
       i18n (~> 0.7)
@@ -55,18 +55,18 @@ GEM
     bootstrap-will_paginate (1.0.0)
       will_paginate
     builder (3.2.3)
-    byebug (10.0.0)
-    capybara (2.13.0)
+    byebug (10.0.2)
+    capybara (2.18.0)
       addressable
-      mime-types (>= 1.16)
+      mini_mime (>= 0.1.3)
       nokogiri (>= 1.3.3)
       rack (>= 1.0.0)
       rack-test (>= 0.5.4)
-      xpath (~> 2.0)
-    capybara-webkit (1.14.0)
-      capybara (>= 2.3.0, < 2.14.0)
+      xpath (>= 2.0, < 4.0)
+    capybara-webkit (1.15.0)
+      capybara (>= 2.3, < 4.0)
       json
-    childprocess (0.8.0)
+    childprocess (0.9.0)
       ffi (~> 1.0, >= 1.0.11)
     choice (0.1.6)
     coderay (1.1.2)
@@ -79,18 +79,18 @@ GEM
     coffee-script-source (1.12.2)
     comma (3.0.4)
     concurrent-ruby (1.0.5)
-    crass (1.0.3)
-    database_cleaner (1.6.2)
+    crass (1.0.4)
+    database_cleaner (1.7.0)
     diff-lcs (1.3)
     dynamic_form (1.1.4)
-    erubi (1.7.0)
+    erubi (1.7.1)
     execjs (2.7.0)
-    ffi (1.9.18)
+    ffi (1.9.23)
     globalid (0.4.1)
       activesupport (>= 4.2.0)
     i18n (0.9.5)
       concurrent-ruby (~> 1.0)
-    jquery-rails (4.3.1)
+    jquery-rails (4.3.3)
       rails-dom-testing (>= 1, < 3)
       railties (>= 4.2.0)
       thor (>= 0.14, < 2.0)
@@ -99,29 +99,26 @@ GEM
     json (2.1.0)
     json-schema (2.8.0)
       addressable (>= 2.4)
-    loofah (2.2.0)
+    loofah (2.2.2)
       crass (~> 1.0.2)
       nokogiri (>= 1.5.9)
     mail (2.7.0)
       mini_mime (>= 0.1.1)
     memoist (0.16.0)
     method_source (0.9.0)
-    mime-types (3.1)
-      mime-types-data (~> 3.2015)
-    mime-types-data (3.2016.0521)
     mini_mime (1.0.0)
     mini_portile2 (2.3.0)
     minitest (5.11.3)
     multi_json (1.13.1)
     mustache (1.0.5)
     narray (0.6.0.4)
-    nio4r (2.2.0)
+    nio4r (2.3.0)
     nokogiri (1.8.2)
       mini_portile2 (~> 2.3.0)
     passenger (5.1.12)
       rack
       rake (>= 0.8.1)
-    pg (0.21.0)
+    pg (1.0.0)
     protected_attributes_continued (1.3.0)
       activemodel (~> 5.0)
     pry (0.11.3)
@@ -132,11 +129,11 @@ GEM
       pry (~> 0.10)
     pry-rails (0.3.6)
       pry (>= 0.10.4)
-    public_suffix (3.0.1)
+    public_suffix (3.0.2)
     rabl (0.13.1)
       activesupport (>= 2.3.14)
     rack (2.0.4)
-    rack-test (0.8.3)
+    rack-test (1.0.0)
       rack (>= 1.0, < 3)
     railroad (0.5.0)
     rails (5.1.5)
@@ -158,8 +155,8 @@ GEM
     rails-dom-testing (2.0.3)
       activesupport (>= 4.2.0)
       nokogiri (>= 1.6)
-    rails-html-sanitizer (1.0.3)
-      loofah (~> 2.0)
+    rails-html-sanitizer (1.0.4)
+      loofah (~> 2.2, >= 2.2.2)
     rails3-restful-authentication (3.0.1)
     railties (5.1.5)
       actionpack (= 5.1.5)
@@ -167,8 +164,8 @@ GEM
       method_source
       rake (>= 0.8.7)
       thor (>= 0.18.1, < 2.0)
-    rake (12.3.0)
-    rb-fsevent (0.10.2)
+    rake (12.3.1)
+    rb-fsevent (0.10.3)
     rb-inotify (0.9.10)
       ffi (>= 0.5.0, < 2)
     recaptcha (0.3.4)
@@ -196,7 +193,7 @@ GEM
       rspec-expectations (~> 3.7.0)
       rspec-mocks (~> 3.7.0)
       rspec-support (~> 3.7.0)
-    rspec-support (3.7.0)
+    rspec-support (3.7.1)
     rspec_api_documentation (5.1.0)
       activesupport (>= 3.0.0)
       mustache (~> 1.0, >= 0.99.4)
@@ -205,7 +202,7 @@ GEM
     rubyzip (1.2.1)
     safe_attributes (1.0.10)
       activerecord (>= 3.0.0)
-    sass (3.5.5)
+    sass (3.5.6)
       sass-listen (~> 4.0.0)
     sass-listen (4.0.0)
       rb-fsevent (~> 0.9, >= 0.9.4)
@@ -217,9 +214,9 @@ GEM
       sprockets-rails (>= 2.0, < 4.0)
       tilt (>= 1.1, < 3)
     seer (0.10.0)
-    selenium-webdriver (3.8.0)
+    selenium-webdriver (3.11.0)
       childprocess (~> 0.5)
-      rubyzip (~> 1.0)
+      rubyzip (~> 1.2)
     sprockets (3.7.1)
       concurrent-ruby (~> 1.0)
       rack (> 1, < 3)
@@ -233,14 +230,14 @@ GEM
     trollop (2.1.2)
     tzinfo (1.2.5)
       thread_safe (~> 0.1)
-    uglifier (4.1.6)
+    uglifier (4.1.9)
       execjs (>= 0.3.0, < 3)
     websocket-driver (0.6.5)
       websocket-extensions (>= 0.1.0)
     websocket-extensions (0.1.3)
     will_paginate (3.1.6)
-    xpath (2.1.0)
-      nokogiri (~> 1.3)
+    xpath (3.0.0)
+      nokogiri (~> 1.8)
     yajl-ruby (1.3.1)
     yard (0.9.12)
 
@@ -250,7 +247,7 @@ PLATFORMS
 DEPENDENCIES
   activerecord-postgis-adapter
   activerecord-session_store
-  apipie-rails
+  apipie-rails (= 0.5.6)
   bootstrap-will_paginate
   capybara (~> 2.8)
   capybara-webkit (~> 1.7)

From ec7416f2a73ac69b0b39b51bd2bbc39074dd9c20 Mon Sep 17 00:00:00 2001
From: Scott Rohde <srohde@igb.illinois.edu>
Date: Fri, 27 Apr 2018 11:29:10 -0500
Subject: [PATCH 35/44] Now that Rails uses strong parameters, convert them to
 a Hash before using in query.

---
 app/controllers/api/base_controller.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/app/controllers/api/base_controller.rb b/app/controllers/api/base_controller.rb
index 3a4b95af6..6b75dff5a 100644
--- a/app/controllers/api/base_controller.rb
+++ b/app/controllers/api/base_controller.rb
@@ -47,7 +47,7 @@ def bad_url
   # clause "key = value" is replaced by "key::text ~ value*", where "value*" is
   # "value" with the tilde removed.
   def query(model, params)
-    where_params = params.slice(*model.column_names)
+    where_params = params.permit!.to_hash.slice(*model.column_names)
 
     limit = nil
     if params.has_key? "limit"

From 8012561c7a211bbbfc3652c18bfe4b2ad88b2208 Mon Sep 17 00:00:00 2001
From: Rob Kooper <kooper@illinois.edu>
Date: Mon, 30 Apr 2018 13:32:48 -0500
Subject: [PATCH 36/44] fixes to work with rails5 branch

---
 Dockerfile                |  4 +++-
 README.md                 | 21 ++++++++++++++++++
 config.ru                 |  5 +----
 docker-compose.yml        | 46 +++++++++++++++++++++++++++++++++++++++
 docker/config.ru          |  7 ++++++
 docker/docker-compose.yml | 13 -----------
 docker/entrypoint.sh      | 32 ++++++++-------------------
 7 files changed, 87 insertions(+), 41 deletions(-)
 create mode 100644 docker-compose.yml
 create mode 100644 docker/config.ru
 delete mode 100644 docker/docker-compose.yml

diff --git a/Dockerfile b/Dockerfile
index 792543fe8..c85a7d7f9 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -5,7 +5,9 @@ RUN apt-get update \
     && apt-get install --no-install-recommends -y \
         curl \
         git \
+        libgeos-dev \
         netcat \
+        nodejs \
         postgresql-client \
     && rm -rf /var/lib/apt/lists/*
 
@@ -23,8 +25,8 @@ EXPOSE 8000
 
 # copy rest of the files
 COPY / /home/bety
-COPY /public/javascripts/cache/all.js-sample /home/bety/public/javascripts/cache/all.js
 COPY /docker/database.yml /home/bety/config/database.yml
+COPY /docker/config.ru /home/bety/config.ru
 
 # download dump.bety and load.bety scripts and configure app
 RUN curl -LOs https://raw.githubusercontent.com/PecanProject/pecan/master/scripts/load.bety.sh \
diff --git a/README.md b/README.md
index 9aa4e40a0..4b403331a 100644
--- a/README.md
+++ b/README.md
@@ -9,6 +9,27 @@ This is the source code for the [Biofuel Ecophysiological Traits and Yields data
 The website is primarily written in Ruby-on-Rails, and has a PostgreSQL backend.
 BETYdb provides an interface for contributing and accessing data, and is the informatics backend for the [Predictive Ecosystem Analyzer (PEcAn)](http://www.pecanproject.org).
 
+## Running BETY using Docker
+
+To get started with BETY you can use the docker-compose.yml file included. This will start the database (postgresql with postgis version 9.5) as well as the BETY container. If this is the first time you start it you will need to initialize the database, this can be done using the following commands:
+
+```
+docker-compose -p bety up -d postgres
+docker run --rm --network bety_bety pecan/bety initialize
+```
+
+Once bety finishes inializing the database, or to restart BETY, you can bring up the all the containers using:
+
+```
+docker-compose -p bety up -d
+```
+
+To change the path BETY runs under you can change the path using the environment variable RAILS_RELATIVE_URL_ROOT, for example to just run bety you can use the following command. This will precompile any of the static assets and run BETY.
+
+```
+docker run -e RAILS_RELATIVE_URL_ROOT="/bety" pecan/bety
+```
+
 ## Documentation.
 
 * Technical Documentation: https://pecan.gitbooks.io/betydb-documentation/content/
diff --git a/config.ru b/config.ru
index 6e715ca17..52aeeab9d 100644
--- a/config.ru
+++ b/config.ru
@@ -1,7 +1,4 @@
 # This file is used by Rack-based servers to start the application.
 
 require ::File.expand_path('../config/environment',  __FILE__)
-
-map (ENV['RAILS_RELATIVE_URL_ROOT'] || "") + "/" do
-    run BetyRails3::Application
-end
+run BetyRails3::Application
diff --git a/docker-compose.yml b/docker-compose.yml
new file mode 100644
index 000000000..e85ac47c2
--- /dev/null
+++ b/docker-compose.yml
@@ -0,0 +1,46 @@
+version: "3"
+
+services:
+  # BETY rails frontend to the database
+  bety:
+    image: pecan/bety:unicorn
+    networks:
+      - bety
+    ports:
+      - 8000
+    environment:
+      - UNICORN_WORKER_PROCESSES=1
+      - SECRET_KEY_BASE=thisissomereallllllylongsecretkeyandshouldbelongerthanthis
+    depends_on:
+      - postgres
+    restart: unless-stopped
+    deploy:
+      mode: replicated
+      restart_policy:
+        condition: any
+      placement:
+        constraints: [node.role == manager]
+
+  # postgresql + postgis to hold all the data
+  postgres:
+    image: mdillon/postgis:9.5
+    networks:
+      - bety
+    #ports:
+    #  - 5432
+    volumes:
+      - postgres:/var/lib/postgresql/data
+    restart: unless-stopped
+    deploy:
+      mode: replicated
+      restart_policy:
+        condition: any
+      placement:
+        constraints: [node.role == worker]
+
+networks:
+  bety:
+
+volumes:
+  postgres:
+
diff --git a/docker/config.ru b/docker/config.ru
new file mode 100644
index 000000000..6e715ca17
--- /dev/null
+++ b/docker/config.ru
@@ -0,0 +1,7 @@
+# This file is used by Rack-based servers to start the application.
+
+require ::File.expand_path('../config/environment',  __FILE__)
+
+map (ENV['RAILS_RELATIVE_URL_ROOT'] || "") + "/" do
+    run BetyRails3::Application
+end
diff --git a/docker/docker-compose.yml b/docker/docker-compose.yml
deleted file mode 100644
index 1ca4e4d45..000000000
--- a/docker/docker-compose.yml
+++ /dev/null
@@ -1,13 +0,0 @@
-# ruby & bety
-bety:
-  image: pecan/bety:develop
-  ports:
-    - "3000"
-  links:
-    - postgres:pg
-
-# postgres database
-postgres:
-  image: mdillon/postgis:9.4
-  ports:
-    - "5432"
diff --git a/docker/entrypoint.sh b/docker/entrypoint.sh
index 87c057957..3b7551474 100755
--- a/docker/entrypoint.sh
+++ b/docker/entrypoint.sh
@@ -1,32 +1,14 @@
 #!/bin/bash
 
-function wait_for_postgres() {
-    echo "Waiting for postgres"
-    # Wait for Postgres to start
-    # http://www.onegeek.com.au/articles/waiting-for-dependencies-in-docker-compose
-    WAIT=0
-    while ! nc -w 1 -z postgres 5432; do
-      sleep 1
-      WAIT=$(($WAIT + 1))
-      echo "Try ${WAIT}"
-      if [ "$WAIT" -gt 15 ]; then
-        echo "Error: Timeout wating for Postgres to start"
-        exit 1
-      fi
-    done
-}
-
 # start right job
 case $1 in
     "initialize" )
-        wait_for_postgres
         echo "Create new database, initialized from all data."
         psql -h postgres -p 5432 -U postgres -c "CREATE ROLE bety WITH LOGIN CREATEDB NOSUPERUSER NOCREATEROLE PASSWORD 'bety'"
         psql -h postgres -p 5432 -U postgres -c "CREATE DATABASE bety WITH OWNER bety"
         ./load.bety.sh -a "postgres" -d "bety" -p "-h postgres -p 5432" -o bety -c -u -g -m ${LOCAL_SERVER} -r 0 -w https://ebi-forecast.igb.illinois.edu/pecan/dumpall/bety.tar.gz
         ;;
     "sync" )
-        wait_for_postgres
         echo "Synchronize with servers ${REMOTE_SERVERS}"
         for r in ${REMOTE_SERVERS}; do
             echo "Synchronizing with server ${r}"
@@ -34,29 +16,32 @@ case $1 in
         done
         ;;
     "dump" )
-        wait_for_postgres
         echo "Dump data from server ${LOCAL_SERVER}"
         ./dump.bety.sh -d "bety" -p "-h postgres -p 5432 -U postgres" -m ${LOCAL_SERVER} -o dump
         ;;
     "migrate" )
-        wait_for_postgres
         echo "Migrate database."
         rake db:migrate SKIP_SCHEMASPY=YES
         ;;
     "server" )
-        wait_for_postgres
         echo "Start running BETY (rails server)"
         exec rails s
         ;;
     "unicorn" )
-        wait_for_postgres
+        if [ "$RAILS_RELATIVE_URL_ROOT" != "" ]; then
+            echo "Compiling assests."
+            bundle exec rake assets:precompile
+        fi
         echo "Start running BETY (unicorn)"
         exec bundle exec unicorn -c config/unicorn.rb
         ;;
     "autoserver" )
-        wait_for_postgres
         echo "Migrate database."
         rake db:migrate SKIP_SCHEMASPY=YES
+        if [ "$RAILS_RELATIVE_URL_ROOT" != "" ]; then
+            echo "Compiling assests."
+            bundle exec rake assets:precompile
+        fi
         echo "Start running BETY (unicorn)"
         exec bundle exec unicorn -c config/unicorn.rb
         ;;
@@ -74,4 +59,5 @@ case $1 in
         ;;
     * )
         exec "$@"
+        ;;
 esac

From 27e8a352ba5528d182f0fb156e8216d874d0fd23 Mon Sep 17 00:00:00 2001
From: Rob Kooper <kooper@illinois.edu>
Date: Tue, 1 May 2018 16:32:16 -0500
Subject: [PATCH 37/44] Add Maintainer for now back.

---
 Dockerfile | 1 +
 1 file changed, 1 insertion(+)

diff --git a/Dockerfile b/Dockerfile
index c85a7d7f9..48c079548 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,4 +1,5 @@
 FROM ruby:2.3
+MAINTAINER Max Burnette <mburnet2@illinois.edu>
 
 # Install dependencies
 RUN apt-get update \

From a9b64d50f9bef772e66488aebcf12b39542c2629 Mon Sep 17 00:00:00 2001
From: Scott Rohde <srohde@igb.illinois.edu>
Date: Thu, 10 May 2018 11:30:00 -0500
Subject: [PATCH 38/44] Fixes for experiments table issues: Issues #488 and
 #581.

---
 app/models/experiment.rb               | 1 +
 app/views/layouts/application.html.erb | 1 +
 2 files changed, 2 insertions(+)

diff --git a/app/models/experiment.rb b/app/models/experiment.rb
index 20bea7b1d..38e7532e8 100644
--- a/app/models/experiment.rb
+++ b/app/models/experiment.rb
@@ -1,4 +1,5 @@
 class Experiment < ActiveRecord::Base
+  attr_protected []
 
   extend SimpleSearch
 
diff --git a/app/views/layouts/application.html.erb b/app/views/layouts/application.html.erb
index 8b5a4e2cc..450989e8d 100644
--- a/app/views/layouts/application.html.erb
+++ b/app/views/layouts/application.html.erb
@@ -178,6 +178,7 @@
                 <li><%= link_to "Citations", citations_path %></li>
                 <li><%= link_to "Covariates", covariates_path %></li>
                 <li><%= link_to "Cultivars", cultivars_path %></li>
+                <li><%= link_to "Experiments", experiments_path %></li>
                 <li><%= link_to "Managements", managements_path %></li>
                 <% if current_user.page_access_level <= 2 %>
                   <li><%= link_to "Methods", methods_path %></li>

From 79cb2980626927497ca5a2a24f4732551c846d93 Mon Sep 17 00:00:00 2001
From: Scott Rohde <srohde@igb.illinois.edu>
Date: Thu, 12 Jul 2018 16:31:46 -0500
Subject: [PATCH 39/44] In observe_field helper function, allow specifying the
 observed event both in the case where there is a :url key and in the case
 where there is a :function key.

Up to now, the function only ran on "keyup" events.
---
 app/helpers/application_helper.rb | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/app/helpers/application_helper.rb b/app/helpers/application_helper.rb
index 79e21f407..8a5fdc5f2 100644
--- a/app/helpers/application_helper.rb
+++ b/app/helpers/application_helper.rb
@@ -160,13 +160,15 @@ def commit_date
 
 # Replacement for the Prototype method of this name.
 def observe_field(element_id, **options)
+
+  observed_event = options[:event_name] || "keyup"
+
   # We assume options has either the key :url or the key :function (but not
   # both).
   if options.has_key? :url
     url = url_for(options[:url])
     connector = url.match(/\?/) ? '&' : '?'
     confirmation = options[:confirmation] || "true"
-    observed_event = options[:event_name] || "keyup"
     raw(
       %Q{<script>
              var data_access_level = #{current_user.access_level};
@@ -224,7 +226,7 @@ def observe_field(element_id, **options)
     raw(
       %Q{<script>
              jQuery(document).ready(function() {
-                 jQuery("##{element_id.to_s}").bind("keyup", function() {
+                 jQuery("##{element_id.to_s}").bind("#{observed_event}", function() {
                      #{options[:function]}
                  })
              })

From 62ef61847484f0d91f5482d1e650753334bbd960 Mon Sep 17 00:00:00 2001
From: Scott Rohde <srohde@igb.illinois.edu>
Date: Thu, 12 Jul 2018 16:33:53 -0500
Subject: [PATCH 40/44] Fix for issue #592: Modify observe_field's function to
 be compatible with the jQuery library now that we don't use Prototype.

---
 app/views/users/edit.html.erb | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/app/views/users/edit.html.erb b/app/views/users/edit.html.erb
index c10acca02..847701451 100644
--- a/app/views/users/edit.html.erb
+++ b/app/views/users/edit.html.erb
@@ -98,8 +98,8 @@
 
 <%= observe_field("change_password",
                   :frequency => 1,
-                  :function => "var u = $('user_password'); u.disabled = !u.disabled;$('user_password_confirmation').disabled = u.disabled;") %>
-
+                  :event_name => "change",
+                  :function => "var u = jQuery('#user_password')[0]; u.disabled = !u.disabled; jQuery('#user_password_confirmation')[0].disabled = u.disabled;") %>
 
 
 

From e4bb02cc0f3a14c8501853b6180e65e1d0cf06c1 Mon Sep 17 00:00:00 2001
From: Scott Rohde <srohde@igb.illinois.edu>
Date: Tue, 17 Jul 2018 14:51:48 -0500
Subject: [PATCH 41/44] Changed app name from BetyRail3 to BetyRails5.

Make update-betydb.sh download load.bety.sh script from the develop branch
rather than the master branch.
---
 Rakefile                | 2 +-
 config.ru               | 2 +-
 config/application.rb   | 2 +-
 docker/config.ru        | 2 +-
 script/update-betydb.sh | 2 +-
 5 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/Rakefile b/Rakefile
index f01e21ae9..8309d623a 100644
--- a/Rakefile
+++ b/Rakefile
@@ -4,4 +4,4 @@
 require File.expand_path('../config/application', __FILE__)
 require 'rake'
 
-BetyRails3::Application.load_tasks
+BetyRails5::Application.load_tasks
diff --git a/config.ru b/config.ru
index 52aeeab9d..762cedca0 100644
--- a/config.ru
+++ b/config.ru
@@ -1,4 +1,4 @@
 # This file is used by Rack-based servers to start the application.
 
 require ::File.expand_path('../config/environment',  __FILE__)
-run BetyRails3::Application
+run BetyRails5::Application
diff --git a/config/application.rb b/config/application.rb
index 3b9e24684..d25f4194b 100644
--- a/config/application.rb
+++ b/config/application.rb
@@ -6,7 +6,7 @@
 # you've limited to :test, :development, or :production.
 Bundler.require(*Rails.groups)
 
-module BetyRails3
+module BetyRails5
   class Application < Rails::Application
 
     # Enable Hash#deep_symbolize_keys method defined in lib/symbolize_helper.rb.
diff --git a/docker/config.ru b/docker/config.ru
index 6e715ca17..bbdec59fd 100644
--- a/docker/config.ru
+++ b/docker/config.ru
@@ -3,5 +3,5 @@
 require ::File.expand_path('../config/environment',  __FILE__)
 
 map (ENV['RAILS_RELATIVE_URL_ROOT'] || "") + "/" do
-    run BetyRails3::Application
+    run BetyRails5::Application
 end
diff --git a/script/update-betydb.sh b/script/update-betydb.sh
index d1984562b..4aaa12e6d 100755
--- a/script/update-betydb.sh
+++ b/script/update-betydb.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 
 # The source for load.bety.sh:
-SCRIPT_SOURCE_LOCATION=https://raw.githubusercontent.com/PecanProject/pecan/master/scripts/load.bety.sh
+SCRIPT_SOURCE_LOCATION=https://raw.githubusercontent.com/PecanProject/pecan/develop/scripts/load.bety.sh
 
 # These are options we want to pass through to load.bety.sh.  Update this as
 # needed if load.bety.sh is revised:

From a5c5b38b3a044fa845cc360c7f7bac104378bb28 Mon Sep 17 00:00:00 2001
From: Scott Rohde <srohde@igb.illinois.edu>
Date: Tue, 17 Jul 2018 16:26:13 -0500
Subject: [PATCH 42/44] Change the name of the RVM Gem set from betydb_rails3
 to betydb_rails5.

---
 .ruby-gemset | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.ruby-gemset b/.ruby-gemset
index b37d060df..1d2770e17 100644
--- a/.ruby-gemset
+++ b/.ruby-gemset
@@ -1 +1 @@
-betydb_rails3
+betydb_rails5

From 1cd385637cac4f8849c361af409a81c1fd7f3a65 Mon Sep 17 00:00:00 2001
From: Scott Rohde <srohde@illinois.edu>
Date: Thu, 19 Jul 2018 17:08:00 -0500
Subject: [PATCH 43/44] Move the preview directory for Priors preview images
 from app/assets/images/ back to public/images/ since these aren't served up
 as assets.

Added to the global .gitignore file
---
 .gitignore                                    | 5 ++++-
 {app/assets => public}/images/prev/.gitignore | 0
 2 files changed, 4 insertions(+), 1 deletion(-)
 rename {app/assets => public}/images/prev/.gitignore (100%)

diff --git a/.gitignore b/.gitignore
index 56172aaff..c834d231d 100644
--- a/.gitignore
+++ b/.gitignore
@@ -18,5 +18,8 @@ orig.public
 public/maps/*
 config/initializers/site_keys.rb
 .Rproj.user
+public/assets
+script/load.bety.sh
 
-
+# Ignore encrypted secrets key file.
+config/secrets.yml.key
diff --git a/app/assets/images/prev/.gitignore b/public/images/prev/.gitignore
similarity index 100%
rename from app/assets/images/prev/.gitignore
rename to public/images/prev/.gitignore

From 4323e8eebef8ce716902429990c54003e947606c Mon Sep 17 00:00:00 2001
From: Scott Rohde <srohde@igb.illinois.edu>
Date: Wed, 1 Aug 2018 16:50:57 -0500
Subject: [PATCH 44/44] Updated the version of Phusion Passenger used.

---
 Gemfile      | 5 +----
 Gemfile.lock | 9 +++------
 2 files changed, 4 insertions(+), 10 deletions(-)

diff --git a/Gemfile b/Gemfile
index edbee6ba0..2d9206e10 100644
--- a/Gemfile
+++ b/Gemfile
@@ -84,11 +84,8 @@ group :debug do
   gem "pry"
 end
 
-# Comment this out if you can't or don't wish to install capybara-webkit:
-
 group :production do
-  #  gem "rmagick", "2.13.1"
-  gem "passenger", "5.1.12"
+  gem "passenger"
 end
 
 group :docker do
diff --git a/Gemfile.lock b/Gemfile.lock
index 084f6f0e3..0a77f2f08 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -116,7 +116,7 @@ GEM
     nio4r (2.3.0)
     nokogiri (1.8.2)
       mini_portile2 (~> 2.3.0)
-    passenger (5.1.12)
+    passenger (5.3.4)
       rack
       rake (>= 0.8.1)
     pg (1.0.0)
@@ -133,7 +133,7 @@ GEM
     public_suffix (3.0.2)
     rabl (0.13.1)
       activesupport (>= 2.3.14)
-    rack (2.0.4)
+    rack (2.0.5)
     rack-test (1.0.0)
       rack (>= 1.0, < 3)
     railroad (0.5.0)
@@ -270,7 +270,7 @@ DEPENDENCIES
   multi_json
   narray (= 0.6.0.4)
   nokogiri
-  passenger (= 5.1.12)
+  passenger
   pg
   protected_attributes_continued
   pry
@@ -298,6 +298,3 @@ DEPENDENCIES
   will_paginate
   yajl-ruby (~> 1.3.1)
   yard
-
-BUNDLED WITH
-   1.16.1