Upgrading to mongoid 3.0.6, the latest health-data-standards and devi…

…se_oauth2_providable code

Gemfile

@@ -2,17 +2,15 @@ source 'http://rubygems.org'
 
 
 gem 'rails', '3.2.8'
-gem "health-data-standards", :git => "http://github.com/projectcypress/health-data-standards.git", :branch => "develop"
+gem "health-data-standards", :git => "https://github.com/eedrummer/health-data-standards.git", :branch => "develop"
 gem 'ruby-openid'
-gem "mongoid"
-gem "bson_ext"
+gem "mongoid", '~> 3.0.6'
 gem "pry"
 gem 'pry-nav'
 gem "capistrano"
-gem 'heroku'
-gem "nokogiri"
+gem "nokogiri", '~> 1.5.5'
 gem 'devise'
-gem 'devise_oauth2_providable', :git => 'http://github.com/rdingwell/devise_oauth2_providable.git' #,:branch => "master" 
+gem 'devise_oauth2_providable', :git => 'https://github.com/project-rhex/devise_oauth2_providable.git' #,:branch => "master" 
 gem 'omniauth_openid_connect', :git => "https://github.com/project-rhex/omniauth_openid_connect.git"
 
 gem 'omniauth'

Gemfile.lock

@@ -1,18 +1,18 @@
 GIT
-  remote: http://github.com/projectcypress/health-data-standards.git
-  revision: e2a73f19322e6ef9115e932dbba9b11751afa745
+  remote: https://github.com/eedrummer/health-data-standards.git
+  revision: efd8445676b1ff0575f3c617cd54f4b6d791a7fc
   branch: develop
   specs:
-    health-data-standards (1.0.1)
+    health-data-standards (2.0.0)
       builder (~> 3.0.0)
-      erubis (~> 2.6)
-      mongoid (~> 2.4.2)
-      nokogiri (>= 1.4.4)
-      uuid (~> 2.3.4)
+      erubis (~> 2.7.0)
+      mongoid (~> 3.0.6)
+      nokogiri (~> 1.5.5)
+      uuid (~> 2.3.5)
 
 GIT
-  remote: http://github.com/rdingwell/devise_oauth2_providable.git
-  revision: 99d0ca56786f86a8e28875d462c99f9e344ac2f9
+  remote: https://github.com/project-rhex/devise_oauth2_providable.git
+  revision: 1e3b7f5553e0b5b957b876fa8e42a593c7ebaa32
   specs:
     devise_oauth2_providable (1.0.5)
       devise (>= 1.4.3)
@@ -63,9 +63,6 @@ GEM
     arel (3.0.2)
     attr_required (0.0.5)
     bcrypt-ruby (3.0.1)
-    bson (1.7.0)
-    bson_ext (1.7.0)
-      bson (~> 1.7.0)
     builder (3.0.3)
     capistrano (2.13.4)
       highline
@@ -96,7 +93,6 @@ GEM
       warden (~> 1.2.1)
     erubis (2.7.0)
     eventmachine (1.0.0)
-    excon (0.16.2)
     execjs (1.4.0)
       multi_json (~> 1.0)
     factory_girl (4.1.0)
@@ -112,14 +108,6 @@ GEM
       nokogiri (> 0.0.0)
       sax-machine (>= 0.0.12)
     hashie (1.2.0)
-    heroku (2.31.2)
-      heroku-api (~> 0.3.4)
-      launchy (>= 0.3.2)
-      netrc (~> 0.7.7)
-      rest-client (~> 1.6.1)
-      rubyzip
-    heroku-api (0.3.5)
-      excon (~> 0.16.1)
     highline (1.6.15)
     hike (1.2.1)
     httpclient (2.2.7)
@@ -128,6 +116,7 @@ GEM
     jquery-rails (2.1.2)
       railties (>= 3.1.0, < 5.0)
       thor (~> 0.14)
+    jruby-pageant (1.1.1)
     json (1.7.5)
     json-jwt (0.1.8)
       activesupport (>= 2.3)
@@ -137,8 +126,6 @@ GEM
     kaminari (0.14.1)
       actionpack (>= 3.0.0)
       activesupport (>= 3.0.0)
-    launchy (2.1.2)
-      addressable (~> 2.3)
     libv8 (3.3.10.4)
     loofah (1.2.1)
       nokogiri (>= 1.4.4)
@@ -151,21 +138,21 @@ GEM
     method_source (0.8)
     mime-types (1.19)
     minitest (3.4.0)
-    mongo (1.3.1)
-      bson (>= 1.3.1)
-    mongoid (2.4.12)
+    mongoid (3.0.6)
       activemodel (~> 3.1)
-      mongo (<= 1.6.2)
+      moped (~> 1.1)
+      origin (~> 1.0)
       tzinfo (~> 0.3.22)
+    moped (1.2.2)
     multi_json (1.3.6)
     net-scp (1.0.4)
       net-ssh (>= 1.99.1)
     net-sftp (2.0.5)
       net-ssh (>= 2.0.9)
-    net-ssh (2.5.2)
+    net-ssh (2.6.0)
+      jruby-pageant (>= 1.1.1)
     net-ssh-gateway (1.1.0)
       net-ssh (>= 1.99.1)
-    netrc (0.7.7)
     nokogiri (1.5.5)
     omniauth (1.1.1)
       hashie (~> 1.2)
@@ -183,6 +170,7 @@ GEM
       tzinfo
       validate_email
       validate_url
+    origin (1.0.8)
     orm_adapter (0.4.0)
     polyglot (0.3.3)
     pry (0.9.10)
@@ -226,10 +214,7 @@ GEM
     rake (0.9.2.2)
     rdoc (3.12)
       json (~> 1.4)
-    rest-client (1.6.7)
-      mime-types (>= 1.16)
     ruby-openid (2.2.0)
-    rubyzip (0.9.9)
     sass (3.2.1)
     sass-rails (3.2.5)
       railties (~> 3.2.0)
@@ -286,7 +271,6 @@ PLATFORMS
   ruby
 
 DEPENDENCIES
-  bson_ext
   capistrano
   coffee-rails (~> 3.2.1)
   cover_me
@@ -295,12 +279,11 @@ DEPENDENCIES
   factory_girl_rails
   feedzirra
   health-data-standards!
-  heroku
   jquery-rails
   kaminari
   minitest
-  mongoid
-  nokogiri
+  mongoid (~> 3.0.6)
+  nokogiri (~> 1.5.5)
   omniauth
   omniauth-openid
   omniauth_openid_connect!

app/controllers/application_controller.rb

@@ -43,7 +43,7 @@ def add_breadcrumb title, link = nil
   # parameter. Make sure to add exceptions for methods that don't.
   def find_record
     record_id = params[:record_id] || params[:id]
-    @record = Record.first(conditions: {medical_record_number: record_id})
+    @record = Record.where(medical_record_number: record_id).first
     raise RequestError.new(404) if @record.nil?
   end
 

app/controllers/entries_controller.rb

@@ -86,8 +86,8 @@ def set_up_section
   end
 
   def find_entry
-    if BSON::ObjectId.legal?(params[:id])
-      @entry = @record.send(@section_name).find(:first, conditions: {id: params[:id]})
+    if Moped::BSON::ObjectId.legal?(params[:id])
+      @entry = @record.send(@section_name).where(id: params[:id]).first
       raise RequestError.new(404, 'Entry Not Found') unless @entry
     else
       raise RequestError.new(400, 'Not a valid identifier for a section document')

app/controllers/open_id_controller.rb

@@ -63,12 +63,8 @@ def authorize
 
     scope = scope.split(/\s/)
 
-    # Find or create a client that matches the given client id
-    begin
-      client = Devise::Oauth2Providable::Client.first(conditions: {cidentifier: client_id})
-    rescue
-      #
-    end
+
+    client = Devise::Oauth2Providable::Client.where(cidentifier: client_id).first
 
     unless client
       raise OpenId::AuthenticationException.new(value: OpenId::ErrorCodes::INVALID_REQUEST,
@@ -101,8 +97,8 @@ def validate
     end
 
     # Find client and user
-    user = User.first(conditions: {email: credentials[:email]})
-    client = Devise::Oauth2Providable::Client.first(conditions: {cidentifier: client_id})
+    user = User.find_by(email: credentials[:email])
+    client = Devise::Oauth2Providable::Client.where(cidentifier: client_id).first
 
     unless client
       raise Exception.new("Client is missing from the database")
@@ -154,7 +150,7 @@ def confirm
         description: "The user denied access to the website", redirect_uri: redirect_uri, state: state)
     end
 
-    client = Devise::Oauth2Providable::Client.first(conditions: {cidentifier: client_id})
+    client = Devise::Oauth2Providable::Client.where(cidentifier: client_id).first
 
     # Create and store the code in the client along with the scopes the user has enabled
     code = SecureRandom.uuid

app/models/audit_log.rb

@@ -28,14 +28,14 @@ class AuditLog
   ## get list of all audited docs
   def self.review_docs() 
     ## return all log events that end in _access
-    AuditLog.all( conditions: { event: /_access$/i } ).to_a
+    AuditLog.where(event: /_access$/i).to_a
   end
 
 
   ## get list of audited docs with this id
   def self.review_doc(id) 
     ## query and return array of data
-    AuditLog.all( conditions: { event: /_access$/i, obj_id: id } ).to_a
+    AuditLog.where(event: /_access$/i).where(obj_id: id).to_a
   end
 
 

app/models/user.rb

@@ -10,8 +10,8 @@ class User
          :oauth2_authorization_code_grantable
 
   ## Database authenticatable
-  field :email,              type: String, null: false
-  field :encrypted_password, type: String, null: false
+  field :email,              type: String
+  field :encrypted_password, type: String
 
   ## Recoverable
   field :reset_password_token,   type: String

config/mongoid.yml

@@ -1,15 +1,20 @@
 development:
-  host: localhost
-  database: hdata_server_development
+  sessions:
+    default:
+      database: patient_data_server_development
+      hosts:
+        - localhost:27017
 
 test:
-  host: <%= ENV['TEST_DB_HOST'] || 'localhost' %>
-  database: hdata_server_test
-
-staging:
-  host: localhost
-  database: hdata_server_staging
+  sessions:
+    default:
+      database: patient_data_server_test
+      hosts:
+        - <%= ENV['TEST_DB_HOST'] || 'localhost' %>:27017
 
 production:
-  host: localhost
-  database: hdata_server_production
+  sessions:
+    default:
+      database: patient_data_server_production
+      hosts:
+        - localhost:27017

lib/notify/notify_event.rb

@@ -3,7 +3,7 @@ class NotifyEvent
 
   def self.process(user, action)
     # lookup user and action in notify_config
-    notify_configs = NotifyConfig.all( conditions: { user: /#{user}/i, action: action } ).to_a
+    notify_configs = NotifyConfig.where(user: /#{user}/i, action: action).to_a
 
     # for each entry, insert a document into notification table
     notify_configs.each do |nconfig|

test/functional/audit_review_controller_test.rb

@@ -37,21 +37,15 @@ class AuditReviewControllerTest < ActionController::TestCase
   test "audit_review_docs" do
     assert_not_nil @audit_log, "factory girl audit_log is nil"
 
-
-
-
-
-
-
     ## get test obj_id
     test_id = @audit_log.obj_id
 
     ## get list of all review docs (docs that end in _access)
     review_docs = AuditLog.review_docs
     assert_not_nil review_docs, "review_docs query failed"
 
-    assert_equal review_docs.count, 3, "audit_log not populated correctly"
-    assert_equal review_docs[0].obj_id, test_id, "obj_id is not #{test_id} (1)"
+    assert_equal 3, review_docs.count, "audit_log not populated correctly"
+    assert_equal test_id, review_docs[0].obj_id, "obj_id is not #{test_id} (1)"
 
     ## get this specific doc
     review_docs = AuditLog.review_doc(test_id)
@@ -65,8 +59,6 @@ class AuditReviewControllerTest < ActionController::TestCase
     @record.save
     AuditLog.doc("NONE", "c32_access", "test description", @record, @record.version)
     #
-    #
-    #
 
     review_docs = AuditLog.review_doc(@record._id)
     assert_not_nil review_docs, "review_doc query failed(2)"

test/functional/open_id_controller_test.rb

@@ -6,7 +6,7 @@ class OpenIdControllerTest < ActionController::TestCase
   CLIENT_ID = '1570981427089'
 
   def setup
-    @client = Devise::Oauth2Providable::Client.first(conditions: {cidentifier: CLIENT_ID})
+    @client = Devise::Oauth2Providable::Client.find_by(cidentifier: CLIENT_ID)
     @client = FactoryGirl.create(:client) unless @client
     @user = FactoryGirl.create(:user)
     sign_in @user

test/integration/notification_event_test.rb

@@ -19,7 +19,7 @@ class NotificationEventTest < ActionController::TestCase
     NotifyEvent.process("[email protected]", :record_update)
     notifications = Notification.all.to_a
     assert_not_nil notifications, "Notifications is null !"
-    assert_equal notifications.count, 1, "notifications not populated correctly"
+    assert_equal 1, notifications.count, "notifications not populated correctly"
   end
 
 

test/test_helper.rb

@@ -17,7 +17,7 @@ def load_fixtures
 
 
 def dump_database
-   Mongoid::Config.master.collections.each do |collection|
+   Mongoid.session(:default).collections.each do |collection|
      collection.drop unless collection.name.include?('system.')
    end
 end