Remove hipaa identifiers

Gemfile

@@ -4,6 +4,7 @@ source 'https://rubygems.org'
 ruby ENV['CUSTOM_RUBY_VERSION'] || '2.4.4'
 
 gem 'activerecord', '>= 5.1.5' # ORM
+gem 'activerecord-delay_touching', '>= 1.0.1' # Batch Touching Calls
 gem 'audited', '>= 4.7.0', require: false # adds table auiting support
 gem 'bugsnag', '>= 6.6', require: false # online bug reporting
 gem 'bundler-audit', '>= 0.6.0', require: false # check gems for security issues
@@ -56,6 +57,8 @@ end
 
 group :development, :test do
   gem 'annotate', '>= 2.7.2', require: false # annotate models
+  gem 'better_errors', '>= 2.4.0', require: false # better error logging 
+  gem 'binding_of_caller', '>= 0.8.0', require: false # helps better_errors provide more detailed debugging
   # Call 'byebug' anywhere in the code to stop execution and get a debugger console
   gem 'byebug', '>= 10.0.2', platforms: %i[mri mingw x64_mingw]
   gem 'fasterer', require: false # find slow code 

Gemfile.lock

@@ -7,6 +7,8 @@ GEM
       activemodel (= 5.1.6)
       activesupport (= 5.1.6)
       arel (~> 8.0)
+    activerecord-delay_touching (1.0.1)
+      activerecord (>= 4.2)
     activesupport (5.1.6)
       concurrent-ruby (~> 1.0, >= 1.0.2)
       i18n (>= 0.7, < 2)
@@ -27,7 +29,13 @@ GEM
       ice_nine (~> 0.11.0)
       thread_safe (~> 0.3, >= 0.3.1)
     backports (3.11.1)
-    bugsnag (6.6.4)
+    better_errors (2.4.0)
+      coderay (>= 1.0.0)
+      erubi (>= 1.0.0)
+      rack (>= 0.9.0)
+    binding_of_caller (0.8.0)
+      debug_inspector (>= 0.0.1)
+    bugsnag (6.7.0)
       concurrent-ruby (~> 1.0)
     bundler-audit (0.6.0)
       bundler (~> 1.2)
@@ -49,6 +57,7 @@ GEM
       term-ansicolor
       thor
     database_cleaner (1.6.1)
+    debug_inspector (0.0.3)
     descendants_tracker (0.0.4)
       thread_safe (~> 0.3, >= 0.3.1)
     diff-lcs (1.3)
@@ -59,6 +68,7 @@ GEM
       unf (>= 0.0.5, < 1.0.0)
     dotenv (2.2.1)
     equalizer (0.0.11)
+    erubi (1.7.1)
     ethon (0.11.0)
       ffi (>= 1.3.0)
     factory_bot (4.8.2)
@@ -232,7 +242,7 @@ GEM
       rdoc (>= 5.0)
     secure_headers (5.0.5)
       useragent (>= 0.15.0)
-    sexp_processor (4.10.1)
+    sexp_processor (4.11.0)
     shellany (0.0.1)
     simplecov (0.16.1)
       docile (~> 1.1)
@@ -289,7 +299,6 @@ GEM
     unf (0.1.4)
       unf_ext
     unf_ext (0.0.7.5)
-    unf_ext (0.0.7.5-x64-mingw32)
     unicode-display_width (1.3.0)
     useragent (0.16.10)
     valid_email2 (2.2.2)
@@ -310,8 +319,11 @@ PLATFORMS
 
 DEPENDENCIES
   activerecord (>= 5.1.5)
+  activerecord-delay_touching (>= 1.0.1)
   annotate (>= 2.7.2)
   audited (>= 4.7.0)
+  better_errors (>= 2.4.0)
+  binding_of_caller (>= 0.8.0)
   bugsnag (>= 6.6)
   bundler-audit (>= 0.6.0)
   byebug (>= 10.0.2)

app/models/choice.rb

@@ -29,7 +29,7 @@
 
 # Model to represent choices in a rating scale
 class Choice < ApplicationRecord
-  belongs_to :response_scale, inverse_of: :choices
+  belongs_to :response_scale, inverse_of: :choices, touch: true
   has_many :responses, inverse_of: :choice
 
   validates :response_scale, presence: true

app/models/init.rb

@@ -12,7 +12,6 @@
 require_relative 'assessment_instrument'
 require_relative 'choice'
 require_relative 'folder'
-require_relative 'hipaa_identifier'
 require_relative 'instrument'
 require_relative 'item'
 require_relative 'journal'

app/models/instrument.rb

@@ -4,6 +4,7 @@
 # Similar to a survey or questionnaire
 class Instrument < ApplicationRecord
   include PgSearch
+  include Discard::Model
   multisearchable against: %i[json_content csv_content]
   pg_search_scope :search_json, against: :json_content
   pg_search_scope :search_csv, against: :csv_content

app/models/item.rb

@@ -35,7 +35,7 @@
 # Represents a psychometric item
 # Similar to a question with metadata
 class Item < ApplicationRecord
-  belongs_to :instrument, inverse_of: :items
+  belongs_to :instrument, inverse_of: :items, touch: true
   belongs_to :response_scale, inverse_of: :items, optional: true
   has_many :choices, through: :response_scale  
   validates :name, presence: true

app/models/journal_entry.rb

@@ -2,7 +2,7 @@
 
 # Model to represent patient journals
 class JournalEntry < ApplicationRecord
-  belongs_to :journal, inverse_of: :journal_entries
+  belongs_to :journal, inverse_of: :journal_entries, touch: true
   validates :entry, exclusion: { in: [nil] } # allow '' but not nil
   validates :entry_date, presence: true
   validates_uniqueness_of :entry_date, scope: :journal

app/models/schedule.rb

@@ -2,7 +2,7 @@
 
 # Model to represent visit schedules
 class Schedule < ApplicationRecord
-  belongs_to :study
+  belongs_to :study, touch: true
   has_many :arms, inverse_of: :schedule
 
   validates :name, presence: true

config/initializers/00_better_errors_initializer.rb

@@ -0,0 +1,8 @@
+# frozen_string_literal: true
+
+require "better_errors"
+
+configure :development, :test do
+  use BetterErrors::Middleware
+  BetterErrors.application_root = __dir__
+end

db/migrate/20180408205532_add_discard_to_users.rb

@@ -1,9 +1,12 @@
 # frozen_string_literal: true
 
+require './lib/shared_migration'
+
 # Add soft delete to users table
 class AddDiscardToUsers < ActiveRecord::Migration[5.1]
+  include SharedMigration
+
   def change
-    add_column :users, :discarded_at, :datetime
-    add_index :users, :discarded_at
+    add_discard table_name: :users
   end
 end

db/migrate/20180409004310_add_discard_to_instruments.rb

@@ -0,0 +1,12 @@
+# frozen_string_literal: true
+
+require './lib/shared_migration'
+
+# Add soft delete to users table
+class AddDiscardToInstruments < ActiveRecord::Migration[5.1]
+  include SharedMigration
+
+  def change
+    add_discard table_name: :instruments
+  end
+end

db/schema.rb

@@ -10,7 +10,7 @@
 #
 # It's strongly recommended that you check this file into your version control system.
 
-ActiveRecord::Schema.define(version: 20180408205532) do
+ActiveRecord::Schema.define(version: 20180409004310) do
 
   # These are extensions that must be enabled in order to support this database
   enable_extension "plpgsql"
@@ -106,7 +106,9 @@
     t.datetime "created_at", default: -> { "CURRENT_TIMESTAMP" }, null: false
     t.datetime "updated_at", default: -> { "CURRENT_TIMESTAMP" }, null: false
     t.string "tags", default: [], array: true
+    t.datetime "discarded_at"
     t.index ["csv_content"], name: "index_instruments_on_csv_content"
+    t.index ["discarded_at"], name: "index_instruments_on_discarded_at"
     t.index ["json_content"], name: "instrument_json_content", using: :gin
     t.index ["name"], name: "index_instruments_on_name"
     t.index ["tags"], name: "instrument_tags", using: :gin

db/seeds/all.rb

@@ -11,25 +11,3 @@
 # instrument = InstrumentCsv.new(name: AppConstants::DEFAULT_CSV_INSTRUMENT)
 # InstrumentLoader.instance.load(instrument: instrument, type: :csv)
 # end
-
-unless HipaaIdentifier.count == 18 
-  HipaaIdentifier.delete_all
-  HipaaIdentifier.create! name: 'Name'
-  HipaaIdentifier.create! name: 'Fax number'
-  HipaaIdentifier.create! name: 'Phone number'
-  HipaaIdentifier.create! name: 'E-mail address'
-  HipaaIdentifier.create! name: 'Account numbers'
-  HipaaIdentifier.create! name: 'Social Security number'
-  HipaaIdentifier.create! name: 'Medical Record number'
-  HipaaIdentifier.create! name: 'Health Plan number'
-  HipaaIdentifier.create! name: 'Certificate/license numbers'
-  HipaaIdentifier.create! name: 'URL'
-  HipaaIdentifier.create! name: 'IP address'
-  HipaaIdentifier.create! name: 'Vehicle identifiers'
-  HipaaIdentifier.create! name: 'Device ID'
-  HipaaIdentifier.create! name: 'Biometric ID'
-  HipaaIdentifier.create! name: 'Full face/identifying photo'
-  HipaaIdentifier.create! name: 'Other unique identifying number, characteristic, or code'
-  HipaaIdentifier.create! name: 'Postal address (geographic subdivisions smaller than state)'
-  HipaaIdentifier.create! name: 'Date precision beyond year'
-end

lib/custom_exceptions.rb

@@ -1,8 +1,15 @@
 # frozen_string_literal: true
 
-# class to implement friendly exception for file not found rather than ErrNoEnt
+# class to implement a friendly exception for file not found rather than ErrNoEnt
 class FileNotFoundException < StandardError
   def to_s
     'File not found'
   end
 end
+
+# class to implement an exception for Missing Table Names in migrations
+class MissingTableNameException < StandardError
+  def to_s
+    'Missing Table Name'
+  end
+end

lib/shared_migration.rb

@@ -1,5 +1,7 @@
 # frozen_string_literal: true
 
+require './lib/custom_exceptions'
+
 # Methods to DRY out migrations
 module SharedMigration
   def create_name_table(table_name:) 
@@ -10,4 +12,11 @@ def create_name_table(table_name:)
       tname.timestamps null: false, default: -> { 'CURRENT_TIMESTAMP' }
     end
   end
+
+  def add_discard(table_name:)
+    raise "Missing Table Name: #{table_name}" if table_name.blank?
+
+    add_column table_name, :discarded_at, :datetime
+    add_index table_name, :discarded_at
+  end
 end

spec/factories.rb

@@ -46,11 +46,6 @@
     initialize_with { Folder.find_or_create_by! name: TestConstants::TEST_FOLDER }
   end
 
-  factory :test_hipaa_identifier, class: 'HipaaIdentifier' do
-    name TestConstants::TEST_HIPAA_IDENTIFIER
-    initialize_with { HipaaIdentifier.find_or_create_by! name: TestConstants::TEST_HIPAA_IDENTIFIER }
-  end
-
   factory :test_instrument, class: 'Instrument' do
     name TestConstants::TEST_INSTRUMENT
     initialize_with { Instrument.find_or_create_by! name: TestConstants::TEST_INSTRUMENT }

spec/models/instrument_spec.rb

@@ -36,15 +36,15 @@
   describe '#items' do
     context 'has no items' do 
       it do
-        ins2 = described_class.find_or_create_by! name: 'Instrument 2'
+        ins2 = Instrument.find_or_create_by! name: 'Instrument 2'
         expect(ins2.items.count).to eq 0 
       end
     end
   end
 
   describe '.list_tests' do
     it 'should return a list of instrument names' do
-      expect(described_class.list_tests(limit: 10)).to \
+      expect(Instrument.list_tests(limit: 10)).to \
         include(TestConstants::TEST_INSTRUMENT)
     end
   end
@@ -60,4 +60,30 @@
   describe '#instructions' do
     it { expect(subject.instructions).to include 'felt or behaved' }
   end
+
+  describe '#discard' do
+    let!(:ins2) { Instrument.find_or_create_by! name: 'Instrument 2' }
+    before :each do
+      ins2.discard
+    end
+
+    context 'does not delete' do
+      it timecop: :freeze do
+        expect(ins2.discarded_at.change(usec: 0)).to eq Time.now.change(usec: 0)
+      end
+
+      it do
+        expect(ins2.discarded?).to eq true    
+      end
+
+      it do
+        discarded = Instrument.discarded.first
+        expect(discarded.id).to eq ins2.id
+      end
+
+      it do
+        expect(Instrument.kept.include?(ins2)).to be_falsey
+      end
+    end
+  end
 end

spec/test_constants.rb

@@ -6,7 +6,6 @@ module TestConstants
   TEST_ARM = 'Test Arm'
   TEST_ARM2 = 'Test Arm 2'
   TEST_FOLDER = 'Test Folder'
-  TEST_HIPAA_IDENTIFIER = 'Test Hipaa Identifier'
   TEST_INSTRUMENT = 'Cesd-r'
   TEST_JOURNAL = 'Test Journal'
   TEST_PARTICIPANT_EMAIL = 'test_participant@test.com'