Misc formatting.

Gemfile

@@ -39,8 +39,8 @@ gem 'jquery-turbolinks'
 gem 'jbuilder', '~> 2.0'
 gem 'chronic', '~> 0.10'
 
-gem 'awesome_nested_set',  
-  git: 'https://github.com/collectiveidea/awesome_nested_set.git'
+gem 'awesome_nested_set',
+    git: 'https://github.com/collectiveidea/awesome_nested_set.git'
 #  tag: 'v3.0.0.rc.5', 
 
 # BibTex handling

app/models/asserted_distribution.rb

@@ -12,14 +12,14 @@ class AssertedDistribution < ActiveRecord::Base
   validates_presence_of :source_id, message: 'Source is not selected'
   validates_uniqueness_of :geographic_area_id, scope: [:otu_id, :source_id], message: 'Duplicate record'
 
-  scope :with_otu_id, -> (otu_id) {where(otu_id: otu_id)}
-  scope :with_geographic_area_id, -> (geographic_area_id) {where(geographic_area_id: geographic_area_id)}
-  scope :with_geographic_area_array, -> (geographic_area_array) {where('geographic_area_id IN (?)', geographic_area_array ) }
-  scope :with_is_absent, -> {where('is_absent = true')}
-  scope :without_is_absent, -> {where('is_absent = false OR is_absent is Null')}
+  scope :with_otu_id, -> (otu_id) { where(otu_id: otu_id) }
+  scope :with_geographic_area_id, -> (geographic_area_id) { where(geographic_area_id: geographic_area_id) }
+  scope :with_geographic_area_array, -> (geographic_area_array) { where('geographic_area_id IN (?)', geographic_area_array) }
+  scope :with_is_absent, -> { where('is_absent = true') }
+  scope :without_is_absent, -> { where('is_absent = false OR is_absent is Null') }
 
   # TODO: this should be a housekeeping scope
-  scope :not_self, -> (id) {where('asserted_distribution.id <> ?', id )}
+  scope :not_self, -> (id) { where('asserted_distribution.id <> ?', id) }
 
   soft_validate(:sv_conflicting_geographic_area, set: :conflicting_geographic_area)
 
@@ -32,7 +32,7 @@ def sv_conflicting_geographic_area
         presence = AssertedDistribution.without_is_absent.with_geographic_area_id(self.geographic_area_id) # this returns an array, not a single GA so test below is not right
         soft_validations.add(:geographic_area_id, "Taxon is reported as present in #{presence.first.geographic_area.name}") unless presence.empty?
       else
-        areas = [ga.level0_id, ga.level1_id, ga.level2_id].compact
+        areas    = [ga.level0_id, ga.level1_id, ga.level2_id].compact
         presence = AssertedDistribution.with_is_absent.with_geographic_area_array(areas)
         soft_validations.add(:geographic_area_id, "Taxon is reported as missing in #{presence.first.geographic_area.name}") unless presence.empty?
       end

app/models/project.rb

@@ -4,7 +4,7 @@ class Project < ActiveRecord::Base
   store_accessor :workbench_settings, :worker_tasks, :workbench_starting_path
 
   DEFAULT_WORKBENCH_STARTING_PATH = '/hub'
-  DEFAULT_WORKBENCH_SETTINGS = {
+  DEFAULT_WORKBENCH_SETTINGS      = {
     'workbench_starting_path' => DEFAULT_WORKBENCH_STARTING_PATH
   }
 
@@ -21,9 +21,8 @@ def clear_workbench_settings
     self.update('workbench_settings' => DEFAULT_WORKBENCH_SETTINGS)
   end
 
-
   # TODO: wrap this in an authentication layer, and protect it?
-  
+
   def nuke
     begin
       ActiveRecord::Base.descendants.each do |d|
@@ -33,19 +32,17 @@ def nuke
       end
     rescue
       raise
-    end 
+    end
   end
 
-
-
   protected
-  
+
   def set_default_workbench_settings
     self.workbench_settings = DEFAULT_WORKBENCH_SETTINGS.merge(self.workbench_settings ||= {})
   end
 
   def self.find_for_autocomplete(params)
     where('name LIKE ?', "#{params[:term]}%")
-end
+  end
 
 end

app/models/tag.rb

@@ -1,6 +1,6 @@
 class Tag < ActiveRecord::Base
   include Housekeeping
-  
+
   acts_as_list scope: [:keyword_id]
 
   belongs_to :keyword
@@ -10,32 +10,30 @@ class Tag < ActiveRecord::Base
   validates :keyword, presence: true
   validate :keyword_is_allowed_on_object, :object_can_be_tagged_with_keyword
 
-  validates_uniqueness_of :keyword_id, scope: [ :tag_object_id, :tag_object_type]
+  validates_uniqueness_of :keyword_id, scope: [:tag_object_id, :tag_object_type]
 
   def tag_object_class
     tag_object.class
   end
 
   def self.find_for_autocomplete(params)
-    # todo: @mjy figure out how to reach through the table for a list of controlled_vocabulary_terms.names
     # where('name LIKE ?', "#{params[:term]}%")
-
     # todo: @mjy below code is running but not giving results we want
-    terms = params[:term].split.collect{ |t| "'#{t}%'"}.join(' or ')
+    terms = params[:term].split.collect { |t| "'#{t}%'" }.join(' or ')
     joins(:keyword).where('controlled_vocabulary_terms.name like ?', terms) # "#{params[:term]}%" )
   end
 
   protected
 
   def keyword_is_allowed_on_object
-    return true if keyword.nil? || tag_object.nil? || !keyword.respond_to?(:can_tag) 
+    return true if keyword.nil? || tag_object.nil? || !keyword.respond_to?(:can_tag)
     if !keyword.can_tag.include?(tag_object.class.name)
       errors.add(:keyword, "this keyword class (#{tag_object.class}) can not be attached to a #{tag_object_type}")
     end
   end
 
   def object_can_be_tagged_with_keyword
-    return true if keyword.nil? || tag_object.nil?  || !tag_object.respond_to?(:taggable_with) 
+    return true if keyword.nil? || tag_object.nil? || !tag_object.respond_to?(:taggable_with)
     if !tag_object.taggable_with.include?(keyword.class.name)
       errors.add(:tag_object, "this tag_object_type (#{tag_object.class}) can not be tagged with this keyword class (#{keyword.class})")
     end

app/models/taxon_name.rb

@@ -679,9 +679,9 @@ def validate_parent_rank_is_higher
       end
 
       if (self.rank_class != self.rank_class_was) && # @proceps this catches nothing, as self.rank_class_was is never defined!
-          self.children &&
-          !self.children.empty? &&
-          RANKS.index(self.rank_string) >= self.children.collect { |r| RANKS.index(r.rank_string) }.max
+        self.children &&
+        !self.children.empty? &&
+        RANKS.index(self.rank_string) >= self.children.collect { |r| RANKS.index(r.rank_string) }.max
         errors.add(:rank_class, "The taxon rank (#{self.rank_class.rank_name}) is not higher than child ranks")
       end
     end
@@ -697,7 +697,7 @@ def validate_rank_class_class
 
   # @proceps self.rank_class_was is not a class method anywhere, so this comparison is vs. nil
   def check_new_rank_class
-    if (self.rank_class != self.rank_class_was) && 
+    if (self.rank_class != self.rank_class_was) &&
       !self.rank_class_was.nil?
       old_rank_group = self.rank_class_was.safe_constantize.parent
       if self.rank_class.parent != old_rank_group
@@ -716,11 +716,11 @@ def check_new_parent_class
   end
 
   def validate_source_type
-    errors.add(:source_id, 'Source must be a Bibtex') if self.source && self.source.type != 'Source::Bibtex' 
+    errors.add(:source_id, 'Source must be a Bibtex') if self.source && self.source.type != 'Source::Bibtex'
   end
 
   def validate_one_root_per_project
-    errors.add(:parent_id, 'Only one root allowed per project') if TaxonName.where(parent_id: nil, project_id: self.project_id ).count > 1 
+    errors.add(:parent_id, 'Only one root allowed per project') if TaxonName.where(parent_id: nil, project_id: self.project_id).count > 1
   end
 
   #TODO: validate, that all the ranks in the table could be linked to ranks in classes (if those had changed)

config/environments/test.rb

@@ -5,34 +5,34 @@
   # test suite. You never need to work with it otherwise. Remember that
   # your test database is "scratch space" for the test suite and is wiped
   # and recreated between test runs. Don't rely on the data there!
-  config.cache_classes = false # true
+  config.cache_classes                              = false # true
 
   # Do not eager load code on boot. This avoids loading your whole application
   # just for the purpose of running a single test. If you are using a tool that
   # preloads Rails for running tests, you may have to set it to true.
-  config.eager_load = false
+  config.eager_load                                 = false
 
   # Configure static asset server for tests with Cache-Control for performance.
-  config.serve_static_assets  = true
-  config.static_cache_control = "public, max-age=3600"
+  config.serve_static_assets                        = true
+  config.static_cache_control                       = "public, max-age=3600"
 
   # Show full error reports and disable caching.
-  config.consider_all_requests_local       = true
-  config.action_controller.perform_caching = false
+  config.consider_all_requests_local                = true
+  config.action_controller.perform_caching          = false
 
   # Raise exceptions instead of rendering exception templates.
-  config.action_dispatch.show_exceptions = false
+  config.action_dispatch.show_exceptions            = false
 
   # Disable request forgery protection in test environment.
   config.action_controller.allow_forgery_protection = false
 
   # Tell Action Mailer not to deliver emails to the real world.
   # The :test delivery method accumulates sent emails in the
   # ActionMailer::Base.deliveries array.
-  config.action_mailer.delivery_method = :test
+  config.action_mailer.delivery_method              = :test
 
   # Print deprecation notices to the stderr.
-  config.active_support.deprecation = :stderr
+  config.active_support.deprecation                 = :stderr
 
 
   # Post scaffolding changes 

lib/housekeeping/projects.rb

@@ -1,20 +1,20 @@
 # Concern the provides housekeeping and related methods for models that belong_to a Project
-module Housekeeping::Projects 
+module Housekeeping::Projects
   extend ActiveSupport::Concern
 
   included do
-   # not added to the model, just used to extend models here
-   related_instances = self.name.demodulize.underscore.pluralize.to_sym # if 'One::Two::Three' gives :threes
-   related_class = self.name
+    # not added to the model, just used to extend models here
+    related_instances = self.name.demodulize.underscore.pluralize.to_sym # if 'One::Two::Three' gives :threes
+    related_class     = self.name
 
-   # these are added to the model 
-   belongs_to :project, inverse_of: related_instances 
+    # these are added to the model
+    belongs_to :project, inverse_of: related_instances
 
-   before_validation :set_project_id, on: :create
-   validates :project, presence: true
+    before_validation :set_project_id, on: :create
+    validates :project, presence: true
 
-   before_save :prevent_alteration_in_other_projects
-   before_destroy :prevent_alteration_in_other_projects
+    before_save :prevent_alteration_in_other_projects
+    before_destroy :prevent_alteration_in_other_projects
 
     # Also extend the project 
     Project.class_eval do
@@ -41,10 +41,10 @@ def set_project_id
 
   # This will have to be extended via role exceptions, maybe.  It is a loose
   # check here, ripped right from mx.
-  def prevent_alteration_in_other_projects 
-  # unless (self.project_id == $project_id)
-  #   raise 'Not owned by current project: ' + self.name + '#' + self.id.to_s
-  # end
+  def prevent_alteration_in_other_projects
+    # unless (self.project_id == $project_id)
+    #   raise 'Not owned by current project: ' + self.name + '#' + self.id.to_s
+    # end
   end
 
 end

spec/factories/controlled_vocabulary_term_factory.rb

@@ -1,7 +1,7 @@
 FactoryGirl.define do
 
-  trait :random_name do 
-     name { Utilities::Strings.random_string(10) }
+  trait :random_name do
+    name { Utilities::Strings.random_string(10) }
   end
 
   trait :random_definition do
@@ -10,10 +10,10 @@
 
   factory :controlled_vocabulary_term, traits: [:housekeeping] do
     factory :valid_controlled_vocabulary_term, traits: [:random_name, :random_definition] do
-      type 'Keyword' 
+      type 'Keyword'
     end
 
-    factory :random_controlled_vocabulary_term, traits: [:random_name, :random_definition] 
+    factory :random_controlled_vocabulary_term, traits: [:random_name, :random_definition]
   end
 
 end

spec/factories/data_attribute_factory.rb

@@ -3,8 +3,8 @@
     factory :valid_data_attribute do
       type 'ImportAttribute'
       association :attribute_subject, factory: :valid_otu
-      import_predicate {Faker::Lorem.words(2).join(" ")}
-      value {Faker::Number.number(5)}
+      import_predicate { Faker::Lorem.words(2).join(" ") }
+      value { Faker::Number.number(5) }
     end
   end
 end

spec/factories/houskeeping_traits.rb

@@ -1,17 +1,17 @@
 FactoryGirl.define do
 
   trait :creator_and_updater do
-    created_by_id { $user_id } 
-    updated_by_id { $user_id } 
+    created_by_id { $user_id }
+    updated_by_id { $user_id }
   end
 
   trait :projects do
-    project_id { $project_id } 
-  end 
+    project_id { $project_id }
+  end
 
   trait :housekeeping do
     creator_and_updater
-    projects 
+    projects
   end
 
 end

spec/models/controlled_vocabulary_term_spec.rb

@@ -1,9 +1,9 @@
 require 'rails_helper'
 
 describe ControlledVocabularyTerm, :type => :model do
-  let(:controlled_vocabulary_term) { FactoryGirl.build(:controlled_vocabulary_term)  }
+  let(:controlled_vocabulary_term) { FactoryGirl.build(:controlled_vocabulary_term) }
 
-  context 'validation' do 
+  context 'validation' do
     before(:each) {
       controlled_vocabulary_term.valid?
     }
@@ -33,7 +33,7 @@
 
     let(:uri) { 'http://purl.org/net/foo/1' }
 
-    specify 'name is unique within projects per type'  do
+    specify 'name is unique within projects per type' do
       a = FactoryGirl.create(:valid_controlled_vocabulary_term)
       b = FactoryGirl.build(:controlled_vocabulary_term, a.attributes.merge(definition: 'Something else.', same_as_uri: uri))
       expect(b.valid?).to be_falsey
@@ -50,7 +50,7 @@
 
     specify 'same_as_uri is unique within projects' do
       a = FactoryGirl.create(:valid_controlled_vocabulary_term, same_as_uri: uri)
-      b = FactoryGirl.build(:valid_controlled_vocabulary_term, same_as_uri: uri )
+      b = FactoryGirl.build(:valid_controlled_vocabulary_term, same_as_uri: uri)
       expect(b.valid?).to be_falsey
       expect(b.errors.include?(:same_as_uri)).to be_truthy
     end
@@ -64,6 +64,6 @@
   end
 
   context 'concerns' do
-   it_behaves_like 'alternate_values'
+    it_behaves_like 'alternate_values'
   end
 end