BicurationGroups. Tag positioning. ControlledVocabulary related facto…

…ries and specs.

Gemfile

@@ -8,7 +8,7 @@ gem 'pg', '~> 0.17.0'
 
 # Postgis
 gem 'activerecord-postgis-adapter'
-gem 'squeel'
+gem 'squeel', git: 'https://github.com/nybex/squeel.git'
 
 # rgeo support
 gem 'ffi-geos'

app/models/biocuration_class.rb

@@ -1,6 +1,7 @@
 class BiocurationClass < ControlledVocabularyTerm
-
-  has_many :biocuration_classifications
-  has_many :biological_objects
 
+  include Shared::Taggable
+
+  has_many :biocuration_classifications
+  has_many :biological_collection_objects, through: :biocuration_classifications, class_name: 'CollectionObject::BiologicalCollectionObject'
 end

app/models/biocuration_classification.rb

@@ -6,6 +6,4 @@ class BiocurationClassification < ActiveRecord::Base
 
   validates_presence_of :biocuration_class, :biological_collection_object
 
-  # TODO: scope to 'organismal/biological axis'
-
 end

app/models/biocuration_group.rb

@@ -0,0 +1,7 @@
+class BiocurationGroup < Keyword 
+
+  # Watch out this is borked with squeel
+  has_many :biocuration_classes, through: :tags, source: 'tag_object', source_type: 'ControlledVocabularyTerm'
+
+
+end

app/models/concerns/shared/taggable.rb

@@ -3,6 +3,7 @@ module Shared::Taggable
 
   included do
     has_many :tags, as: :tag_object, validate: false
+    has_many :keywords, through: :tags 
   end 
 
   def tagged?

app/models/container.rb

@@ -4,8 +4,10 @@ class Container < ActiveRecord::Base
   include Housekeeping
   include Shared::Identifiable
   include Shared::Containable
+  include Shared::Taggable
   include SoftValidation
 
+
   # TODO: rethinking this 
   # belongs_to :otu
 

app/models/controlled_vocabulary_term.rb

@@ -1,6 +1,7 @@
 class ControlledVocabularyTerm < ActiveRecord::Base
   include Housekeeping
   include Shared::AlternateValues
+  # include Shared::Taggable <- !! NO
 
   validates_presence_of :name, :definition, :type
   validates_length_of :definition, minimum: 4

app/models/keyword.rb

@@ -1,2 +1,9 @@
 class Keyword < ControlledVocabularyTerm 
+
+  has_many :tags, foreign_key: :keyword_id
+
+ def tagged_objects
+   self.tags.collect{|t| t.tag_object}
+ end
+
 end

app/models/protonym.rb

@@ -55,7 +55,7 @@ class Protonym < TaxonName
   scope :named, -> (name) {where(name: name)}
   scope :with_name_in_array, -> (array) { where('name in (?)', array) }  
 
-  #  find classifications for taxon
+  # find classifications for taxon
   scope :with_taxon_name_classifications_on_taxon_name, -> (t) { includes(:taxon_name_classifications).where('taxon_name_classifications.taxon_name_id = ?', t).references(:taxon_name_classifications) }
 
   # find taxa with classifications

app/models/tag.rb

@@ -1,10 +1,13 @@
 class Tag < ActiveRecord::Base
   include Housekeeping
+
+  acts_as_list scope: [:keyword_id]
 
   belongs_to :keyword
   belongs_to :tag_object, polymorphic: true
+
   validates :tag_object, presence: true
   validates :keyword, presence: true
-  validates_uniqueness_of :keyword_id, scope: [:tag_object]
+  validates_uniqueness_of :keyword_id, scope: [ :tag_object_id, :tag_object_type]
 
 end

db/migrate/20140407134323_add_position_to_tags.rb

@@ -0,0 +1,5 @@
+class AddPositionToTags < ActiveRecord::Migration
+  def change
+    add_column :tags, :position, :integer
+  end
+end

spec/factories/biocuration_classification_factory.rb

@@ -1,7 +1,8 @@
 FactoryGirl.define do
   factory :biocuration_classification, traits: [:housekeeping] do
-    biocuration_class nil
-    biological_collection_object nil
-    position 1
+    factory :valid_biocuration_classification do
+      association :biocuration_class, factory: :valid_biocuration_class
+      association :biological_collection_object, factory: :valid_specimen
+    end
   end
 end

spec/factories/biocuration_group_factory.rb

@@ -0,0 +1,8 @@
+FactoryGirl.define do
+  factory :biocuration_group, traits: [:housekeeping] do
+    factory :valid_biocuration_group do
+      name 'life stage'
+      definition 'A group of life stages.'
+    end
+  end
+end

spec/factories/container/box_factory.rb

@@ -0,0 +1,5 @@
+FactoryGirl.define do
+  factory :container_box, class: Container::Box, traits: [:housekeeping] do
+    factory :valid_container_box 
+  end
+end

spec/models/biocuration_class_spec.rb

@@ -7,21 +7,16 @@
   context 'associations' do
     context 'has_many' do
       specify 'biocuration_classifications' do
-        expect(biocuration_class).to respond_to(:biocuration_classifications)
+        expect(biocuration_class.biocuration_classifications << FactoryGirl.build(:valid_biocuration_classification)).to be_true
       end
 
       specify 'biological_objects' do
-        expect(biocuration_class).to respond_to(:biological_objects)
+        expect(biocuration_class.biological_collection_objects << FactoryGirl.build(:valid_specimen)).to be_true
       end
-    end
-  end
 
-  context 'validations' do
-    before(:each) do
-      biocuration_class.valid?
-    end
-    specify 'name is required' do
-      expect(biocuration_class.errors.include?(:name)).to be_true
+      specify 'tags' do
+        expect(biocuration_class.tags << FactoryGirl.build(:valid_tag)).to be_true
+      end
     end
   end
 

spec/models/biocuration_group_spec.rb

@@ -0,0 +1,31 @@
+require 'spec_helper'
+
+describe BiocurationGroup do
+
+  let(:biocuration_group) {FactoryGirl.build(:biocuration_group)}
+
+  context 'has many' do
+    before(:each) {
+      @biocuration_group = FactoryGirl.create(:valid_biocuration_group, name: 'Stages.', definition: 'Life stages.')
+      @bc1 = BiocurationClass.create(name: 'Adult', definition: 'A mature indivdiual.') 
+      @bc2 = BiocurationClass.create(name: 'Larva', definition: 'Not a mature indivdiual.') 
+    }
+
+    specify 'tags (through Keywords)' do
+      expect(biocuration_group.tags << Tag.new(keyword: FactoryGirl.create(:valid_keyword))).to be_true
+    end
+
+    specify 'biocuration_classes' do
+      expect(biocuration_group).to respond_to(:biocuration_classes)
+      t1 =Tag.create(keyword: @biocuration_group, tag_object: @bc1)
+      t2 = Tag.create(keyword: @biocuration_group, tag_object: @bc2)
+
+      # Something to not match 
+      t3 = Tag.create(keyword: FactoryGirl.create(:valid_keyword), tag_object: @bc1) 
+
+      expect(@biocuration_group.biocuration_classes).to have(2).things
+      expect(@biocuration_group.biocuration_classes.to_a.map(&:class)).to eq([BiocurationClass, BiocurationClass])
+    end
+  end
+end
+

spec/models/keyword_spec.rb

@@ -1,15 +1,39 @@
 require 'spec_helper'
 
 describe Keyword do
-  let(:topic) { Keyword.new }
+  let(:keyword) { FactoryGirl.build(:keyword) }
 
-  context "associations" do
+  context "validation" do
+    before(:each) {  @k = FactoryGirl.create(:valid_keyword) }
+
+    specify "can be used for tags" do
+      t = Tag.new(keyword: @k, tag_object: FactoryGirl.build(:valid_otu))
+      expect(t.save).to be_true
+    end
+
+    specify "can not be used for other things" do
+      expect {c = CitationTopic.new(topic: @k)}.to raise_error
+    end
   end
 
-  context "validation" do
-    specify "can be used for tags"
-    specify "can not be used for citations"
+  context 'associations' do
+    context 'has_many' do
+      specify 'tags' do
+        expect(keyword.tags << FactoryGirl.build(:valid_tag)).to be_true
+      end
+    end
   end
 
+  specify 'tagged_objects' do
+    expect(keyword).to respond_to(:tagged_objects)
+    k = FactoryGirl.create(:valid_keyword)
+    t1 = Tag.create(keyword: k, tag_object: FactoryGirl.create(:valid_otu))
+    t2 = Tag.create(keyword: k, tag_object: FactoryGirl.create(:valid_specimen))
+    expect(k.tagged_objects).to have(2).things
+    expect(k.tags).to have(2).things
+  end
+
+
+
 end
 

spec/models/tag_spec.rb

@@ -6,7 +6,11 @@
 
   context 'associations' do
     specify 'tag_object' do 
-      expect(tag).to respond_to(:tag_object)
+      expect(tag.tag_object = FactoryGirl.create(:valid_biocuration_class)).to be_true
+    end
+
+    specify 'keyword' do
+      expect(tag.keyword = FactoryGirl.create(:valid_keyword)).to be_true
     end
   end
 
@@ -24,7 +28,8 @@
     end
 
     specify 'a topic can not be used' do
-      pending
+      t = Topic.new(name: 'foo', definition: 'Something about foo')
+      expect{tag.keyword = t}.to raise_error
     end
 
     specify 'a tagged object is only tagged once per keyword' do
@@ -41,6 +46,36 @@
       expect(dupe_tag.errors.include?(:keyword_id)).to be_true
     end
 
+    context 'STI based tag behaviour' do
+      before(:each) {
+        tag.keyword = FactoryGirl.create(:valid_keyword) 
+        tag.tag_object = FactoryGirl.create(:valid_specimen)
+      }
+
+      specify 'tagging an subclass of an STI model instance *stores* the tag_type as the superclass' do
+        expect(tag.save).to be_true
+        expect(tag.tag_object_type).to eq('CollectionObject')
+      end
+
+      specify 'tagging an subclass of an STI model instance, with subclass namespace, *stores* the tag_type as the superclass' do
+        tag.tag_object = FactoryGirl.create(:valid_container_box)
+        expect(tag.save).to be_true
+        expect(tag.tag_object_type).to eq('Container')
+      end
+
+      specify 'tagging a subclass of an STI model *returns* the subclassed object' do
+        expect(tag.save).to be_true
+        expect(tag.tag_object.class).to eq(Specimen) 
+      end
+    end
+
+    context 'acts_as_list' do
+      specify 'position is set' do
+        t1 = FactoryGirl.create(:valid_tag)
+        expect(t1.position).to eq(1)
+      end
+    end
+
     # TODO: Determine if we want to tag individual fields. 
     #  specify 'a attribute is actually a attribute of the tag object'
   end