taxonomite 0.1.0 → 0.2.3

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data/spec/factories/taxonomy_taxon.rb

@@ -1,45 +1,56 @@
 
+require 'factory_girl_rails'
 require 'faker'
 
 FactoryGirl.define do
   factory :taxonomite_node, :class => 'Taxonomite::Node' do
     name { Faker::Lorem.word.capitalize }
-    description { Faker::Lorem.paragraph }
   end
 
   factory :taxonomite_species, :class => 'Taxonomite::Species' do
     name { "#{Faker::Lorem.word.capitalize} #{Faker::Lorem.word}" }
-    description { Faker::Lorem.paragraph }
   end
 
   factory :taxonomite_genus, :class => 'Taxonomite::Genus' do
-    name { "#{Faker::Lorem.word.capitalize} #{Faker::Lorem.word}" }
-    description { Faker::Lorem.paragraph }
+    name { "#{Faker::Lorem.word.capitalize}" }
   end
 
   factory :taxonomite_family, :class => 'Taxonomite::Family' do
-    name { "#{Faker::Lorem.word.capitalize} #{Faker::Lorem.word}" }
-    description { Faker::Lorem.paragraph }
+    name { "#{Faker::Lorem.word.capitalize}" }
   end
 
   factory :taxonomite_order, :class => 'Taxonomite::Order' do
-    name { "#{Faker::Lorem.word.capitalize} #{Faker::Lorem.word}" }
-    description { Faker::Lorem.paragraph }
+    name { "#{Faker::Lorem.word.capitalize}" }
   end
 
   factory :taxonomite_class, :class => 'Taxonomite::Class' do
-    name { "#{Faker::Lorem.word.capitalize} #{Faker::Lorem.word}" }
-    description { Faker::Lorem.paragraph }
+    name { "#{Faker::Lorem.word.capitalize}" }
   end
 
   factory :taxonomite_phylum, :class => 'Taxonomite::Phylum' do
-    name { "#{Faker::Lorem.word.capitalize} #{Faker::Lorem.word}" }
-    description { Faker::Lorem.paragraph }
+    name { "#{Faker::Lorem.word.capitalize}" }
   end
 
   factory :taxonomite_kingdom, :class => 'Taxonomite::Kingdom' do
-    name { "#{Faker::Lorem.word.capitalize} #{Faker::Lorem.word}" }
-    description { Faker::Lorem.paragraph }
+    name { "#{Faker::Lorem.word.capitalize}" }
+  end
+
+  factory :taxonomite_down_taxonomy, :class => 'Taxonomite::Taxonomy' do
+    down_taxonomy { { 'kingdom' => 'phylum', 'phylum' => 'class', 'class' => 'order',
+          'order' => 'family', 'family' => 'genus', 'genus' => 'species' } }
   end
 
+  factory :taxonomite_up_taxonomy, :class => 'Taxonomite::Taxonomy' do
+    up_taxonomy { { 'kingdom' => 'phylum', 'phylum' => 'class', 'class' => 'order',
+          'order' => 'family', 'family' => 'genus', 'genus' => 'species' }.invert }
+  end
+
+  factory :taxonomite_empty_taxonomy, :class => 'Taxonomite::Taxonomy' do
+  end
+
+  factory :taxonomite_single_wildcard_taxonomy, :class => 'Taxonomite::Taxonomy' do
+    down_taxonomy { { 'kingdom' => '*', 'phylum' => 'class' } }
+  end
+
+
 end

data/spec/models/taxonomite/hierarchy_spec.rb

@@ -3,32 +3,125 @@ require 'models/taxonomite/zoology'
 
 module Taxonomite
     RSpec.describe Tree, type: :model do
+        describe 'enforce hierarchy' do
+            context 'without Taxonomy object' do
+                before(:each) do
+                    @family = FactoryGirl.build(:taxonomite_family)
+                    @genus = FactoryGirl.build(:taxonomite_genus)
+                    @species = FactoryGirl.build(:taxonomite_species)
+                end
 
-      context 'sample hierarchy enforcement' do
-          before(:each) do
-              @family = FactoryGirl.build(:taxonomite_family)
-              @genus = FactoryGirl.build(:taxonomite_genus)
-              @species = FactoryGirl.build(:taxonomite_species)
-          end
+                it 'to allow species in genus when no taxonomy present' do
+                    expect { @genus.add_child(@species) }.not_to raise_error
+                end
 
-          it 'to allow species in genus' do
-              expect { @genus.children << @species }.not_to raise_error
-          end
+                it 'to allow genus in family when no taxonomy present' do
+                    expect { @family.add_child(@genus) }.not_to raise_error
+                end
 
-          it 'to allow genus in family' do
-              expect { @family.children << @genus }.not_to raise_error
-          end
+                it 'to allow genus in species when no taxonomy present' do
+                    expect { @species.add_child(@genus) }.not_to raise_error
+                end
 
-          it 'not to allow genus in species' do
-              expect { @species.children << @genus }.to raise_error
-          end
+                it 'to allow species in family when no taxonomy present' do
+                    expect { @family.add_child(@species) }.not_to raise_error
+                end
+            end
 
-          it 'not to allow species in family' do
-              expect { @family.children << @species }.to raise_error
-          end
+            context 'specific taxonomy rejections, with wildcard' do
+              before(:each) do
+                @taxonomy = FactoryGirl.build(:taxonomite_single_wildcard_taxonomy)
+                @kingdom = FactoryGirl.build(:taxonomite_kingdom)
+                @phylum = FactoryGirl.build(:taxonomite_phylum)
+                @class = FactoryGirl.build(:taxonomite_class)
+                @species = FactoryGirl.build(:taxonomite_species)
+              end
 
-      end
+              it 'to allow anything in kingdom (under "*")' do
+                expect { @taxonomy.add(@kingdom, @phylum) }.not_to raise_error
+                expect { @taxonomy.add(@kingdom, @class) }.not_to raise_error
+                expect { @taxonomy.add(@kingdom, @species) }.not_to raise_error
+              end
 
-    end
+              it 'to allow only class under phylum' do
+                expect { @taxonomy.add(@phylum, @class) }.not_to raise_error
+                expect { @taxonomy.add(@phylum, @species) }.to raise_error
+                expect { @taxonomy.add(@phylum, @kingdom) }.to raise_error
+              end
+
+              it 'to allow only nothing under class (empty)' do
+                expect { @taxonomy.add(@class, @phylum) }.to raise_error
+                expect { @taxonomy.add(@class, @species) }.to raise_error
+                expect { @taxonomy.add(@class, @kingdom) }.to raise_error
+              end
+            end
+
+            context 'empty Taxonomy object' do
+              before(:each) do
+                  @taxonomy = FactoryGirl.build(:taxonomite_empty_taxonomy)
+                  @family = FactoryGirl.build(:taxonomite_family)
+                  @genus = FactoryGirl.build(:taxonomite_genus)
+                  @species = FactoryGirl.build(:taxonomite_species)
+              end
+
+              it 'to allow anything anywhere' do
+                  expect { @taxonomy.add(@genus, @species) }.not_to raise_error
+                  expect { @taxonomy.add(@family, @genus) }.not_to raise_error
+                  expect { @taxonomy.add(@species, @genus) }.to raise_error # circular reference
+                  expect { @taxonomy.add(@family, @species) }.not_to raise_error
+              end
+            end
+
+            context 'with down-looking Taxonomy object' do
+              before(:each) do
+                  @taxonomy = FactoryGirl.build(:taxonomite_down_taxonomy)
+                  @family = FactoryGirl.build(:taxonomite_family)
+                  @genus = FactoryGirl.build(:taxonomite_genus)
+                  @species = FactoryGirl.build(:taxonomite_species)
+              end
+
+              it 'to allow species in genus with taxonomy present' do
+                  expect { @taxonomy.add(@genus, @species) }.not_to raise_error
+              end
+
+              it 'to allow genus in family with taxonomy present' do
+                  expect { @taxonomy.add(@family, @genus) }.not_to raise_error
+              end
+
+              it 'not to allow genus in species with taxonomy present' do
+                  expect { @taxonomy.add(@species, @genus) }.to raise_error
+              end
 
+              it 'not to allow species in family with taxonomy present' do
+                  expect { @taxonomy.add(@family, @species) }.to raise_error
+              end
+            end
+
+            context 'with up-looking Taxonomy object' do
+              before(:each) do
+                  @taxonomy = FactoryGirl.build(:taxonomite_up_taxonomy)
+                  @family = FactoryGirl.build(:taxonomite_family)
+                  @genus = FactoryGirl.build(:taxonomite_genus)
+                  @species = FactoryGirl.build(:taxonomite_species)
+              end
+
+              it 'to allow species in genus with taxonomy present' do
+                  expect { @taxonomy.add(@genus, @species) }.not_to raise_error
+              end
+
+              it 'to allow genus in family with taxonomy present' do
+                  expect { @taxonomy.add(@family, @genus) }.not_to raise_error
+              end
+
+              it 'not to allow genus in species with taxonomy present' do
+                  expect { @taxonomy.add(@species, @genus) }.to raise_error
+              end
+
+              it 'not to allow species in family with taxonomy present' do
+                  expect { @taxonomy.add(@family, @species) }.to raise_error
+              end
+            end
+
+      end
+    end
 end

data/spec/models/taxonomite/model_spec.rb

@@ -20,11 +20,6 @@ module Taxonomite
                 expect(node.name).to eq("new_name")
             end
 
-            it 'sets the description' do
-                node.description = "new_description"
-                expect(node.description).to eq("new_description")
-            end
-
             it 'allow access to children' do
                 expect { node.children }.not_to raise_error
             end

data/spec/models/taxonomite/tree_spec.rb

@@ -7,30 +7,52 @@ module Taxonomite
       context 'tree creation' do
           let!(:nodes) { Array.new(3){ |index| build(:taxonomite_node)} }
 
+          it 'allows addition of children' do
+              expect { nodes[0].add_child(nodes[1]) }.not_to raise_error
+          end
+
+          it 'allows addition of parent' do
+              expect { nodes[0].add_parent(nodes[1]) }.not_to raise_error
+          end
+
           it 'to disallow direct circular reference' do
-              # rephrase to check validity
-              expect { nodes[0].children << nodes[0] }.to raise_error
+              expect { nodes[0].add_child(nodes[0]) }.to raise_error
           end
 
           it 'to disallow circular reference (one deep)' do
-               nodes[0].children << nodes[1]
-               expect { nodes[1].children << nodes[0] }.to raise_error
+               nodes[0].add_child(nodes[1])
+               expect { nodes[1].add_child(nodes[0]) }.to raise_error
           end
+
+          it 'remove parent works as expected, parents child becomes nil' do
+               nodes[0].add_child(nodes[1])
+               expect { nodes[1].remove_parent }.not_to raise_error
+               expect(nodes[0].children.size).to eq(0)
+          end
+
+          it 'remove child works as expected, child parent becomes nil' do
+               nodes[0].add_child(nodes[1])
+               expect { nodes[0].remove_child(nodes[1]) }.not_to raise_error
+               expect(nodes[0].children.size).to eq(0)
+               expect(nodes[1].parent).nil?
+          end
+
       end
 
       context 'tree structure' do
         before(:each) do
-          @nodes = Array.new(3) { build(:taxonomite_node) }
-          @nodes[0].children << @nodes[1]
-          @nodes[1].children << @nodes[2]
+          @nodes = Array.new(4) { build(:taxonomite_node) }
+          @nodes[0].add_child(@nodes[1])
+          @nodes[1].add_child(@nodes[2])
+          @nodes[0].add_child(@nodes[3])
         end
 
-          it 'has appropriate children' do
-            expect(@nodes[0].children.size).to eq(1)
+          it 'has appropriate number of children' do
+            expect(@nodes[0].children.size).to eq(2)
           end
 
           it 'to disallow circular reference (two deep)' do
-              expect { @nodes[2].children << @nodes[0] }.to raise_error
+              expect { @nodes[2].add_child(@nodes[0]) }.to raise_error
           end
 
           it 'to iterate children' do
@@ -48,6 +70,94 @@ module Taxonomite
               expect { @nodes[0].destroy }.not_to raise_error
               expect(@nodes[1].parent).to eq(nil)
               expect(@nodes[2].parent).not_to eq(nil)
+              expect(@nodes[3].parent).to eq(nil)
+          end
+
+          it 'successfully finds leaves of the tree' do
+              expect(@nodes[0].leaves.size).to eq(2)
+              expect(@nodes[0].leaves.find(@nodes[3])).not_to eq(nil)
+          end
+
+          it 'successfully finds the root of the tree' do
+              expect(@nodes[2].root).to eq(@nodes[0])
+              expect(@nodes[3].root).to eq(@nodes[0])
+          end
+
+          it 'successfully identifies anscestor' do
+              expect(@nodes[2].descendant_of?(@nodes[0])).to eq(true)
+              expect(@nodes[0].descendant_of?(@nodes[2])).to eq(false)
+          end
+
+          it 'successfully identifies descendant' do
+              expect(@nodes[2].ancestor_of?(@nodes[0])).to eq(false)
+              expect(@nodes[0].ancestor_of?(@nodes[2])).to eq(true)
+          end
+
+          it 'can aggregate ancestors' do
+            expect { @nodes[0].ancestors.map { |n| n.evaluate('name') } }.not_to raise_error
+          end
+
+          it 'accurately aggregates self and ancestors' do
+              a = @nodes[2].self_and_ancestors.map { |n| n.evaluate ('name') }
+              expect(a.size).to eq(3)
+              expect(a.include?(@nodes[3].name)).not_to eq(true)
+              expect(a.include?(@nodes[2].name)).to eq(true)
+              expect(a.include?(@nodes[1].name)).to eq(true)
+              expect(a.include?(@nodes[0].name)).to eq(true)
+          end
+
+          it 'accurately aggregates ancestors without self' do
+              a = @nodes[2].ancestors.map { |n| n.evaluate ('name') }
+              expect(a.size).to eq(2)
+              expect(a.include?(@nodes[3].name)).not_to eq(true)
+              expect(a.include?(@nodes[2].name)).not_to eq(true)
+              expect(a.include?(@nodes[1].name)).to eq(true)
+              expect(a.include?(@nodes[0].name)).to eq(true)
+          end
+
+          it 'can aggregate self and descendants' do
+              expect { @nodes[0].self_and_descendants.map { |n| n.evaluate('name') } }.not_to raise_error
+          end
+
+          it 'accurately aggregates self and descendants' do
+              a = @nodes[0].self_and_descendants.map { |n| n.evaluate ('name') }
+              expect(a.size).to eq(4)
+              expect(a.include?(@nodes[3].name)).to eq(true)
+              expect(a.include?(@nodes[2].name)).to eq(true)
+              expect(a.include?(@nodes[1].name)).to eq(true)
+              expect(a.include?(@nodes[0].name)).to eq(true)
+          end
+
+          it 'accurately aggregates descendants without self' do
+            a = @nodes[0].descendants.map { |n| n.evaluate ('name') }
+            expect(a.size).to eq(3)
+            expect(a.include?(@nodes[3].name)).to eq(true)
+            expect(a.include?(@nodes[2].name)).to eq(true)
+            expect(a.include?(@nodes[1].name)).to eq(true)
+            expect(a.include?(@nodes[0].name)).not_to eq(true)
+          end
+
+          it 'aggregates leaf values without causing exception' do
+            expect { @nodes[0].leaves.map { |n| n.evaluate('name') } }.not_to raise_error
+          end
+
+          it 'accurately aggregates leaf values' do
+              a = @nodes[0].leaves.map { |n| n.evaluate('name') }
+
+              # i = 0
+              # @nodes.each do |n|
+              #   print "Node[#{i}]: #{n.name} children: ["; n.children.each { |c| print " #{c.name}" }; puts " ]"
+              #   puts "\t aggregated value: #{a.find_index(n.name)}"
+              #   i += 1
+              # end
+              # puts "nodes: #{@nodes[0].aggregate('name')}"
+              # print "leaves: ["; @nodes[0].leaves.each { |l| print " #{l.name}" }; puts " ]"
+              # puts "aggregated leaves: #{a}"
+
+              expect(a.include?(@nodes[3].name)).to eq(true)
+              expect(a.include?(@nodes[2].name)).to eq(true)
+              expect(a.include?(@nodes[1].name)).not_to eq(true)
+              expect(a.include?(@nodes[0].name)).not_to eq(true)
           end
 
       end