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taxon_spec.rb
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taxon_spec.rb
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# coding: UTF-8
require 'spec_helper'
describe Taxon do
it "should require a name" do
Factory.build(:taxon).should_not be_valid
taxon = FactoryGirl.create :taxon, :name => 'Cerapachynae'
taxon.name.should == 'Cerapachynae'
taxon.should be_valid
end
it "should be (Rails) valid with a nil status" do
Taxon.new(:name => 'Cerapachynae').should be_valid
Taxon.new(:name => 'Cerapachynae', :status => 'valid').should be_valid
end
it "when status 'valid', should not be invalid" do
taxon = FactoryGirl.create :taxon, :name => 'Cerapachynae'
taxon.should_not be_invalid
end
it "should be able to be unidentifiable" do
taxon = FactoryGirl.create :taxon, :name => 'Cerapachynae'
taxon.should_not be_unidentifiable
taxon.update_attribute :status, 'unidentifiable'
taxon.should be_unidentifiable
taxon.should be_invalid
end
it "should be able to be unavailable" do
taxon = FactoryGirl.create :taxon, :name => 'Cerapachynae'
taxon.should_not be_unavailable
taxon.should be_available
taxon.update_attribute :status, 'unavailable'
taxon.should be_unavailable
taxon.should_not be_available
taxon.should be_invalid
end
it "should be able to be excluded" do
taxon = FactoryGirl.create :taxon, :name => 'Cerapachynae'
taxon.should_not be_excluded
taxon.update_attribute :status, 'excluded'
taxon.should be_excluded
taxon.should be_invalid
end
it "should be able to be a synonym" do
taxon = FactoryGirl.create :taxon, :name => 'Cerapachynae'
taxon.should_not be_synonym
taxon.update_attribute :status, 'synonym'
taxon.should be_synonym
taxon.should be_invalid
end
it "should be able to be a fossil" do
taxon = FactoryGirl.create :taxon, :name => 'Cerapachynae'
taxon.should_not be_fossil
taxon.fossil.should == false
taxon.update_attribute :fossil, true
taxon.should be_fossil
end
it "should raise if anyone calls #children directly" do
lambda {Taxon.new.children}.should raise_error NotImplementedError
end
it "should be able to be a synonym of something else" do
gauromyrmex = FactoryGirl.create :taxon, :name => 'Gauromyrmex'
acalama = FactoryGirl.create :taxon, :name => 'Acalama', :status => 'synonym', :synonym_of => gauromyrmex
acalama.reload
acalama.should be_synonym
acalama.reload.synonym_of.should == gauromyrmex
end
it "should be able to be a homonym of something else" do
neivamyrmex = FactoryGirl.create :taxon, :name => 'Neivamyrmex'
acamatus = FactoryGirl.create :taxon, :name => 'Acamatus', :status => 'homonym', :homonym_replaced_by => neivamyrmex
acamatus.reload
acamatus.should be_homonym
acamatus.homonym_replaced_by.should == neivamyrmex
end
it "should be able to have an incertae_sedis_in" do
myanmyrma = FactoryGirl.create :taxon, :name => 'Myanmyrma', :incertae_sedis_in => 'family'
myanmyrma.reload
myanmyrma.incertae_sedis_in.should == 'family'
myanmyrma.should_not be_invalid
end
it "should be able to say whether it is incertae sedis in a particular rank" do
myanmyrma = FactoryGirl.create :taxon, :name => 'Myanmyrma', :incertae_sedis_in => 'family'
myanmyrma.reload
myanmyrma.should be_incertae_sedis_in('family')
end
it "should be able to store tons of text in taxonomic history" do
camponotus = FactoryGirl.create :taxon, :name => 'Camponotus', :taxonomic_history => '1234' * 100_000
camponotus.reload.taxonomic_history.size.should == 4 * 100_000
end
describe "Current valid name" do
it "if it's not a synonym: it's just the name" do
taxon = Taxon.create! :name => 'Name'
taxon.current_valid_name.should == 'Name'
end
it "if it is a synonym: the name of the target" do
target = Taxon.create! :name => 'Target'
taxon = Taxon.create! :name => 'Taxon', :status => 'synonym', :synonym_of => target
taxon.current_valid_name.should == 'Target'
end
it "if it is a synonym of a synonym: the name of the target's target" do
target_target = Taxon.create! :name => 'Target_Target'
target = Taxon.create! :name => 'Target', :status => 'synonym', :synonym_of => target_target
taxon = Taxon.create! :name => 'Taxon', :status => 'synonym', :synonym_of => target
taxon.current_valid_name.should == 'Target_Target'
end
end
describe "Find name" do
before do
FactoryGirl.create :genus, :name => 'Monomorium'
@monoceros = FactoryGirl.create :genus, :name => 'Monoceros'
@rufa = FactoryGirl.create :species, :name => 'rufa', :genus => @monoceros
end
it "should return [] if nothing matches" do
Taxon.find_name('sdfsdf').should == []
end
it "should return an exact match" do
Taxon.find_name('Monomorium').first.name.should == 'Monomorium'
end
it "should return a prefix match" do
Taxon.find_name('Monomor', 'beginning with').first.name.should == 'Monomorium'
end
it "should return a substring match" do
Taxon.find_name('iu', 'containing').first.name.should == 'Monomorium'
end
it "should return multiple matches" do
results = Taxon.find_name('Mono', 'containing')
results.size.should == 2
end
it "should not return anything but subfamilies, tribes, genera and species" do
FactoryGirl.create :subfamily, :name => 'Lepto'
FactoryGirl.create :tribe, :name => 'Lepto'
FactoryGirl.create :genus, :name => 'Lepto'
FactoryGirl.create :subgenus, :name => 'Lepto'
FactoryGirl.create :species, :name => 'Lepto'
FactoryGirl.create :subspecies, :name => 'Lepto'
results = Taxon.find_name 'Lepto'
results.size.should == 4
end
it "should sort results by name" do
FactoryGirl.create :subfamily, :name => 'Lepti'
FactoryGirl.create :subfamily, :name => 'Lepta'
FactoryGirl.create :subfamily, :name => 'Lepte'
results = Taxon.find_name 'Lept', 'beginning with'
results.map(&:name).should == ['Lepta', 'Lepte', 'Lepti']
end
describe "Finding full species name" do
it "should search for full species name" do
results = Taxon.find_name 'Monoceros rufa'
results.first.should == @rufa
end
it "should search for partial species name" do
results = Taxon.find_name 'Monoceros ruf', 'beginning with'
results.first.should == @rufa
end
end
end
describe ".rank" do
it "should return a lowercase version" do
FactoryGirl.create(:subfamily).rank.should == 'subfamily'
end
end
describe "being a synonym of" do
it "should not think it's a synonym of something when it's not" do
genus = FactoryGirl.create :genus
another_genus = FactoryGirl.create :genus
genus.should_not be_synonym_of another_genus
end
it "should think it's a synonym of something when it is" do
senior_synonym = FactoryGirl.create :genus
junior_synonym = FactoryGirl.create :genus, :synonym_of => senior_synonym, :status => 'synonym'
junior_synonym.should be_synonym_of senior_synonym
end
end
describe "being a homonym replaced by something" do
it "should not think it's a homonym replaced by something when it's not" do
genus = FactoryGirl.create :genus
another_genus = FactoryGirl.create :genus
genus.should_not be_homonym_replaced_by another_genus
genus.homonym_replaced.should be_nil
end
it "should think it's a homonym replaced by something when it is" do
replacement = FactoryGirl.create :genus
homonym = FactoryGirl.create :genus, :homonym_replaced_by => replacement, :status => 'homonym'
homonym.should be_homonym_replaced_by replacement
replacement.homonym_replaced.should == homonym
end
end
describe "the 'valid' scope" do
it "should only include valid taxa" do
subfamily = FactoryGirl.create :subfamily
replacement = FactoryGirl.create :genus, :subfamily => subfamily
homonym = FactoryGirl.create :genus, :homonym_replaced_by => replacement, :status => 'homonym', :subfamily => subfamily
synonym = FactoryGirl.create :genus, :synonym_of => replacement, :status => 'synonym', :subfamily => subfamily
subfamily.genera.valid.should == [replacement]
end
end
describe "the 'extant' scope" do
it "should only include extant taxa" do
subfamily = FactoryGirl.create :subfamily
extant_genus = FactoryGirl.create :genus, :subfamily => subfamily
FactoryGirl.create :genus, :subfamily => subfamily, :fossil => true
subfamily.genera.extant.should == [extant_genus]
end
end
describe "ordered by name" do
it "should order by name" do
zymacros = FactoryGirl.create :subfamily, :name => 'Zymacros'
atta = FactoryGirl.create :subfamily, :name => 'Atta'
Taxon.ordered_by_name.should == [atta, zymacros]
end
end
describe "statistics (for the whole family)" do
it "should return the statistics for each status of each rank" do
subfamily = FactoryGirl.create :subfamily
genus = FactoryGirl.create :genus, :subfamily => subfamily, :tribe => nil
FactoryGirl.create :genus, :subfamily => subfamily, :status => 'homonym', :tribe => nil
2.times {FactoryGirl.create :subfamily, :fossil => true}
Taxon.statistics.should == {
:extant => {:subfamilies => {'valid' => 1}, :genera => {'valid' => 1, 'homonym' => 1}},
:fossil => {:subfamilies => {'valid' => 2}}
}
end
end
describe "Convert asterisks to daggers" do
it "should convert an asterisk to a dagger" do
taxon = FactoryGirl.create :subfamily
taxon.taxonomic_history = '*'
taxon.convert_asterisks_to_daggers!
taxon.taxonomic_history.should == '†'
taxon.reload.taxonomic_history.should == '†'
end
it "work OK if taxonomic history is nil" do
taxon = FactoryGirl.create :subfamily, :taxonomic_history => nil
taxon.convert_asterisks_to_daggers!
taxon.taxonomic_history.should be_nil
taxon.reload.taxonomic_history.should be_nil
end
end
describe "Protonym" do
it "should have a protonym" do
taxon = Family.create! :name => 'Formicidae'
taxon.protonym.should be_nil
taxon.build_protonym :name => 'Formicariae'
end
end
describe "Taxonomic history items" do
it "should have some" do
taxon = FactoryGirl.create :family
taxon.taxonomic_history_items.should be_empty
taxon.taxonomic_history_items.create! :taxt => 'foo'
taxon.reload.taxonomic_history_items.map(&:taxt).should == ['foo']
end
it "should show the items in the order in which they were added to the taxon" do
taxon = FactoryGirl.create :family
taxon.taxonomic_history_items.create! :taxt => '1'
taxon.taxonomic_history_items.create! :taxt => '2'
taxon.taxonomic_history_items.create! :taxt => '3'
taxon.taxonomic_history_items.map(&:taxt).should == ['1','2','3']
taxon.taxonomic_history_items.first.move_to_bottom
taxon.taxonomic_history_items(true).map(&:taxt).should == ['2','3','1']
end
end
describe "Reference sections" do
it "should have some" do
taxon = FactoryGirl.create :family
taxon.reference_sections.should be_empty
taxon.reference_sections.create! :references => 'foo'
taxon.reload.reference_sections.map(&:references).should == ['foo']
end
it "should show the items in the order in which they were added to the taxon" do
taxon = FactoryGirl.create :family
taxon.reference_sections.create! :references => '1'
taxon.reference_sections.create! :references => '2'
taxon.reference_sections.create! :references => '3'
taxon.reference_sections.map(&:references).should == ['1','2','3']
taxon.reference_sections.first.move_to_bottom
taxon.reference_sections(true).map(&:references).should == ['2','3','1']
end
end
describe "Finding a genus or a subgenus" do
it "should find a genus" do
atta = FactoryGirl.create :genus, name: 'Atta'
Taxon.find_genus_group_by_name('Atta').should == atta
end
it "should find a subgenus" do
atta = FactoryGirl.create :subgenus, name: 'Atta'
Taxon.find_genus_group_by_name('Atta').should == atta
end
it "should merely return nil if more than one result is found" do
2.times {FactoryGirl.create :genus, name: 'Atta'}
Taxon.find_genus_group_by_name('Atta').should be_nil
end
end
describe "Child list queries" do
before do
@subfamily = FactoryGirl.create :subfamily, name: 'Dolichoderinae'
end
it "should find all genera for the taxon if there are no conditions" do
FactoryGirl.create :genus, name: 'Atta', subfamily: @subfamily
FactoryGirl.create :genus, name: 'Eciton', subfamily: @subfamily, fossil: true
FactoryGirl.create :genus, name: 'Aneuretus', subfamily: @subfamily, fossil: true, incertae_sedis_in: 'subfamily'
@subfamily.child_list_query(:genera).map(&:name).sort.should == ['Aneuretus', 'Atta', 'Eciton']
@subfamily.child_list_query(:genera, fossil: true).map(&:name).sort.should == ['Aneuretus', 'Eciton']
@subfamily.child_list_query(:genera, incertae_sedis_in: 'subfamily').map(&:name).sort.should == ['Aneuretus']
end
it "should not include invalid taxa" do
FactoryGirl.create :genus, name: 'Atta', subfamily: @subfamily, :status => 'synonym'
FactoryGirl.create :genus, name: 'Eciton', subfamily: @subfamily, fossil: true
FactoryGirl.create :genus, name: 'Aneuretus', subfamily: @subfamily, fossil: true, incertae_sedis_in: 'subfamily'
@subfamily.child_list_query(:genera).map(&:name).sort.should == ['Aneuretus', 'Eciton']
end
end
describe "Cascading delete" do
it "should delete the protonym when the taxon is deleted" do
Taxon.count.should be_zero
Protonym.count.should be_zero
genus = FactoryGirl.create :genus, tribe: nil, subfamily: nil
Taxon.count.should == 1
Protonym.count.should == 1
genus.destroy
Taxon.count.should be_zero
Protonym.count.should be_zero
end
it "should delete history and reference sections when the taxon is deleted" do
Taxon.count.should be_zero
ReferenceSection.count.should be_zero
genus = FactoryGirl.create :genus, tribe: nil, subfamily: nil
genus.reference_sections.create! title: 'title', references: 'references'
ReferenceSection.count.should == 1
genus.destroy
ReferenceSection.count.should be_zero
end
end
end