taxonifi 0.1.0 → 0.2.0

data/test/test_taxonifi_name_collection.rb

@@ -1,8 +1,13 @@
 require File.expand_path(File.join(File.dirname(__FILE__), 'helper'))
-require File.expand_path(File.join(File.dirname(__FILE__), '../lib/models/name_collection')) 
 
 class TestTaxonifiNameCollection < Test::Unit::TestCase
 
+  def test_that_name_collections_have_collections
+    c = Taxonifi::Model::NameCollection.new
+    assert c.respond_to?(:collection)
+    assert_equal([], c.collection)
+  end
+
   def test_that_add_objects_adds_to_collection
     c = Taxonifi::Model::NameCollection.new
     n = Taxonifi::Model::Name.new
@@ -10,12 +15,6 @@ class TestTaxonifiNameCollection < Test::Unit::TestCase
     assert_equal(1, c.collection.size)
   end
 
-  def test_that_name_collections_have_collections
-    c = Taxonifi::Model::NameCollection.new
-    assert c.respond_to?(:collection)
-    assert_equal([], c.collection)
-  end
-
   def test_that_name_collection_returns_encompassing_rank
     c = Taxonifi::Model::NameCollection.new
     n = Taxonifi::Model::Name.new
@@ -108,21 +107,58 @@ class TestTaxonifiNameCollection < Test::Unit::TestCase
     assert_equal "Fooidae", c.by_name_index['family'].keys.first
   end
 
+
   def test_name_exists?
     c = Taxonifi::Model::NameCollection.new
-    n1 = Taxonifi::Model::Name.new(:name => "Fooidae", :rank => "family")
-    n2 = Taxonifi::Model::Name.new(:name => "Bar",     :rank => "genus", :parent => n1)
-    n3 = Taxonifi::Model::Name.new(:name => "Bar",     :rank => "genus", :parent => n1)
-    n4 = Taxonifi::Model::Name.new(:name => "Bar",     :rank => "subgenus", :parent => n2)
-    n5 = Taxonifi::Model::Name.new(:name => "foo",     :rank => "species", :parent => n2)
-    n6 = Taxonifi::Model::Name.new(:name => "foo",     :rank => "species", :parent => n2)
+    n1 = Taxonifi::Model::Name.new(name: "Fooidae", rank: "family",   author: nil ,    year: nil)   
+    n2 = Taxonifi::Model::Name.new(name: "Bar",     rank: "genus",    author: nil ,    year: nil,   :parent => n1)
+    n3 = Taxonifi::Model::Name.new(name: "Bar",     rank: "genus",    author: nil ,    year: nil,   :parent => n1)
+    n4 = Taxonifi::Model::Name.new(name: "Bar",     rank: "subgenus", author: nil ,    year: nil,   :parent => n2)
+    n5 = Taxonifi::Model::Name.new(name: "foo",     rank: "species",  author: 'Smith', year: 1920,  :parent => n2)
+    n6 = Taxonifi::Model::Name.new(name: "foo",     rank: "species",  author: 'Smith', year: 1920,  :parent => n2)
+    n7  = Taxonifi::Model::Name.new(name: "Blorf",  rank: "genus",      author: 'Smith', year: 1920,  :parent => n1)
+    n8  = Taxonifi::Model::Name.new(name: "foo",    rank: "species",    author: 'Smith', year: 1920,  :parent => n7)
+    n9  = Taxonifi::Model::Name.new(name: "foo",    rank: "species",    author: 'Jones', year: nil,   :parent => n7)
+    n10 = Taxonifi::Model::Name.new(name: "foo",    rank: "species",    author: 'Jones', year: nil,   :parent => n7)
+    n11 = Taxonifi::Model::Name.new(name: "foo",    rank: "species",    author: nil    , year: 1920,  :parent => n7)
+    n12 = Taxonifi::Model::Name.new(name: "foo",    rank: "species",    author: nil    , year: 1920,  :parent => n7)
+    n13 = Taxonifi::Model::Name.new(name: "foo",    rank: "subspecies", author: nil    , year: 1920,  :parent => n11)
+
+    # Given this set test that the following are identical (and that all others are not):
+    # n2 =  n3  # parent/name/rank
+    # n5  = n6  # parent/name/rank/author/year 
+    # n9  = n10 # parent/name/rank/author      
+    # n11 = n12 # parent/name/year        
+    # n13 = n11 # parent/nominotypic name 
+
     c.add_object(n1) 
+
     c.add_object(n2) 
+    assert c.name_exists?(n3),  "Name exists, but not caught."
+
+    assert c.name_exists?(n4),  "Nominotypical subgenus exists."
+
     c.add_object(n5) 
-    assert c.name_exists?(n3), "Name exists, but not caught."
-    assert c.name_exists?(n6), "Name exists, but not caught."
-    assert !c.name_exists?(n4), "Name doesn't exist, but asserted to."
-    assert_equal n2.id, c.name_exists?(n3) 
+    assert c.name_exists?(n6),  "Name exists, but not caught."
+
+    assert !c.name_exists?(n7), "Name doesn't exist, but asserted to."
+    c.add_object(n7)
+
+    assert !c.name_exists?(n8), "Name doesn't exist, but asserted to."
+    c.add_object(n8)
+    assert !c.name_exists?(n9), "Name doesn't exist, but asserted to."
+    c.add_object(n9)
+    assert c.name_exists?(n10), "Name exists and wasn't caught."
+    
+    assert !c.name_exists?(n11)
+    c.add_object(n11)
+    assert c.name_exists?(n12)
+
+    assert c.name_exists?(n13)
+
+    assert_equal n2.id, c.name_exists?(n3)
+    assert_equal n9.id, c.name_exists?(n10)
+    assert_equal n11.id, c.name_exists?(n12)
   end
 
   def test_that_name_collection_generate_ref_collection
@@ -154,5 +190,6 @@ class TestTaxonifiNameCollection < Test::Unit::TestCase
     foo = 1
   end
 
+
 end
 

data/test/test_taxonifi_species_name.rb

@@ -88,7 +88,7 @@ class TestTaxonifiSpeciesName < Test::Unit::TestCase
     sn3 = Taxonifi::Model::SpeciesName.new(:genus => g, :subgenus => sg, :species => s, :subspecies => ss) 
     assert_equal "Foo (Bar) stuff things Jones, 2012", sn3.display_name
   
-    ss.parens = false
+    ss.parens = true 
     assert_equal "Foo (Bar) stuff things (Jones, 2012)", sn3.display_name
   end
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: taxonifi
 version: !ruby/object:Gem::Version
-  version: 0.1.0
+  version: 0.2.0
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-06-07 00:00:00.000000000 Z
+date: 2013-03-27 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rdoc
@@ -59,6 +59,22 @@ dependencies:
     - - ~>
       - !ruby/object:Gem::Version
         version: 1.8.3
+- !ruby/object:Gem::Dependency
+  name: activerecord
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 3.2.8
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 3.2.8
 - !ruby/object:Gem::Dependency
   name: debugger
   requirement: !ruby/object:Gem::Requirement
@@ -96,7 +112,10 @@ files:
 - lib/assessor/row_assessor.rb
 - lib/export/export.rb
 - lib/export/format/base.rb
+- lib/export/format/obo_nomenclature.rb
+- lib/export/format/prolog.rb
 - lib/export/format/species_file.rb
+- lib/lumper/clump.rb
 - lib/lumper/lumper.rb
 - lib/lumper/lumps/parent_child_name_collection.rb
 - lib/models/author_year.rb
@@ -110,6 +129,7 @@ files:
 - lib/models/person.rb
 - lib/models/ref.rb
 - lib/models/ref_collection.rb
+- lib/models/shared_class_methods.rb
 - lib/models/species_name.rb
 - lib/splitter/builder.rb
 - lib/splitter/lexer.rb
@@ -117,26 +137,35 @@ files:
 - lib/splitter/splitter.rb
 - lib/splitter/tokens.rb
 - lib/taxonifi.rb
+- lib/utils/array.rb
+- lib/utils/hash.rb
+- taxonifi.gemspec
+- test/file_fixtures/Fossil.csv
 - test/file_fixtures/Lygaeoidea.csv
+- test/file_fixtures/names.csv
 - test/helper.rb
+- test/test_export_prolog.rb
 - test/test_exporter.rb
+- test/test_lumper_clump.rb
 - test/test_lumper_geogs.rb
 - test/test_lumper_hierarchical_collection.rb
 - test/test_lumper_names.rb
 - test/test_lumper_parent_child_name_collection.rb
 - test/test_lumper_refs.rb
+- test/test_obo_nomenclature.rb
 - test/test_parser.rb
 - test/test_splitter.rb
 - test/test_splitter_tokens.rb
 - test/test_taxonifi.rb
 - test/test_taxonifi_accessor.rb
+- test/test_taxonifi_base.rb
 - test/test_taxonifi_geog.rb
 - test/test_taxonifi_name.rb
 - test/test_taxonifi_name_collection.rb
 - test/test_taxonifi_ref.rb
 - test/test_taxonifi_ref_collection.rb
 - test/test_taxonifi_species_name.rb
-homepage: http://github.com/mjy/taxonifi
+homepage: http://github.com/SpeciesFile/taxonifi
 licenses:
 - MIT
 post_install_message: 
@@ -151,7 +180,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: 3742775100880240863
+      hash: -2473283969605789743
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements:
@@ -160,7 +189,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.21
+rubygems_version: 1.8.25
 signing_key: 
 specification_version: 3
 summary: A general purpose framework for scripted handling of taxonomic names