taxonifi 0.4.0 → 0.5.0

checksums.yaml

@@ -1,7 +1,7 @@
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data/.ruby-version

@@ -1 +1 @@
-2.3.1
+2.6.5

data/.travis.yml

@@ -1,6 +1,6 @@
 language: ruby
 rvm:
-  - 2.1.5
+  - 2.3.1
 bundler_args: --without development
 before_install: ./travis/before_install.sh
 branches:

data/Gemfile.lock

@@ -1,36 +1,34 @@
 PATH
   remote: .
   specs:
-    taxonifi (0.4.0)
-      require_all (~> 1.3.3)
+    taxonifi (0.5.0)
+      require_all (~> 3.0)
 
 GEM
   remote: https://rubygems.org/
   specs:
-    awesome_print (1.6.1)
-    builder (3.2.2)
-    byebug (8.2.5)
-    json (1.8.3)
-    power_assert (0.3.0)
-    rake (11.1.2)
-    rdoc (4.2.2)
-      json (~> 1.4)
-    require_all (1.3.3)
-    test-unit (3.1.8)
+    awesome_print (1.8.0)
+    builder (3.2.4)
+    byebug (11.1.1)
+    power_assert (1.1.5)
+    rake (13.0.1)
+    rdoc (6.2.1)
+    require_all (3.0.0)
+    test-unit (3.3.5)
       power_assert
 
 PLATFORMS
   ruby
 
 DEPENDENCIES
-  awesome_print (~> 1.6)
+  awesome_print (~> 1.8)
   builder (~> 3.2)
   bundler (~> 1.12)
-  byebug (~> 8.2)
-  rake (~> 11.1)
-  rdoc (~> 4.2.2)
+  byebug (~> 11)
+  rake (~> 13.0)
+  rdoc (~> 6.2)
   taxonifi!
-  test-unit (~> 3.1.8)
+  test-unit (~> 3.3.5)
 
 BUNDLED WITH
-   1.12.3
+   1.17.3

data/README.md

@@ -1,11 +1,11 @@
 
-[![Continuous Integration Status][1]][2]
+[![Build Status](https://travis-ci.org/SpeciesFileGroup/taxonifi.svg?branch=master)](https://travis-ci.org/SpeciesFileGroup/taxonifi)
 [![Dependency Status][7]][8]
 
 
 taxonifi
 ========
-There will always be "legacy" taxonomic data that needs shuffling around. The taxonifi gem is a suite of general purpose tools that act as a middle layer for data-conversion purposes (e.g. migrating legacy taxonomic databases).  It's first application was to convert DwC-style data downloaded from EoL into a Species File.  The code is well documented in unit tests, poke around to see if it might be useful.  In particular, if you've considered building a collection of regular expressions particular to biodiversity data look at the Tokens code and related tests. 
+There will always be "legacy" taxonomic data that needs shuffling around. The taxonifi gem is a suite of general purpose tools that act as a middle layer for data-conversion purposes (e.g. migrating legacy taxonomic databases).  Its first application was to convert DwC-style data downloaded from EoL into a Species File.  The code is well documented in unit tests, poke around to see if it might be useful.  In particular, if you've considered building a collection of regular expressions particular to biodiversity data look at the Tokens code and related tests. 
 
 Overall, the goal is to provide well documented (and unit-tested) coded that is broadly useful, and vanilla enough to encourage other to fork and hack on their own.
 
@@ -16,9 +16,9 @@ Source is available at https://github.com/SpeciesFile/taxonifi .  The rdoc API i
 What's next?
 ------------
 
-Before you jump on board you should also check out similar code from the Global Names team at https://github.com/GlobalNamesArchitecture. Future integration and merging of shared functionality is planned.  Code will be released in an "early-and-often" approach.
+Before you jump on board you should also check out similar code from the Global Names team at https://github.com/GlobalNamesArchitecture. Future integration and merging of shared functionality is planned. 
 
-Taxonifi is presently coded for convience, not speed (though it's not necessarily slow). It assumes that conversion processes are typically one-offs that can afford to run over a longer period of time (read minutes rather than seconds). Reading, and fully parsing into objects, around 25k rows of nomenclature (class to species, inc. author year, = ~45k names) in to memory as Taxonifi objects benchmarks at around 2 minutes. Faster indexing is planned as needed, likely using Redis (see GNA link above).
+Taxonifi is presently coded for convience, not speed (though it's not necessarily slow). It assumes that conversion processes are typically one-offs that can afford to run over a longer period of time (read minutes rather than seconds). Reading, and fully parsing into objects, around 25k rows of nomenclature (class to species, inc. author year, = ~45k names) in to memory as Taxonifi objects benchmarks at around 2 minutes. 
 
 Getting started
 ---------------

data/lib/taxonifi.rb

@@ -7,7 +7,7 @@ module Taxonifi
 
   class TaxonifiError < StandardError; end;
 
-  # Taxonomic ranks. 
+  # Taxonomic ranks.
   RANKS = %w{
       kingdom
       phylum
@@ -17,7 +17,7 @@ module Taxonifi
       infraclass
       cohort
       superorder
-      order 
+      order
       suborder
       infraorder
       superfamily

data/lib/taxonifi/model/author_year.rb

@@ -1,4 +1,4 @@
-require File.expand_path(File.join(File.dirname(__FILE__), "../model/base.rb"))
+require_rel 'base'
 
 module Taxonifi
   module Model

data/lib/taxonifi/model/base.rb

@@ -1,9 +1,11 @@
+require_rel 'shared_class_methods'
+
 module Taxonifi
   module Model
 
     # A base class for all Taxonifi::Models that represent
-    # "individuals" (as opposed to collections of indviduals).  
-    class Base 
+    # "individuals" (as opposed to collections of indviduals).
+    class Base
 
       include Taxonifi::Model::SharedClassMethods
 
@@ -23,8 +25,8 @@ module Taxonifi
         @properties = {}
       end
 
-      # Assign on new() all attributes for the ATTRIBUTES 
-      # constant in a given subclass. 
+      # Assign on new() all attributes for the ATTRIBUTES
+      # constant in a given subclass.
       # !! Check validity prior to building.
       def build(attributes, opts)
         attributes.each do |c|
@@ -39,12 +41,12 @@ module Taxonifi
 
       # Add a key/value pair to @properties
       def add_property(key, value)
-        if @properties[key] 
+        if @properties[key]
           return false
         else
           @properties.merge!(key => value)
         end
-      end  
+      end
 
       # Replace an existing key/value pair in @properties
       def replace_property(key,value)
@@ -53,19 +55,19 @@ module Taxonifi
        else
         @properties.merge!(key => value)
        end
-      end 
- 
-      # Delete an existing key/value pair in @properties 
+      end
+
+      # Delete an existing key/value pair in @properties
       def delete_property(key)
        if !@properties[key]
-         @properties.delete(key) 
+         @properties.delete(key)
        else
         @properties.merge!(key => value)
        end
       end
 
       def id=(id)
-        raise Taxonifi::ModelError, "Base model objects must have Fixnum ids." if !id.nil? && id.class != Fixnum
+        raise Taxonifi::ModelError, "Base model objects must have Fixnum ids." if !id.nil? && id.class != ::Integer
         @id = id
       end
 
@@ -74,7 +76,7 @@ module Taxonifi
       def ancestor_ids
         i = 0 # check for recursion
         ids = []
-        p = parent 
+        p = parent
         while !p.nil?
           ids.unshift p.id
           p = p.parent
@@ -90,14 +92,14 @@ module Taxonifi
       def ancestors
         i = 0 # check for recursion
         ancestors = []
-        p = parent 
+        p = parent
         while !p.nil?
           ancestors.unshift p
           p = p.parent
           i += 1
           raise Taxonifi::ModelError, "Infite recursion in parent string detected for Base model object #{id.display_name}." if i > 100
         end
-        ancestors 
+        ancestors
       end
     end
 

data/lib/taxonifi/version.rb

@@ -1,3 +1,3 @@
 module Taxonifi 
-  VERSION = "0.4.0"
+  VERSION = "0.5.0"
 end

data/taxonifi.gemspec

@@ -8,7 +8,7 @@ Gem::Specification.new do |s|
   s.version = Taxonifi::VERSION
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
-  s.authors = ["mjy"]
+  s.authors = ["Matt Yoder"]
   s.date = "2013-03-27"
   
   s.summary = "A general purpose framework for scripted handling of taxonomic names or other heirarchical metadata."
@@ -22,20 +22,21 @@ Gem::Specification.new do |s|
   s.files         = `git ls-files -z`.split("\x0")
   s.executables   = s.files.grep(%r{^bin/}) { |f| File.basename(f) }
   s.test_files    = s.files.grep(%r{^(test|spec|features)/})
-  s.homepage = "http://github.com/SpeciesFile/taxonifi"
+  s.homepage = "https://github.com/SpeciesFile/taxonifi"
   s.licenses = ["MIT"]
   s.require_paths = ["lib"]
   s.rubygems_version = "2.4.5"
+  s.metadata = { "source_code_uri" => "https://github.com/SpeciesFileGroup/taxonifi" }
 
-  s.add_dependency "require_all", "~> 1.3.3"
+  s.add_dependency "require_all", "~> 3.0"
+  s.required_ruby_version = '~> 2.6'
 
-  s.add_development_dependency "rake", '~> 11.1'
-  s.add_development_dependency "byebug", "~> 8.2"
+  s.add_development_dependency "rake", '~> 13.0'
+  s.add_development_dependency "byebug", "~> 11"
   s.add_development_dependency "bundler", "~> 1.12"
-  s.add_development_dependency 'awesome_print', '~> 1.6'
-  s.add_development_dependency 'test-unit', '~> 3.1.8'
-  s.add_development_dependency "rdoc", "~> 4.2.2"
+  s.add_development_dependency 'awesome_print', '~> 1.8'
+  s.add_development_dependency 'test-unit', '~> 3.3.5'
+  s.add_development_dependency "rdoc", "~> 6.2"
   s.add_development_dependency "builder", "~> 3.2"
 
 end
-

data/test/helper.rb

@@ -26,14 +26,12 @@ def generic_csv_with_names
 end
 
 def names
-    file = File.expand_path(File.join(File.dirname(__FILE__), 'file_fixtures/names.csv'))
-
-    csv = CSV.read(file, { 
-      headers: true,
-      col_sep: ",",
-      header_converters: :downcase
-    } ) 
-    nc = Taxonifi::Lumper.create_name_collection(:csv => csv, :initial_id => 1) 
+  file = File.expand_path(File.join(File.dirname(__FILE__), 'file_fixtures/names.csv'))
+
+  csv = CSV.read(file, { 
+    headers: true,
+    col_sep: ",",
+    header_converters: :downcase
+  } ) 
+  nc = Taxonifi::Lumper.create_name_collection(csv: csv, initial_id: 1) 
 end
-
-

data/test/test_taxonifi_name.rb

@@ -7,66 +7,66 @@ class TestTaxonifiName < Test::Unit::TestCase
   end
 
   def test_new_name
-    assert n = Taxonifi::Model::Name.new() 
+    assert n = Taxonifi::Model::Name.new()
   end
 
   def test_that_name_has_a_name
-    n = Taxonifi::Model::Name.new() 
+    n = Taxonifi::Model::Name.new()
     assert n.respond_to?(:name)
   end
 
   def test_that_name_has_an_id
-    n = Taxonifi::Model::Name.new() 
+    n = Taxonifi::Model::Name.new()
     assert n.respond_to?(:id)
   end
 
   def test_that_name_has_a_parent
-    n = Taxonifi::Model::Name.new() 
-    assert n.respond_to?(:parent) 
+    n = Taxonifi::Model::Name.new()
+    assert n.respond_to?(:parent)
   end
 
   def test_that_name_has_a_rank
-    n = Taxonifi::Model::Name.new() 
-    assert n.respond_to?(:rank) 
+    n = Taxonifi::Model::Name.new()
+    assert n.respond_to?(:rank)
   end
 
   def test_that_name_has_an_author
-    n = Taxonifi::Model::Name.new() 
-    assert n.respond_to?(:author) 
+    n = Taxonifi::Model::Name.new()
+    assert n.respond_to?(:author)
   end
 
   def test_that_name_has_a_year
-    n = Taxonifi::Model::Name.new() 
-    assert n.respond_to?(:year) 
+    n = Taxonifi::Model::Name.new()
+    assert n.respond_to?(:year)
   end
 
   def test_that_name_returns_false_with_bad_rank
-    n = Taxonifi::Model::Name.new() 
+    n = Taxonifi::Model::Name.new()
     assert_raise Taxonifi::NameError do
       n.rank = "FOO"
-    end 
+    end
   end
 
   def test_that_name_allows_legal_rank
-    n = Taxonifi::Model::Name.new() 
+    n = Taxonifi::Model::Name.new()
     assert n.rank = "genus"
   end
 
   def test_that_name_rank_is_case_insensitive
-    n = Taxonifi::Model::Name.new() 
+    n = Taxonifi::Model::Name.new()
     assert n.rank = "Genus"
     assert n.rank = "GENUS"
   end
 
   def test_that_rank_is_required_before_parent
-    n = Taxonifi::Model::Name.new() 
+    n = Taxonifi::Model::Name.new()
     assert_raise Taxonifi::NameError do
-      n.parent = Taxonifi::Model::Name.new() 
+      n.parent = Taxonifi::Model::Name.new()
     end
   end
 
   def test_that_parent_is_a_taxonifi_name
-    n = Taxonifi::Model::Name.new() 
+    n = Taxonifi::Model::Name.new()
     n.rank = "genus" # avoid that raise
     assert_raise Taxonifi::NameError do
       n.parent = "foo"
@@ -74,15 +74,15 @@ class TestTaxonifiName < Test::Unit::TestCase
   end
 
   def test_that_rank_can_be_set
-    n = Taxonifi::Model::Name.new() 
+    n = Taxonifi::Model::Name.new()
     n.rank = "family"
     assert_equal "family", n.rank
   end
 
   def test_that_parent_is_higher_rank_than_child
-    n = Taxonifi::Model::Name.new() 
+    n = Taxonifi::Model::Name.new()
     n.rank = "genus"
-    p = Taxonifi::Model::Name.new() 
+    p = Taxonifi::Model::Name.new()
     p.rank = "species"
     assert_raise Taxonifi::NameError do
       n.parent = p
@@ -90,9 +90,9 @@ class TestTaxonifiName < Test::Unit::TestCase
   end
 
   def test_that_parent_can_be_set
-    n = Taxonifi::Model::Name.new() 
+    n = Taxonifi::Model::Name.new()
     n.rank = "genus"
-    p = Taxonifi::Model::Name.new() 
+    p = Taxonifi::Model::Name.new()
     p.rank = "species"
     assert p.parent = n
     assert_equal "genus", p.parent.rank
@@ -139,30 +139,30 @@ class TestTaxonifiName < Test::Unit::TestCase
     create_a_few_names
     n5 = Taxonifi::Model::Name.new(:name => "beep", :rank => "Subspecies", :author => "Frank", :year => 2020, :id => 11,  :parent => @n4 )
 
-    assert_equal 'Foo', @n2.nomenclator_name 
+    assert_equal 'Foo', @n2.nomenclator_name
     assert_equal 'Foo (Bar)', @n3.nomenclator_name
     assert_equal 'Foo (Bar) boo', @n4.nomenclator_name
     assert_equal 'Foo (Bar) boo beep', n5.nomenclator_name
   end
 
   def test_ancestors
-    create_a_few_names 
+    create_a_few_names
     assert_equal [@n0, @n1], @n2.ancestors
   end
 
   def test_ancestor_ids
-    create_a_few_names 
+    create_a_few_names
     assert_equal [2,15], @n2.ancestor_ids
   end
 
   # TODO: fix to inject valid id to confirm to SF
   def test_parent_ids_sf_style
-    create_a_few_names 
+    create_a_few_names
     assert_equal '2-15-14g-19s-11', @n4.parent_ids_sf_style
     assert_equal '2-15-14g-19s', @n3.parent_ids_sf_style
     assert_equal '2-15-14g', @n2.parent_ids_sf_style
     assert_equal '2-15', @n1.parent_ids_sf_style
-  end 
+  end
 
   def test_author_year_index
     n = Taxonifi::Model::Name.new(author_year: 'Smith and Jones, 1920')
@@ -170,17 +170,21 @@ class TestTaxonifiName < Test::Unit::TestCase
   end
 
   def test_genus_group_parent
-    n1 = Taxonifi::Model::Name.new(name: "Fooidae", rank: "family", author: nil, year: nil)                      # 
-    n2 = Taxonifi::Model::Name.new(name: "Foo",     rank: "genus",      author: nil ,    year: nil,   :parent => n1)     # Foo
+    n1 = Taxonifi::Model::Name.new(name: "Fooidae", rank: "family", author: nil, year: nil)                              #
+    n2 = Taxonifi::Model::Name.new(name: "Foo",     rank: "genus",      author: nil ,    year: "",   :parent => n1)      # Foo
     n3 = Taxonifi::Model::Name.new(name: "Bar",     rank: "subgenus",   author: nil ,    year: nil,   :parent => n2)     # Foo (Bar)
-    n4 = Taxonifi::Model::Name.new(name: "aus",     rank: "species",    author: nil ,    year: nil,   :parent => n3)     # Foo (Bar) aus 
+    n4 = Taxonifi::Model::Name.new(name: "aus",     rank: "species",    author: nil ,    year: nil,   :parent => n3)     # Foo (Bar) aus
     n5 = Taxonifi::Model::Name.new(name: "bus",     rank: "subspecies", author: 'Smith', year: 1920,  :parent => n4)     # Foo (Bar) aus bus
 
     assert_equal n3, n4.genus_group_parent
     assert_equal n3, n5.genus_group_parent
+
+    # No zeros injected
+    assert_equal nil, n3.year
+    assert_equal "", n2.year
   end
 
-  # 
+  #
   # ICZN Subclass
   #
 

metadata

@@ -1,10 +1,10 @@
 --- !ruby/object:Gem::Specification
 name: taxonifi
 version: !ruby/object:Gem::Version
-  version: 0.4.0
+  version: 0.5.0
 platform: ruby
 authors:
-- mjy
+- Matt Yoder
 autorequire: 
 bindir: bin
 cert_chain: []
@@ -16,42 +16,42 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 1.3.3
+        version: '3.0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 1.3.3
+        version: '3.0'
 - !ruby/object:Gem::Dependency
   name: rake
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '11.1'
+        version: '13.0'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '11.1'
+        version: '13.0'
 - !ruby/object:Gem::Dependency
   name: byebug
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '8.2'
+        version: '11'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '8.2'
+        version: '11'
 - !ruby/object:Gem::Dependency
   name: bundler
   requirement: !ruby/object:Gem::Requirement
@@ -72,42 +72,42 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.6'
+        version: '1.8'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.6'
+        version: '1.8'
 - !ruby/object:Gem::Dependency
   name: test-unit
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 3.1.8
+        version: 3.3.5
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 3.1.8
+        version: 3.3.5
 - !ruby/object:Gem::Dependency
   name: rdoc
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 4.2.2
+        version: '6.2'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 4.2.2
+        version: '6.2'
 - !ruby/object:Gem::Dependency
   name: builder
   requirement: !ruby/object:Gem::Requirement
@@ -202,27 +202,27 @@ files:
 - test/test_taxonifi_ref_collection.rb
 - test/test_taxonifi_species_name.rb
 - travis/before_install.sh
-homepage: http://github.com/SpeciesFile/taxonifi
+homepage: https://github.com/SpeciesFile/taxonifi
 licenses:
 - MIT
-metadata: {}
+metadata:
+  source_code_uri: https://github.com/SpeciesFileGroup/taxonifi
 post_install_message: 
 rdoc_options: []
 require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
-  - - ">="
+  - - "~>"
     - !ruby/object:Gem::Version
-      version: '0'
+      version: '2.6'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
   - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubyforge_project: 
-rubygems_version: 2.5.1
+rubygems_version: 3.0.6
 signing_key: 
 specification_version: 4
 summary: A general purpose framework for scripted handling of taxonomic names or other