taxonifi 0.5.0 → 0.5.1

checksums.yaml

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data/.travis.yml

@@ -1,7 +1,6 @@
 language: ruby
 rvm:
-  - 2.3.1
-bundler_args: --without development
+  - 2.6.5
 before_install: ./travis/before_install.sh
 branches:
   only:

data/README.md

@@ -1,29 +1,23 @@
 
 [![Build Status](https://travis-ci.org/SpeciesFileGroup/taxonifi.svg?branch=master)](https://travis-ci.org/SpeciesFileGroup/taxonifi)
-[![Dependency Status][7]][8]
 
 
-taxonifi
-========
+
+# 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).  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.
 
-Source
-------
+# Source
 Source is available at https://github.com/SpeciesFile/taxonifi .  The rdoc API is also viewable at http://taxonifi.speciesfile.org , (though those docs may lag behind commits to github).
 
-What's next?
-------------
-
+# 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. 
 
 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
----------------
-taxonifi is coded for Ruby 1.9.3, it has not been tested on earlier versions (though it will certainly not work with 1.8.7). 
-Using Ruby Version Manager (RVM, https://rvm.io/ ) is highly recommend. You can test your version of Ruby by doinging "ruby -v" in your terminal.
+# Getting started
+taxonifi is coded for Ruby 2.6.5, 0.4.0 works on 1.9.4.
 
 To install:
 
@@ -110,8 +104,7 @@ Parent/child style nomenclature is also parseable.
 
 There are *lots* more examples of code use in the test suite.
 
-Export/conversion
------------------
+# Export/conversion
 
 The following is an example that translates a DwC style input format as exported by EOL into tables importable to SpeciesFile.  The input file is has id, parent, child, vernacular, synonym columns.  Data are exported by default to a the users home folder in a taxonifi directory.  The export creates 6 tables that can be imported into Species File directly.
 
@@ -144,8 +137,7 @@ csv = CSV.read('input/my_data.tab',  {
               col_sep: "\t"  } ) 
 ```
 
-Code organization
------------------
+# Code organization
 
 ```
 test                # unit tests, quite a few of them
@@ -158,8 +150,7 @@ lib/model           # Taxonifi objects
 lib/splitter        # a parser/lexer/token suite for breaking down data 
 ```
 
-Contributing to taxonifi
-------------------------
+# Contributing to taxonifi
 
 (this is generic)
  
@@ -172,22 +163,17 @@ Contributing to taxonifi
 * All pull requests should test clean.
 * Please try not to mess with the Rakefile, version, or history. If you want to have your own version, or is otherwise necessary, that is fine, but please isolate to its own commit so I can cherry-pick around it.
 
-About
------
+# About
 
 taxonifi is coded by Matt Yoder in consultation with the Species File Group at University of Illinois.
 
-Copyright
----------
+# Copyright
 
-Copyright (c) 2012 Illinois Natural History Survey. See LICENSE.txt for
+Copyright (c) 2012-2020 Illinois Natural History Survey. See LICENSE.txt for
 further details.
 
-
-
 [1]: https://secure.travis-ci.org/SpeciesFileGroup/taxonifi.png?branch=master
 [2]: https://travis-ci.org/SpeciesFileGroup/taxonifi.svg?branch=master
-[7]: https://gemnasium.com/SpeciesFileGroup/taxonifi.png?branch=master
-[8]: https://gemnasium.com/SpeciesFileGroup/taxonifi?branch=master
+
 
 

data/lib/taxonifi/splitter/parser.rb

@@ -25,7 +25,7 @@ class Taxonifi::Splitter::Parser
       @builder.people.push n 
     end
 
-    @builder.year   = t.year.to_i
+    @builder.year = t.year
     @builder.parens = t.parens
   end
 

data/lib/taxonifi/splitter/tokens.rb

@@ -39,7 +39,7 @@ module Taxonifi::Splitter::Tokens
     attr_reader :authors, :year, :parens
     # This is going to hit just everything, should only be used 
     # in one off when you know you have that string.
-    @regexp = Regexp.new(/\A\s*(\(?[^\+\d)]+(\d\d\d\d)?\)?)\s*/i)
+    @regexp = Regexp.new(/\A\s*(\(?[^\+\d)]+(\d{4})?\)?)\s*/i)
 
     def initialize(str)
       str.strip!
@@ -52,9 +52,9 @@ module Taxonifi::Splitter::Tokens
         @parens = false
       end
       # check for year
-      if w =~ /(\d\d\d\d)\Z/
-        @year = $1.to_i
-        w.gsub!(/\d\d\d\d\Z/, "")
+      if w =~ /(\d{4})\Z/
+        @year = $1 ? $1.to_i : nil
+        w.gsub!(/\d{4}\Z/, "")
         w.strip!
       end
       w.gsub!(/,\s*\Z/, '')

data/lib/taxonifi/version.rb

@@ -1,3 +1,3 @@
 module Taxonifi 
-  VERSION = "0.5.0"
+  VERSION = "0.5.1"
 end

data/test/test_parser.rb

@@ -12,7 +12,7 @@ class Test_TaxonifiSplitterParser < Test::Unit::TestCase
     assert_equal "Smith", builder.names.last.author
     assert_equal 1912 ,  builder.names.last.year
     assert_equal false, builder.names.last.parens
-    assert_equal "Foo stuff Smith, 1912", builder.display_name 
+    assert_equal "Foo stuff Smith, 1912", builder.display_name
   end
 
   def test_that_parse_species_name_parses_subspecies
@@ -25,7 +25,7 @@ class Test_TaxonifiSplitterParser < Test::Unit::TestCase
     assert_equal "Smith", builder.names.last.author
     assert_equal 1912 ,  builder.names.last.year
     assert_equal false, builder.names.last.parens
-    assert_equal "Foo stuff things Smith, 1912", builder.display_name 
+    assert_equal "Foo stuff things Smith, 1912", builder.display_name
   end
 
   def test_that_parse_species_name_parses_subgenera
@@ -34,15 +34,15 @@ class Test_TaxonifiSplitterParser < Test::Unit::TestCase
     Taxonifi::Splitter::Parser.new(lexer, builder).parse_species_name
     assert_equal "Foo", builder.genus.name
     assert_equal "Bar", builder.subgenus.name
-    assert_equal builder.genus, builder.subgenus.parent 
+    assert_equal builder.genus, builder.subgenus.parent
     assert_equal "stuff", builder.species.name
-    assert_equal builder.subgenus, builder.species.parent 
+    assert_equal builder.subgenus, builder.species.parent
     assert_equal "things", builder.subspecies.name
-    assert_equal builder.species, builder.subspecies.parent 
+    assert_equal builder.species, builder.subspecies.parent
     assert_equal "Smith", builder.names.last.author
     assert_equal 1912, builder.names.last.year
     assert_equal true, builder.names.last.parens
-    assert_equal "Foo (Bar) stuff things (Smith, 1912)", builder.display_name 
+    assert_equal "Foo (Bar) stuff things (Smith, 1912)", builder.display_name
   end
 
   def test_that_parse_species_name_parses_variety_following_subspecies
@@ -56,7 +56,7 @@ class Test_TaxonifiSplitterParser < Test::Unit::TestCase
     assert_equal "Smith", builder.names.last.author
     assert_equal 1912 ,  builder.names.last.year
     assert_equal false, builder.names.last.parens
-    assert_equal "Foo stuff things var. blorf Smith, 1912", builder.display_name 
+    assert_equal "Foo stuff things var. blorf Smith, 1912", builder.display_name
   end
 
 
@@ -71,10 +71,10 @@ class Test_TaxonifiSplitterParser < Test::Unit::TestCase
     assert_equal "Smith", builder.names.last.author
     assert_equal 1912 ,  builder.names.last.year
     assert_equal false, builder.names.last.parens
-    assert_equal "Foo stuff var. blorf Smith, 1912", builder.display_name 
+    assert_equal "Foo stuff var. blorf Smith, 1912", builder.display_name
   end
 
-  
+
   def test_that_parse_species_name_parses_variety_following_species_without_author_year
     lexer = Taxonifi::Splitter::Lexer.new("Foo stuff v. blorf", :species_name)
     builder = Taxonifi::Model::SpeciesName.new
@@ -84,10 +84,9 @@ class Test_TaxonifiSplitterParser < Test::Unit::TestCase
     assert_equal nil, builder.subspecies
     assert_equal "blorf", builder.variety.name
     assert_equal nil, builder.names.last.parens # not set
-    assert_equal "Foo stuff var. blorf", builder.display_name 
+    assert_equal "Foo stuff var. blorf", builder.display_name
   end
 
-
   def test_that_parse_species_name_parses_variety_following_species_without_author_year_II
     lexer = Taxonifi::Splitter::Lexer.new("Calyptonotus rolandri var. opacus", :species_name)
     builder = Taxonifi::Model::SpeciesName.new
@@ -95,12 +94,32 @@ class Test_TaxonifiSplitterParser < Test::Unit::TestCase
     assert_equal "Calyptonotus", builder.genus.name
     assert_equal "rolandri", builder.species.name
     assert_equal nil, builder.subspecies
+    assert_equal nil, builder.names.last.year
     assert_equal "opacus", builder.variety.name
     assert_equal nil, builder.names.last.parens # not set
-    assert_equal "Calyptonotus rolandri var. opacus", builder.display_name 
+    assert_equal "Calyptonotus rolandri var. opacus", builder.display_name
+  end
+
+  def test_that_parse_family_name_parses_to_nil_year
+    lexer = Taxonifi::Splitter::Lexer.new("Bus aus (Jones)", :species_name)
+    builder = Taxonifi::Model::SpeciesName.new
+    Taxonifi::Splitter::Parser.new(lexer, builder).parse_species_name
+    assert_equal nil, builder.names.last.year
   end
 
+  def test_that_parse_family_name_parses_to_year_2
+    lexer = Taxonifi::Splitter::Lexer.new("Bus aus Jones, 1920", :species_name)
+    builder = Taxonifi::Model::SpeciesName.new
+    Taxonifi::Splitter::Parser.new(lexer, builder).parse_species_name
+    assert_equal 1920, builder.names.last.year
+  end
 
+  def test_that_parse_family_name_parses_to_year_3
+    lexer = Taxonifi::Splitter::Lexer.new("Bus aus (Jones, 1920)", :species_name)
+    builder = Taxonifi::Model::SpeciesName.new
+    Taxonifi::Splitter::Parser.new(lexer, builder).parse_species_name
+    assert_equal 1920, builder.names.last.year
+  end
 
-end 
+end
 

data/test/test_splitter_tokens.rb

@@ -88,7 +88,7 @@ class Test_TaxonifiSplitterTokens < Test::Unit::TestCase
             lexer = Taxonifi::Splitter::Lexer.new(s)
             assert t = lexer.pop(Taxonifi::Splitter::Tokens::AuthorYear)
             assert_equal a.strip, t.authors
-            assert_equal (y.size > 0 ? y.strip.to_i : nil), t.year
+            assert_equal (y.size > 0 ? y.strip.to_i : nil), t.year # bad test
             assert_equal p, t.parens
             s = nil
           end
@@ -425,8 +425,6 @@ class Test_TaxonifiSplitterTokens < Test::Unit::TestCase
     assert_equal "33", t.pg_end
     assert_equal "ix 14, 19", t.remainder
 
-
   end
-
 end 
 

data/travis/before_install.sh

@@ -1,2 +1,2 @@
 #!/bin/sh
-gem install bundler -v=1.9.4
+gem install bundler -v=1.17.3

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: taxonifi
 version: !ruby/object:Gem::Version
-  version: 0.5.0
+  version: 0.5.1
 platform: ruby
 authors:
 - Matt Yoder