dwc-archive 0.9.6 → 0.9.10
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- checksums.yaml +7 -0
- data/.gitignore +30 -0
- data/.rspec +2 -0
- data/.ruby-version +1 -0
- data/.travis.yml +6 -4
- data/CHANGELOG +2 -0
- data/Gemfile +1 -15
- data/README.md +17 -5
- data/Rakefile +6 -24
- data/] +40 -0
- data/dwc-archive.gemspec +33 -0
- data/lib/dwc-archive.rb +33 -21
- data/lib/dwc-archive/archive.rb +5 -2
- data/lib/dwc-archive/classification_normalizer.rb +4 -0
- data/lib/dwc-archive/core.rb +2 -2
- data/lib/dwc-archive/expander.rb +6 -2
- data/lib/dwc-archive/generator.rb +18 -8
- data/lib/dwc-archive/generator_eml_xml.rb +16 -14
- data/lib/dwc-archive/generator_meta_xml.rb +19 -11
- data/lib/dwc-archive/ingester.rb +1 -1
- data/lib/dwc-archive/metadata.rb +8 -2
- data/lib/dwc-archive/version.rb +3 -0
- data/lib/dwc-archive/xml_reader.rb +9 -9
- data/spec/lib/classification_normalizer_spec.rb +223 -0
- data/spec/lib/core_spec.rb +98 -0
- data/spec/lib/darwin_core_spec.rb +279 -0
- data/spec/lib/generator_eml_xml_spec.rb +21 -0
- data/spec/lib/generator_meta_xml_spec.rb +21 -0
- data/spec/lib/generator_spec.rb +116 -0
- data/spec/lib/gnub_taxon_spec.rb +34 -0
- data/spec/lib/metadata_spec.rb +80 -0
- data/spec/lib/taxon_normalized_spec.rb +145 -0
- data/spec/lib/xml_reader_spec.rb +13 -10
- data/spec/spec_helper.rb +72 -3
- metadata +133 -62
- data/Gemfile.lock +0 -155
- data/VERSION +0 -1
- data/lib/dwc-archive/.expander.rb.swo +0 -0
- data/lib/dwc-archive/utf_regex_ruby18.rb +0 -10
- data/spec/lib/dwc-archive_spec.rb +0 -250
- data/spec/spec.opts +0 -1
data/Gemfile.lock
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GEM
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remote: https://rubygems.org/
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specs:
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abstract (1.0.0)
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i18n (~> 0.5.0)
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activesupport (3.0.8)
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archive-tar-minitar (0.5.2)
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awesome_print (1.1.0)
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binding_of_caller (0.7.1)
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debug_inspector (>= 0.0.1)
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biodiversity (3.1.0)
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parallel
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coderay (1.0.9)
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columnize (0.3.6)
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coolline (0.4.2)
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cucumber (1.3.1)
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mime-types (~> 1.15)
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awesome_print (~> 1.1.0)
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git (>= 1.2.5)
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rdoc
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method_source (0.8.1)
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mime-types (1.23)
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nokogiri (1.5.9)
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parallel (0.7.0)
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parsley-store (0.3.2)
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biodiversity (~> 3.1.0)
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jeweler (~> 1.8)
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redis (~> 3.0)
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yard (>= 0.8)
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rack-test (0.5.7)
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activesupport (= 3.0.8)
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thor (~> 0.14.4)
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redis (3.0.4)
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rspec (2.13.0)
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rspec-expectations (2.13.0)
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diff-lcs (>= 1.1.3, < 2.0)
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rspec-mocks (2.13.1)
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slop (3.4.4)
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thor (0.14.6)
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treetop (1.4.14)
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polyglot
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polyglot (>= 0.3.1)
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tzinfo (0.3.37)
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unicode_utils (1.4.0)
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PLATFORMS
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ruby
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DEPENDENCIES
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archive-tar-minitar (~> 0.5)
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bundler (~> 1.3)
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cucumber (~> 1.3)
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debugger (~> 1.3)
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jazz_hands (~> 0.5)
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jeweler (~> 1.8)
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nokogiri (~> 1.5)
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rspec (~> 2.13)
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data/VERSION
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0.9.6
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UTF8RGX = /\A(
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[\x09\x0A\x0D\x20-\x7E] # ASCII
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| [\xC2-\xDF][\x80-\xBF] # non-overlong 2-byte
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| \xE0[\xA0-\xBF][\x80-\xBF] # excluding overlongs
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| [\xE1-\xEC\xEE\xEF][\x80-\xBF]{2} # straight 3-byte
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)*\z/x
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# encoding: utf-8
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require File.expand_path(File.dirname(__FILE__) + "/../spec_helper")
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describe DarwinCore do
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before(:all) do
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@file_dir = File.join(File.dirname(__FILE__), '..', 'files')
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end
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describe "VERSION" do
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it "should return VERSION number" do
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DarwinCore::VERSION.split('.').join('').to_i.should > 41
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end
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end
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describe "::nil_field?" do
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it "should return true for entries which normally mean nil" do
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[nil, '/N', ''].each do |i|
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DarwinCore.nil_field?(i).should be_true
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end
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end
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it "should return false for fields that are not nil" do
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[0, '0', '123', 123, 'dsdfs434343/N'].each do |i|
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DarwinCore.nil_field?(i).should be_false
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end
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end
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end
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describe ".new" do
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it "should create DarwinCore instance out of archive file" do
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['data.zip', 'data.tar.gz', 'minimal.tar.gz', 'junk_dir_inside.zip'].each do |file|
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file = File.join(@file_dir, file)
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dwc = DarwinCore.new(file)
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dwc.archive.valid?.should be_true
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end
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end
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it "should raise an error if archive file does not exist" do
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file = 'not_a_file'
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lambda { DarwinCore.new(file) }.should raise_error(DarwinCore::FileNotFoundError)
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end
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it "should raise an error if archive is broken" do
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file = File.join(@file_dir, 'broken.tar.gz')
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lambda { DarwinCore.new(file) }.should raise_error(DarwinCore::UnpackingError)
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end
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it "should raise an error if archive is invalid" do
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file = File.join(@file_dir, 'invalid.tar.gz')
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lambda { DarwinCore.new(file) }.should raise_error(DarwinCore::InvalidArchiveError)
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end
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it "should raise an error if archive is not in utf-8" do
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file = File.join(@file_dir, 'latin1.tar.gz')
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lambda { DarwinCore.new(file) }.should raise_error(DarwinCore::EncodingError)
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end
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it "should work with files that have non-alfanumeric characters and spaces" do
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file = File.join(@file_dir, 'file with characters(3).gz')
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dwc = DarwinCore.new(file)
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dwc.archive.valid?.should be_true
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end
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end
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describe ".normalize_classification" do
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it "should return flat list if file has no parent id information" do
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file = File.join(@file_dir, 'flat_list.tar.gz')
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dwc = DarwinCore.new(file)
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cn = DarwinCore::ClassificationNormalizer.new(dwc)
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cn.normalize
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cn.normalized_data.should_not be_nil
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cn.normalized_data.size.should > 0
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end
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it "should return array or hash of name_strings back" do
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file = File.join(@file_dir, 'data.tar.gz')
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dwc = DarwinCore.new(file)
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cn = DarwinCore::ClassificationNormalizer.new(dwc)
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cn.normalize
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name_strings = cn.name_strings
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name_strings.is_a?(Array).should be_true
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name_strings.size.should > 1
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name_strings = cn.name_strings(with_hash: true)
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name_strings.size.should > 1
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name_strings.is_a?(Hash).should be_true
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name_strings.is_a?(Hash).should be_true
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name_strings.values.uniq.should == [1]
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vernacular_name_strings = cn.vernacular_name_strings
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vernacular_name_strings.is_a?(Array).should be_true
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vernacular_name_strings.size.should > 0
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vernacular_name_strings = cn.vernacular_name_strings(with_hash: true)
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vernacular_name_strings.size.should > 0
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vernacular_name_strings.is_a?(Hash).should be_true
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vernacular_name_strings.values.uniq.should == [1]
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end
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it "should traverse DarwinCore files and assemble data for every node in memory" do
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file = File.join(@file_dir, 'data.tar.gz')
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dwc = DarwinCore.new(file)
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norm = dwc.normalize_classification
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norm.class.should == Hash
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path_encodings = []
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norm.each do |taxon_id, taxon|
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taxon.classification_path.each {|p| path_encodings << p.encoding}
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end
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path_encodings.uniq!
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path_encodings.size.should == 1
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path_encodings[0].to_s.should == "UTF-8"
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norm['leptogastrinae:tid:2857'].class.should == DarwinCore::TaxonNormalized
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norm['leptogastrinae:tid:2857'].source.should == 'http://leptogastrinae.lifedesks.org/pages/2857'
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end
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it "should assemble synonyms from core" do
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file = File.join(@file_dir, 'data.tar.gz')
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dwc = DarwinCore.new(file)
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norm = dwc.normalize_classification
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syn = norm.values.select {|n| n.synonyms.size > 0}[0].synonyms[0]
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syn.id.should == 'leptogastrinae:tid:127'
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syn.name.should == "Leptogastridae"
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syn.source.should == 'http://leptogastrinae.lifedesks.org/pages/127'
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end
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it "should be able to assemble vernacular names from an extension" do
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file = File.join(@file_dir, 'data.tar.gz')
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dwc = DarwinCore.new(file)
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norm = dwc.normalize_classification
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norm.select { |k,v| !v.vernacular_names.empty? }.map { |k,v| v.vernacular_names }.size.should > 0
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end
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it "should be able to assemble synonyms from extension" do
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file = File.join(@file_dir, 'synonyms_in_extension.tar.gz')
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dwc = DarwinCore.new(file)
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norm = dwc.normalize_classification
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norm.select { |k,v| !v.synonyms.empty? }.map { |k,v| v.synonyms }.size.should > 0
|
135
|
-
end
|
136
|
-
|
137
|
-
it "should not assemble synonyms from extension with scientificName, and file name not matching 'synonym'" do
|
138
|
-
file = File.join(@file_dir, 'not_synonym_in_extension.tar.gz')
|
139
|
-
dwc = DarwinCore.new(file)
|
140
|
-
norm = dwc.normalize_classification
|
141
|
-
norm.select { |k,v| !v.synonyms.empty? }.map { |k,v| v.synonyms }.size.should == 0
|
142
|
-
end
|
143
|
-
|
144
|
-
it "should not attempt to assemble extensions with with_extensions opts set to false" do
|
145
|
-
file = File.join(@file_dir, 'data.tar.gz')
|
146
|
-
dwc = DarwinCore.new(file)
|
147
|
-
cn = DarwinCore::ClassificationNormalizer.new(dwc)
|
148
|
-
norm = cn.normalize(:with_extensions => false)
|
149
|
-
norm.select { |k,v| !v.vernacular_names.empty? }.size.should == 0
|
150
|
-
norm = cn.normalize()
|
151
|
-
norm.select { |k,v| !v.vernacular_names.empty? }.size.should > 0
|
152
|
-
file = File.join(@file_dir, 'synonyms_in_extension.tar.gz')
|
153
|
-
dwc = DarwinCore.new(file)
|
154
|
-
cn = DarwinCore::ClassificationNormalizer.new(dwc)
|
155
|
-
norm = cn.normalize(:with_extensions => false)
|
156
|
-
norm.select { |k,v| !v.synonyms.empty? }.size.should == 0
|
157
|
-
norm = cn.normalize()
|
158
|
-
norm.select { |k,v| !v.synonyms.empty? }.size.should > 0
|
159
|
-
end
|
160
|
-
|
161
|
-
it "should assemble linnean classification if terms for it exists" do
|
162
|
-
file = File.join(@file_dir, 'linnean.tar.gz')
|
163
|
-
dwc = DarwinCore.new(file)
|
164
|
-
cn = DarwinCore::ClassificationNormalizer.new(dwc)
|
165
|
-
norm = cn.normalize
|
166
|
-
cn.normalized_data.first.last.linnean_classification_path.should == [["Animalia", :kingdom], ["Arthropoda", :phylum], ["Insecta", :class], ["Diptera", :order], ["Cecidomyiidae", :family], ["Resseliella", :genus]]
|
167
|
-
end
|
168
|
-
|
169
|
-
it "should keep linnean classification empty if terms are not there" do
|
170
|
-
file = File.join(@file_dir, 'data.tar.gz')
|
171
|
-
dwc = DarwinCore.new(file)
|
172
|
-
cn = DarwinCore::ClassificationNormalizer.new(dwc)
|
173
|
-
norm = cn.normalize
|
174
|
-
cn.normalized_data.first.last.linnean_classification_path.should == []
|
175
|
-
end
|
176
|
-
|
177
|
-
it "should be able to assemble synonyms from core" do
|
178
|
-
file = File.join(@file_dir, 'synonyms_in_core_accepted_name_field.tar.gz')
|
179
|
-
dwc = DarwinCore.new(file)
|
180
|
-
norm = dwc.normalize_classification
|
181
|
-
norm.select { |k,v| !v.synonyms.empty? }.map { |k,v| v.synonyms }.size.should > 0
|
182
|
-
end
|
183
|
-
|
184
|
-
it "should be able to assemble synonyms from extension" do
|
185
|
-
file = File.join(@file_dir, 'data.tar.gz')
|
186
|
-
dwc = DarwinCore.new(file)
|
187
|
-
norm = dwc.normalize_classification
|
188
|
-
nodes_with_syn = norm.select { |k,v| !v.synonyms.empty? }
|
189
|
-
nodes_with_syn.map { |k,v| v.synonyms }.size.should > 0
|
190
|
-
nodes_with_syn.first[1].synonyms.first.status.should == 'synonym'
|
191
|
-
end
|
192
|
-
|
193
|
-
it "should be able work with files which have scientificNameAuthorship" do
|
194
|
-
file = File.join(@file_dir, 'sci_name_authorship.tar.gz')
|
195
|
-
dwc = DarwinCore.new(file)
|
196
|
-
cn = DarwinCore::ClassificationNormalizer.new(dwc)
|
197
|
-
norm = cn.normalize
|
198
|
-
path_encodings = norm.map {|taxon_id, taxon| taxon.classification_path}.flatten.map { |name| name.encoding.to_s }.uniq
|
199
|
-
path_encodings.size.should == 1
|
200
|
-
path_encodings[0].should == "UTF-8"
|
201
|
-
taxa = norm.select{|k,v| v.current_name_canonical.match " "}.select{|k,v| [v.current_name.split(" ").size > v.current_name_canonical.split(" ").size]}
|
202
|
-
taxa.size.should == 507
|
203
|
-
syn = norm.select{|k,v| v.synonyms.size > 0}.map {|k,v| v.synonyms}.flatten.select {|s| s.name.split(" ").size > s.canonical_name.split(" ").size}
|
204
|
-
syn.size.should == 50
|
205
|
-
end
|
206
|
-
|
207
|
-
it "should be able work with files which repeat scientificNameAuthorship value in scientificName field" do
|
208
|
-
file = File.join(@file_dir, 'sci_name_authorship_dup.tar.gz')
|
209
|
-
dwc = DarwinCore.new(file)
|
210
|
-
norm = dwc.normalize_classification
|
211
|
-
taxa = norm.select{|k,v| v.current_name_canonical.match " "}.select{|k,v| [v.current_name.split(" ").size > v.current_name_canonical.split(" ").size]}
|
212
|
-
taxa.size.should == 507
|
213
|
-
syn = norm.select{|k,v| v.synonyms.size > 0}.map {|k,v| v.synonyms}.flatten.select {|s| s.name.split(" ").size > s.canonical_name.split(" ").size}
|
214
|
-
syn.size.should == 50
|
215
|
-
end
|
216
|
-
|
217
|
-
it "should be able open files where coreid is empty" do
|
218
|
-
file = File.join(@file_dir, 'empty_coreid.tar.gz')
|
219
|
-
dwc = DarwinCore.new(file)
|
220
|
-
norm = dwc.normalize_classification
|
221
|
-
taxa = norm.select{|k,v| v.current_name_canonical.match " "}.select{|k,v| [v.current_name.split(" ").size > v.current_name_canonical.split(" ").size]}
|
222
|
-
taxa.size.should == 2
|
223
|
-
end
|
224
|
-
|
225
|
-
it "should be able to get language and locality fields for vernacular names" do
|
226
|
-
file = File.join(@file_dir, 'language_locality.tar.gz')
|
227
|
-
dwc = DarwinCore.new(file)
|
228
|
-
cn = DarwinCore::ClassificationNormalizer.new(dwc)
|
229
|
-
cn.normalize
|
230
|
-
vn = cn.normalized_data['leptogastrinae:tid:42'].vernacular_names.first
|
231
|
-
vn.language.should == 'en'
|
232
|
-
vn.locality.should == 'New England'
|
233
|
-
end
|
234
|
-
|
235
|
-
it 'should be able to get uuids from gnub dataset' do
|
236
|
-
file = File.join(@file_dir, 'gnub.tar.gz')
|
237
|
-
dwc = DarwinCore.new(file)
|
238
|
-
cn = DarwinCore::ClassificationNormalizer.new(dwc)
|
239
|
-
cn.normalize
|
240
|
-
vn = cn.normalized_data['9c399f90-cfb8-5a7f-9a21-18285a473488']
|
241
|
-
vn.class.should == DarwinCore::GnubTaxon
|
242
|
-
vn.uuid.should == '8faa91f6-663f-4cfe-b785-0ab4e9415a51'
|
243
|
-
vn.uuid_path.should == [
|
244
|
-
"9a9f9eeb-d5f9-4ff6-b6cb-a5ad345e33c3",
|
245
|
-
"bf4c91c0-3d1f-44c7-9d3b-249382182a26",
|
246
|
-
"8faa91f6-663f-4cfe-b785-0ab4e9415a51"]
|
247
|
-
end
|
248
|
-
end
|
249
|
-
|
250
|
-
end
|
data/spec/spec.opts
DELETED
@@ -1 +0,0 @@
|
|
1
|
-
--color
|