dwc-archive 0.5.18 → 0.6.0

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Files changed (5) hide show
  1. data/VERSION +1 -1
  2. data/lib/dwc-archive/classification_normalizer.rb +18 -2
  3. data/spec/files/sci_name_authorship_dup.tar.gz +0 -0
  4. data/spec/lib/dwc-archive_spec.rb +22 -10
  5. metadata +22 -21
data/VERSION CHANGED
@@ -1 +1 @@
1
- 0.5.18
1
+ 0.6.0
data/lib/dwc-archive/classification_normalizer.rb CHANGED
@@ -89,13 +89,29 @@ class DarwinCore
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  def set_scientific_name(row, fields)
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  row[fields[:scientificname]] = 'N/A' unless row[fields[:scientificname]]
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- canonical_name = get_canonical_name(row[fields[:scientificname]])
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+ canonical_name = ''
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+ scientific_name = row[fields[:scientificname]].strip
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+ if separate_canonical_and_authorship?(row, fields)
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+ canonical_name = row[fields[:scientificname]].strip
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+ scientific_name += " #{row[fields[:scientificnameauthorship]].strip}"
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+ else
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+ canonical_name = get_canonical_name(row[fields[:scientificname]])
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+ end
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  fields[:canonicalname] = row.size
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  row << canonical_name
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- scientific_name = row[fields[:scientificname]].strip
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  row[fields[:scientificname]] = scientific_name
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  end
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+ def separate_canonical_and_authorship?(row, fields)
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+ authorship = ''
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+ if fields[:scientificnameauthorship]
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+ authorship = row[fields[:scientificnameauthorship]].to_s.strip
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+ end
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+ !(authorship.empty? || row[fields[:scientificname]].index(authorship))
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+ end
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+
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+
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+
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  def ingest_core
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  raise RuntimeError, "Darwin Core core fields must contain taxon id and scientific name" unless (@core_fields[:id] && @core_fields[:scientificname])
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  @dwc.core.read do |rows|
data/spec/lib/dwc-archive_spec.rb CHANGED
@@ -101,16 +101,28 @@ describe DarwinCore do
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  nodes_with_syn.first[1].synonyms.first.status.should == 'synonym'
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  end
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- # it "should be able work with files which have scientificNameAuthorship" do
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- # file = File.join(@file_dir, 'sci_name_authorship.tar.gz')
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- # dwc = DarwinCore.new(file)
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- # $lala = 1
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- # norm = dwc.normalize_classification
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- # taxa = norm.select{|k,v| v.current_name_canonical.match " "}.select{|k,v| [v.current_name.split(" ").size > v.current_name_canonical.split(" ").size]}
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- # taxa.size.should == 507
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- # 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}
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- # syn.size.should == 50
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- # end
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+ it "should be able work with files which have scientificNameAuthorship" do
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+ file = File.join(@file_dir, 'sci_name_authorship.tar.gz')
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+ dwc = DarwinCore.new(file)
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+ $lala = 1
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+ norm = dwc.normalize_classification
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+ require 'ruby-debug'; debugger
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+ taxa = norm.select{|k,v| v.current_name_canonical.match " "}.select{|k,v| [v.current_name.split(" ").size > v.current_name_canonical.split(" ").size]}
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+ taxa.size.should == 507
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+ 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}
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+ syn.size.should == 50
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+ end
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+
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+ it "should be able work with files which repeat scientificNameAuthorship value in scientificName field" do
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+ file = File.join(@file_dir, 'sci_name_authorship_dup.tar.gz')
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+ dwc = DarwinCore.new(file)
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+ $lala = 1
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+ norm = dwc.normalize_classification
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+ taxa = norm.select{|k,v| v.current_name_canonical.match " "}.select{|k,v| [v.current_name.split(" ").size > v.current_name_canonical.split(" ").size]}
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+ taxa.size.should == 507
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+ 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}
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+ syn.size.should == 50
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+ end
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  it "should be able to get language and locality fields for vernacular names" do
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  file = File.join(@file_dir, 'language_locality.tar.gz')
metadata CHANGED
@@ -1,7 +1,7 @@
1
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  --- !ruby/object:Gem::Specification
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  name: dwc-archive
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  version: !ruby/object:Gem::Version
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- version: 0.5.18
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+ version: 0.6.0
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  prerelease:
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  platform: ruby
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  authors:
@@ -13,7 +13,7 @@ date: 2011-11-04 00:00:00.000000000Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: parsley-store
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- requirement: &70273545347720 !ruby/object:Gem::Requirement
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+ requirement: &70322001068080 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ! '>='
@@ -21,10 +21,10 @@ dependencies:
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  version: '0'
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  type: :runtime
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  prerelease: false
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- version_requirements: *70273545347720
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+ version_requirements: *70322001068080
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  - !ruby/object:Gem::Dependency
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  name: rspec
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- requirement: &70273545347240 !ruby/object:Gem::Requirement
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+ requirement: &70322001067600 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ~>
@@ -32,10 +32,10 @@ dependencies:
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  version: 2.3.0
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  type: :development
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  prerelease: false
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- version_requirements: *70273545347240
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+ version_requirements: *70322001067600
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  - !ruby/object:Gem::Dependency
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  name: nokogiri
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- requirement: &70273545345720 !ruby/object:Gem::Requirement
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+ requirement: &70322001067120 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ! '>='
@@ -43,10 +43,10 @@ dependencies:
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  version: '0'
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  type: :development
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  prerelease: false
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- version_requirements: *70273545345720
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+ version_requirements: *70322001067120
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  - !ruby/object:Gem::Dependency
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  name: cucumber
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- requirement: &70273545345120 !ruby/object:Gem::Requirement
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+ requirement: &70322001066640 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ! '>='
@@ -54,10 +54,10 @@ dependencies:
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  version: '0'
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  type: :development
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  prerelease: false
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- version_requirements: *70273545345120
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+ version_requirements: *70322001066640
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  - !ruby/object:Gem::Dependency
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  name: bundler
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- requirement: &70273545344540 !ruby/object:Gem::Requirement
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+ requirement: &70322001066140 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ~>
@@ -65,10 +65,10 @@ dependencies:
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  version: 1.0.0
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  type: :development
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  prerelease: false
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- version_requirements: *70273545344540
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+ version_requirements: *70322001066140
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  - !ruby/object:Gem::Dependency
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  name: jeweler
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- requirement: &70273545344060 !ruby/object:Gem::Requirement
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+ requirement: &70322001065660 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ~>
@@ -76,10 +76,10 @@ dependencies:
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  version: 1.6.4
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  type: :development
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  prerelease: false
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- version_requirements: *70273545344060
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+ version_requirements: *70322001065660
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  - !ruby/object:Gem::Dependency
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  name: ruby-debug19
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- requirement: &70273545343580 !ruby/object:Gem::Requirement
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+ requirement: &70322001065180 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ! '>='
@@ -87,10 +87,10 @@ dependencies:
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  version: '0'
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  type: :development
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  prerelease: false
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- version_requirements: *70273545343580
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+ version_requirements: *70322001065180
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  - !ruby/object:Gem::Dependency
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  name: parsley-store
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- requirement: &70273545343100 !ruby/object:Gem::Requirement
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+ requirement: &70322001064700 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ! '>='
@@ -98,10 +98,10 @@ dependencies:
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  version: 0.2.0
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  type: :runtime
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  prerelease: false
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- version_requirements: *70273545343100
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+ version_requirements: *70322001064700
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  - !ruby/object:Gem::Dependency
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  name: rspec
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- requirement: &70273545342620 !ruby/object:Gem::Requirement
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+ requirement: &70322001064220 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ! '>='
@@ -109,10 +109,10 @@ dependencies:
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  version: 1.2.9
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  type: :development
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  prerelease: false
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- version_requirements: *70273545342620
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+ version_requirements: *70322001064220
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  - !ruby/object:Gem::Dependency
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  name: cucumber
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- requirement: &70273545328540 !ruby/object:Gem::Requirement
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+ requirement: &70322001063720 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ! '>='
@@ -120,7 +120,7 @@ dependencies:
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  version: '0'
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  type: :development
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  prerelease: false
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- version_requirements: *70273545328540
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+ version_requirements: *70322001063720
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  description: Darwin Core Archive is the current standard exchange format for GLobal
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  Names Architecture modules. This gem makes it easy to incorporate files in Darwin
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  Core Archive format into a ruby project.
@@ -172,6 +172,7 @@ files:
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  - spec/files/meta.xml
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  - spec/files/minimal.tar.gz
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  - spec/files/sci_name_authorship.tar.gz
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+ - spec/files/sci_name_authorship_dup.tar.gz
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  - spec/files/synonyms_in_core_accepted_name_field.tar.gz
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  - spec/files/synonyms_in_extension.tar.gz
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  - spec/files/uncompressed