dwc-archive 0.7.18 → 0.8.0
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- data/CHANGELOG +1 -0
- data/VERSION +1 -1
- data/lib/dwc-archive/classification_normalizer.rb +11 -1
- data/spec/files/linnean.tar.gz +0 -0
- data/spec/lib/dwc-archive_spec.rb +16 -0
- metadata +75 -23
data/CHANGELOG
ADDED
@@ -0,0 +1 @@
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1
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+
0.8.0 Added linnean classification path to normalized data from DwCA. It consists of data associated with clades like 'kingdom', 'order' etc.
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data/VERSION
CHANGED
@@ -1 +1 @@
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1
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-
0.
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1
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+
0.8.0
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@@ -4,7 +4,7 @@ require 'parsley-store'
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class DarwinCore
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class TaxonNormalized
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7
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-
attr_accessor :id, :local_id, :global_id, :source, :parent_id, :classification_path_id, :classification_path, :current_name, :current_name_canonical, :synonyms, :vernacular_names, :rank, :status
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7
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attr_accessor :id, :local_id, :global_id, :source, :parent_id, :classification_path_id, :classification_path, :linnean_classification_path, :current_name, :current_name_canonical, :synonyms, :vernacular_names, :rank, :status
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8
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def initialize
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@id = @parent_id = @rank = @status = nil
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@@ -17,6 +17,7 @@ class DarwinCore
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@classification_path_id = []
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@synonyms = []
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@vernacular_names = []
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@linnean_classification_path = []
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end
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end
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@@ -165,6 +166,7 @@ class DarwinCore
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taxon.status = r[@core_fields[:taxonomicstatus]] if @core_fields[:taxonomicstatus]
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taxon.source = r[@core_fields[:source]] if @core_fields[:source]
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taxon.local_id = r[@core_fields[:localid]] if @core_fields[:localid]
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+
taxon.linnean_classification_path = get_linnean_classification_path(r)
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taxon.global_id = r[@core_fields[:globalid]] if @core_fields[:globalid]
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add_name_string(taxon.current_name)
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add_name_string(taxon.current_name_canonical) if taxon.current_name_canonical && !taxon.current_name_canonical.empty?
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@@ -312,5 +314,13 @@ class DarwinCore
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end
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end
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def get_linnean_classification_path(row)
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res = []
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[:kingdom, :phylum, :class, :order, :family, :genus, :subgenus].each do |clade|
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res << [row[@core_fields[clade]], clade] if @core_fields[clade]
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end
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res
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end
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end
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end
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Binary file
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@@ -152,6 +152,22 @@ describe DarwinCore do
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norm.select { |k,v| !v.synonyms.empty? }.size.should > 0
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end
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it "should assemble linnean classification if terms for it exists" do
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file = File.join(@file_dir, 'linnean.tar.gz')
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dwc = DarwinCore.new(file)
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cn = DarwinCore::ClassificationNormalizer.new(dwc)
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norm = cn.normalize
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cn.normalized_data.first.last.linnean_classification_path.should == [["Animalia", :kingdom], ["Arthropoda", :phylum], ["Insecta", :class], ["Diptera", :order], ["Cecidomyiidae", :family], ["Resseliella", :genus]]
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end
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it "should keep linnean classification empty if terms are not there" 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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norm = cn.normalize
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cn.normalized_data.first.last.linnean_classification_path.should == []
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end
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it "should be able to assemble synonyms from core" do
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file = File.join(@file_dir, 'synonyms_in_core_accepted_name_field.tar.gz')
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dwc = DarwinCore.new(file)
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metadata
CHANGED
@@ -1,7 +1,7 @@
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1
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.
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4
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version: 0.8.0
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prerelease:
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platform: ruby
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authors:
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@@ -9,11 +9,11 @@ authors:
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autorequire:
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bindir: bin
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cert_chain: []
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-
date: 2012-
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12
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+
date: 2012-07-25 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: nokogiri
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requirement:
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requirement: !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ~>
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@@ -21,10 +21,15 @@ dependencies:
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version: 1.5.0
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type: :runtime
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prerelease: false
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version_requirements:
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version_requirements: !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ~>
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- !ruby/object:Gem::Version
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version: 1.5.0
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- !ruby/object:Gem::Dependency
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name: parsley-store
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requirement:
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requirement: !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ~>
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@@ -32,10 +37,15 @@ dependencies:
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version: 0.3.0
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type: :runtime
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prerelease: false
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version_requirements:
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version_requirements: !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ~>
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- !ruby/object:Gem::Version
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version: 0.3.0
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- !ruby/object:Gem::Dependency
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name: rspec
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requirement:
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requirement: !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ~>
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@@ -43,10 +53,15 @@ dependencies:
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version: 2.7.0
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type: :development
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prerelease: false
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version_requirements:
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version_requirements: !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ~>
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- !ruby/object:Gem::Version
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version: 2.7.0
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- !ruby/object:Gem::Dependency
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name: cucumber
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requirement:
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requirement: !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ~>
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@@ -54,10 +69,15 @@ dependencies:
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version: 1.1.3
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type: :development
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prerelease: false
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version_requirements:
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version_requirements: !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ~>
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- !ruby/object:Gem::Version
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version: 1.1.3
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- !ruby/object:Gem::Dependency
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name: bundler
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requirement:
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requirement: !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ~>
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@@ -65,10 +85,15 @@ dependencies:
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version: '1.0'
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type: :development
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prerelease: false
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version_requirements:
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version_requirements: !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ~>
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- !ruby/object:Gem::Version
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version: '1.0'
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- !ruby/object:Gem::Dependency
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name: jeweler
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requirement:
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requirement: !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ~>
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@@ -76,10 +101,15 @@ 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:
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version_requirements: !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ~>
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- !ruby/object:Gem::Version
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version: 1.6.4
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- !ruby/object:Gem::Dependency
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name: ruby-debug19
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requirement:
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requirement: !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ~>
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@@ -87,10 +117,15 @@ dependencies:
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version: 0.11.6
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type: :development
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prerelease: false
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version_requirements:
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version_requirements: !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ~>
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- !ruby/object:Gem::Version
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version: 0.11.6
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- !ruby/object:Gem::Dependency
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name: parsley-store
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requirement:
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requirement: !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ! '>='
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@@ -98,10 +133,15 @@ dependencies:
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version: 0.3.0
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type: :runtime
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prerelease: false
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version_requirements:
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version_requirements: !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ! '>='
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- !ruby/object:Gem::Version
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version: 0.3.0
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- !ruby/object:Gem::Dependency
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name: rspec
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requirement:
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requirement: !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ! '>='
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@@ -109,10 +149,15 @@ 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:
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version_requirements: !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ! '>='
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- !ruby/object:Gem::Version
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version: 1.2.9
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- !ruby/object:Gem::Dependency
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name: cucumber
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requirement:
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requirement: !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ! '>='
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@@ -120,7 +165,12 @@ 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:
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version_requirements: !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ! '>='
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- !ruby/object:Gem::Version
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version: '0'
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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.
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@@ -133,6 +183,7 @@ extra_rdoc_files:
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files:
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- .document
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- .rvmrc
|
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+
- CHANGELOG
|
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187
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- Gemfile
|
137
188
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- Gemfile.lock
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138
189
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- LICENSE
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@@ -169,6 +220,7 @@ files:
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- spec/files/invalid.tar.gz
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221
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- spec/files/junk_dir_inside.zip
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171
222
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- spec/files/language_locality.tar.gz
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223
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+
- spec/files/linnean.tar.gz
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224
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- spec/files/meta.xml
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173
225
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- spec/files/minimal.tar.gz
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226
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- spec/files/not_synonym_in_extension.tar.gz
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@@ -206,7 +258,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
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version: '0'
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207
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requirements: []
|
208
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rubyforge_project:
|
209
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-
rubygems_version: 1.8.
|
261
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+
rubygems_version: 1.8.24
|
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signing_key:
|
211
263
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specification_version: 3
|
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summary: Handler of Darwin Core Archive files
|