ols 0.2.0 → 0.2.1

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Files changed (4) hide show
  1. data/History.txt +4 -0
  2. data/lib/ols/cache.rb +24 -32
  3. data/lib/ols/version.rb +1 -1
  4. metadata +17 -17
data/History.txt CHANGED
@@ -1,3 +1,7 @@
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+ === 0.2.1 2011-11-07
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+
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+ * Cache bugfix. Removed the use of 'Dir.chdir' as it was firing warnings.
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+
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  === 0.2.0 2011-11-07
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  * Addition of a basic cache layer. Users can now cache regularly used ontologies on disk.
data/lib/ols/cache.rb CHANGED
@@ -12,6 +12,7 @@ module OLS
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  def initialize(args={})
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  options = { :directory => Dir.getwd }.merge(args)
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  @cache_directory = options[:directory]
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+ @cache_directory.sub!(/\/$/,'')
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  prepare_cache
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  end
@@ -25,10 +26,8 @@ module OLS
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  filename = @term_id_to_files[term_id].to_s
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  unless filename.nil? || filename.empty?
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- Dir.chdir(@cache_directory) do
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- root_term = Marshal.load( File.open(filename) )
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- found_term = root_term.send(:find_in_graph,term_id)
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- end
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+ root_term = Marshal.load( File.open("#{@cache_directory}/#{filename}") )
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+ found_term = root_term.send(:find_in_graph,term_id)
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  end
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  found_term
@@ -50,17 +49,14 @@ module OLS
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  new_filenames = []
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- Dir.chdir(@cache_directory) do
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- OLS.root_terms(ontology).each do |term|
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- term_filename = "#{term.term_id.gsub(':','')}.marshal"
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- term.focus_graph!
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- File.open("#{term_filename}",'w') { |f| f << Marshal.dump(term) }
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- @cached_ontologies[ontology] ||= { :filenames => [], :date => Date.today }
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- @cached_ontologies[ontology][:filenames].push(term_filename) unless @cached_ontologies[ontology][:filenames].include? term_filename
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- new_filenames.push(term_filename)
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- end
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+ OLS.root_terms(ontology).each do |term|
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+ term_filename = "#{term.term_id.gsub(':','')}.marshal"
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+ term.focus_graph!
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+ File.open("#{@cache_directory}/#{term_filename}",'w') { |f| f << Marshal.dump(term) }
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+ @cached_ontologies[ontology] ||= { :filenames => [], :date => Date.today }
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+ @cached_ontologies[ontology][:filenames].push(term_filename) unless @cached_ontologies[ontology][:filenames].include? term_filename
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+ new_filenames.push(term_filename)
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  end
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-
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  @cached_ontologies[ontology][:filenames].delete_if { |file| !new_filenames.include?(file) }
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  write_cached_ontologies_to_disk
@@ -76,10 +72,8 @@ module OLS
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  def remove_ontology_from_cache(ontology)
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  raise ArgumentError, "'#{ontology}' is not part of the cache" unless OLS.ontologies.include?(ontology)
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- Dir.chdir(@cache_directory) do
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- @cached_ontologies[ontology][:filenames].each do |file|
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- File.delete(file)
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- end
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+ @cached_ontologies[ontology][:filenames].each do |file|
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+ File.delete("#{@cache_directory}/#{file}")
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  end
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  @cached_ontologies.delete(ontology)
@@ -92,9 +86,7 @@ module OLS
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  # writes the @cached_ontologies variable to disk
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  def write_cached_ontologies_to_disk
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- Dir.chdir(@cache_directory) do
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- File.open('cached_ontologies.yaml','w') { |f| f << @cached_ontologies.to_yaml }
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- end
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+ File.open("#{@cache_directory}/cached_ontologies.yaml",'w') { |f| f << @cached_ontologies.to_yaml }
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  end
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  # Utility function to prepare the cache.
@@ -103,18 +95,18 @@ module OLS
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  @term_id_to_files = {}
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  Dir.mkdir(@cache_directory) unless Dir.exists?(@cache_directory)
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- Dir.chdir(@cache_directory) do
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- @cached_ontologies = YAML.load( File.open('cached_ontologies.yaml') ) if File.exists?('cached_ontologies.yaml')
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-
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- @cached_ontologies.each do |ontology,details|
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- details[:filenames].each do |filename|
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- root_term = Marshal.load( File.open(filename) )
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- next unless root_term.is_a? OLS::Term
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- @term_id_to_files[ root_term.term_id ] = filename.to_sym
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- root_term.all_child_ids.each { |term_id| @term_id_to_files[term_id] = filename.to_sym }
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- end
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+
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+ @cached_ontologies = YAML.load( File.open("#{@cache_directory}/cached_ontologies.yaml") ) if File.exists?("#{@cache_directory}/cached_ontologies.yaml")
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+
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+ @cached_ontologies.each do |ontology,details|
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+ details[:filenames].each do |filename|
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+ root_term = Marshal.load( File.open("#{@cache_directory}/#{filename}") )
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+ next unless root_term.is_a? OLS::Term
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+ @term_id_to_files[ root_term.term_id ] = filename.to_sym
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+ root_term.all_child_ids.each { |term_id| @term_id_to_files[term_id] = filename.to_sym }
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  end
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  end
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  end
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  end
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- end
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+ end
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+
data/lib/ols/version.rb CHANGED
@@ -2,5 +2,5 @@
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  module OLS
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  # OLS::VERSION - The OLS gem version
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- VERSION = "0.2.0"
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+ VERSION = "0.2.1"
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  end
metadata CHANGED
@@ -1,7 +1,7 @@
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  --- !ruby/object:Gem::Specification
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  name: ols
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  version: !ruby/object:Gem::Version
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- version: 0.2.0
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+ version: 0.2.1
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  prerelease:
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  platform: ruby
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  authors:
@@ -13,7 +13,7 @@ date: 2011-11-07 00:00:00.000000000 Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: savon
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- requirement: &2152592920 !ruby/object:Gem::Requirement
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+ requirement: &2156971680 !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: *2152592920
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+ version_requirements: *2156971680
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  - !ruby/object:Gem::Dependency
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  name: rake
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- requirement: &2152592420 !ruby/object:Gem::Requirement
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+ requirement: &2156971240 !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: '0'
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  type: :development
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  prerelease: false
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- version_requirements: *2152592420
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+ version_requirements: *2156971240
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  - !ruby/object:Gem::Dependency
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  name: shoulda
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- requirement: &2152591680 !ruby/object:Gem::Requirement
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+ requirement: &2156970820 !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: *2152591680
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+ version_requirements: *2156970820
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  - !ruby/object:Gem::Dependency
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  name: vcr
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- requirement: &2152590620 !ruby/object:Gem::Requirement
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+ requirement: &2156970400 !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: *2152590620
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+ version_requirements: *2156970400
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  - !ruby/object:Gem::Dependency
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  name: webmock
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- requirement: &2152589180 !ruby/object:Gem::Requirement
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+ requirement: &2156969980 !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: '0'
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  type: :development
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  prerelease: false
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- version_requirements: *2152589180
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+ version_requirements: *2156969980
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  - !ruby/object:Gem::Dependency
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  name: simplecov
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- requirement: &2152587220 !ruby/object:Gem::Requirement
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+ requirement: &2156969560 !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: '0'
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  type: :development
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  prerelease: false
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- version_requirements: *2152587220
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+ version_requirements: *2156969560
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  - !ruby/object:Gem::Dependency
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  name: simplecov-rcov
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- requirement: &2152585760 !ruby/object:Gem::Requirement
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+ requirement: &2156969140 !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: *2152585760
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+ version_requirements: *2156969140
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  - !ruby/object:Gem::Dependency
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  name: mocha
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- requirement: &2152584200 !ruby/object:Gem::Requirement
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+ requirement: &2156968720 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ! '>='
@@ -98,7 +98,7 @@ 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: *2152584200
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+ version_requirements: *2156968720
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  description: ! "\n OLS provides a simple interface to the EBI's Ontology Lookup
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  Service (http://www.ebi.ac.uk/ontology-lookup/).\n It provides an easy lookup
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  of ontology terms and automagically builds up ontology trees for you.\n "