Maven migration (first draft)
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Graham Triggs
parent
da79ac3e1d
commit
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1711 changed files with 662 additions and 0 deletions
44
legacy/utilities/languageSupport/translateLabelsInOntology/label_common.rb
Executable file
44
legacy/utilities/languageSupport/translateLabelsInOntology/label_common.rb
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#!/usr/bin/ruby
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=begin
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--------------------------------------------------------------------------------
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--------------------------------------------------------------------------------
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=end
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require 'rubygems'
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require 'rdf'
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require 'rdf/rdfxml'
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require 'rdf/ntriples'
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require 'rdf/n3'
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include RDF
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class UsageError < StandardError; end
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class FilterError < StandardError; end
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class LabelCommon
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# ------------------------------------------------------------------------------------
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private
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# ------------------------------------------------------------------------------------
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# ------------------------------------------------------------------------------------
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public
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# ------------------------------------------------------------------------------------
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def self.load_filter(filter_file)
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return lambda{|s| true} unless filter_file
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return eval(IO.read(filter_file))
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rescue
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raise FilterError.new($!.message)
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end
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def initialize(rdf_file, &filter)
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@filter = filter.nil? ? lambda{true} : filter
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@graph = Graph.load(rdf_file)
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end
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def process(query, &filter)
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solutions = query.execute(@graph)
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solutions.filter!(&filter)
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solutions.order(:prop)
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end
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end
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118
legacy/utilities/languageSupport/translateLabelsInOntology/label_inserter.rb
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legacy/utilities/languageSupport/translateLabelsInOntology/label_inserter.rb
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#!/usr/bin/ruby
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=begin
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--------------------------------------------------------------------------------
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A utility that reads an RDF file, builds a model, sorts all of the URIs that have
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labels, and associates those URIs with the labels in a supplied text file, one line
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per label.
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These labels are assigned the language specified on the command line, and the
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resulting RDF statements are sent to standard output as N3.
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On the command line provide the path to the RDF file, the path to the labels file,
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and the desired language/locale. E.g.:
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label_inserter.rb ../../vivo-core-1.5-annotations.rdf labels.file es_ES
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--------------------------------------------------------------------------------
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=end
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$: << File.dirname(File.expand_path(__FILE__))
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require 'rubygems'
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require 'rdf'
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require 'label_common'
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include RDF
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class LabelInserter
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# ------------------------------------------------------------------------------------
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private
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# ------------------------------------------------------------------------------------
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#
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# Parse the arguments and complain if they don't make sense.
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#
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def sanity_check_arguments(args)
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raise UsageError, "usage is: label_inserter.rb <rdf_file> <labels_input_file> <locale> [filter_file] <n3_output_file> [ok]" unless (3..5).include?(args.length)
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if args[-1].downcase == 'ok'
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ok = true
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args.pop
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else
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ok = false
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end
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n3_output_file = args.pop
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raise UsageError, "File '#{n3_output_file}' already exists. specify 'ok' to overwrite it." if File.exist?(n3_output_file) && !ok
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rdf_file = args[0]
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raise UsageError, "File '#{rdf_file}' does not exist." unless File.exist?(rdf_file)
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labels_input_file = args[1]
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raise UsageError, "File '#{labels_input_file}' does not exist." unless File.exist?(labels_input_file)
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locale = args[2]
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raise UsageError, "Locale should be like 'ab' or 'ab-CD'." unless /^[a-z]{2}(-[A-Z]{2})?$/ =~ locale
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filter_file = args[3]
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raise UsageError, "File '#{filter_file}' does not exist." if filter_file && !File.exist?(filter_file)
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filter = LabelCommon.load_filter(filter_file)
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return rdf_file, labels_input_file, locale, filter, n3_output_file
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end
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# ------------------------------------------------------------------------------------
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public
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# ------------------------------------------------------------------------------------
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def initialize(args)
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@rdf_file, @labels_input_file, @locale, @filter, @n3_output_file = sanity_check_arguments(args)
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rescue UsageError => e
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puts "\n----------------\nUsage error\n----------------\n\n#{e}\n\n----------------\n\n"
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exit
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rescue FilterError => e
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puts "\n----------------\nFilter file is invalid\n----------------\n\n#{e}\n\n----------------\n\n"
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exit
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end
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def process()
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query = Query.new({
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:prop => {
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RDFS.label => :label,
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}
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})
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solutions = LabelCommon.new(@rdf_file).process(query, &@filter)
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labels = IO.readlines(@labels_input_file)
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raise "Number of labels (#{labels.length}) doesn't match number of URIs (#{solutions.length})" unless labels.length == solutions.length
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graph = Graph.new
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solutions.zip(labels).each do |data|
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s = data[0].prop
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p = RDFS.label
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o = Literal.new(data[1].chomp, :language => @locale)
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graph << Statement.new(s, p, o)
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end
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File.open(@n3_output_file, 'w') do |f|
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f.puts graph.dump(:ntriples)
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end
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end
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end
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#
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#
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# ------------------------------------------------------------------------------------
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# Standalone calling.
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#
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# Do this if this program was called from the command line. That is, if the command
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# expands to the path of this file.
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# ------------------------------------------------------------------------------------
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#
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if File.expand_path($0) == File.expand_path(__FILE__)
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inserter = LabelInserter.new(ARGV)
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inserter.process()
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end
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101
legacy/utilities/languageSupport/translateLabelsInOntology/label_stripper.rb
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legacy/utilities/languageSupport/translateLabelsInOntology/label_stripper.rb
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#!/usr/bin/ruby
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=begin
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--------------------------------------------------------------------------------
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A utility that reads an RDF file, builds a model, sorts all of the URIs that have
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labels, and produces a file of those labels, one per line. The idea is that this
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file could be translated, and the result could be put into RDF by label_inserter.rb
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This required the RDF.rb gem: sudo gem install rdf
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On the command line provide the path to the RDF file. E.g.:
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label_stripper.rb '../../vivo-core-1.5-annotations.rdf'
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--------------------------------------------------------------------------------
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=end
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$: << File.dirname(File.expand_path(__FILE__))
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require 'rubygems'
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require 'rdf'
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require 'label_common'
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require 'rdf/n3'
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include RDF
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class LabelStripper
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# ------------------------------------------------------------------------------------
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private
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# ------------------------------------------------------------------------------------
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#
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# Parse the arguments and complain if they don't make sense.
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#
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def sanity_check_arguments(args)
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raise UsageError, "usage is: label_stripper.rb <rdf_file> [filter_file] <labels_output_file> [ok]" unless (2..3).include?(args.length)
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if args[-1].downcase == 'ok'
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ok = true
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args.pop
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else
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ok = false
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end
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output_file = args.pop
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raise UsageError, "File '#{output_file}' already exists. specify 'ok' to overwrite it." if File.exist?(output_file) && !ok
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rdf_file = args[0]
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raise UsageError, "File '#{rdf_file}' does not exist." unless File.exist?(rdf_file)
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filter_file = args[1]
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raise UsageError, "File '#{filter_file}' does not exist." if filter_file && !File.exist?(filter_file)
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filter = LabelCommon.load_filter(filter_file)
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return rdf_file, filter, output_file
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end
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# ------------------------------------------------------------------------------------
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public
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# ------------------------------------------------------------------------------------
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def initialize(args)
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@rdf_file, @filter, @labels_output_file = sanity_check_arguments(args)
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rescue UsageError => e
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puts "\n----------------\nUsage error\n----------------\n\n#{e}\n\n----------------\n\n"
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exit
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rescue FilterError => e
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puts "\n----------------\nFilter file is invalid\n----------------\n\n#{e}\n\n----------------\n\n"
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exit
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end
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def process()
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query = Query.new({
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:prop => {
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RDFS.label => :label,
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}
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})
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solutions = LabelCommon.new(@rdf_file).process(query, &@filter)
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File.open(@labels_output_file, 'w') do |f|
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solutions.each do |s|
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f.puts s.label
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end
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end
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end
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end
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#
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#
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# ------------------------------------------------------------------------------------
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# Standalone calling.
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#
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# Do this if this program was called from the command line. That is, if the command
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# expands to the path of this file.
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# ------------------------------------------------------------------------------------
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#
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if File.expand_path($0) == File.expand_path(__FILE__)
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stripper = LabelStripper.new(ARGV)
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stripper.process()
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end
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@ -0,0 +1,12 @@
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lambda {|s|
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(
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s.prop.start_with?("http://vivoweb.org/ontology/core#") ||
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s.prop.start_with?("http://vitro.mannlib.cornell.edu/ns/") ||
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s.prop.start_with?("http://purl.org/ontology/bibo/") ||
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s.prop.start_with?("http://xmlns.com/foaf/0.1/") ||
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s.prop.start_with?("http://purl.org/dc/terms/") ||
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s.prop.start_with?("http://purl.org/dc/elements/1.1/") ||
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s.prop.start_with?("http://purl.org/NET/c4dm/event.owl#") ) &&
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!s.label.to_s.strip.empty?
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}
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