bel 0.3.0.beta1-x86-mingw32
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- data/INSTALL.md +19 -0
- data/INSTALL_RUBY.md +107 -0
- data/LICENSE +191 -0
- data/README.md +319 -0
- data/bel.gemspec +67 -0
- data/bin/bel2rdf +134 -0
- data/bin/bel_compare +177 -0
- data/bin/bel_parse +60 -0
- data/bin/bel_rdfschema +72 -0
- data/bin/bel_summarize +86 -0
- data/bin/bel_upgrade +175 -0
- data/bin/bel_upgrade_term +163 -0
- data/ext/mri/bel-ast.c +221 -0
- data/ext/mri/bel-ast.h +82 -0
- data/ext/mri/bel-node-stack.c +83 -0
- data/ext/mri/bel-node-stack.h +26 -0
- data/ext/mri/bel-parse-statement.c +122296 -0
- data/ext/mri/bel-parse-term.c +117670 -0
- data/ext/mri/bel-parser.c +91 -0
- data/ext/mri/bel-parser.h +13 -0
- data/ext/mri/bel-token.c +161 -0
- data/ext/mri/bel-token.h +58 -0
- data/ext/mri/bel-tokenize-term.c +391 -0
- data/ext/mri/extconf.rb +8 -0
- data/ext/mri/libbel.c +5 -0
- data/ext/mri/libbel.def +26 -0
- data/lib/bel.rb +17 -0
- data/lib/bel/completion.rb +53 -0
- data/lib/bel/completion_rule.rb +236 -0
- data/lib/bel/language.rb +1052 -0
- data/lib/bel/namespace.rb +323 -0
- data/lib/bel/quoting.rb +29 -0
- data/lib/bel/rdf.rb +314 -0
- data/lib/bel/script.rb +239632 -0
- data/lib/features.rb +21 -0
- data/lib/libbel.rb +201 -0
- data/lib/libbel.so +0 -0
- data/lib/util.rb +125 -0
- metadata +269 -0
data/bel.gemspec
ADDED
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Gem::Specification.new do |spec|
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spec.name = 'bel'
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spec.version = '0.3.0.beta1'
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spec.summary = '''
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Process BEL with ruby.
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'''.gsub(%r{^\s+}, ' ').gsub(%r{\n}, '')
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spec.description = '''
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The BEL gem allows the reading, writing,
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and processing of BEL (Biological Expression
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Language) with a natural DSL.
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'''.gsub(%r{^\s+}, ' ').gsub(%r{\n}, '')
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spec.license = 'Apache-2.0'
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spec.authors = [
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'Anthony Bargnesi',
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'Natalie Catlett',
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'Nick Bargnesi',
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'William Hayes'
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]
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spec.email = [
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'abargnesi@selventa.com',
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'ncatlett@selventa.com',
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'nbargnesi@selventa.com',
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'whayes@selventa.com'
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]
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spec.files = [
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Dir.glob("lib/**/*.rb"),
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Dir.glob("ext/**/*.{c,h,def}"),
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__FILE__,
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'LICENSE',
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'INSTALL.md',
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'INSTALL_RUBY.md',
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'README.md'
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].flatten!
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spec.executables = Dir.glob('bin/*').map(&File.method(:basename))
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spec.homepage = 'https://github.com/OpenBEL/bel.rb'
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spec.rdoc_options = [
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'--title', 'BEL Ruby Documentation',
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'--main', 'README.md',
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'--line-numbers',
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'--exclude', 'lib/bel/script.rb',
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'README.md',
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'INSTALL.md',
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'INSTALL_RUBY.md',
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'LICENSE'
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]
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spec.extensions << 'ext/mri/extconf.rb'
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spec.required_ruby_version = '>= 1.9.2'
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# runtime
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spec.add_dependency 'ffi', '~> 1.9'
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# test rdf functionality
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spec.add_development_dependency 'uuid', '~> 2.3'
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spec.add_development_dependency 'addressable', '~> 2.3'
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spec.add_development_dependency 'rdf', '~> 1.1'
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# development gems
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spec.add_development_dependency 'bundler', '~> 1.7'
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spec.add_development_dependency 'rake', '~> 10.4'
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spec.add_development_dependency 'rake-compiler', '~> 0.9'
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spec.add_development_dependency 'rspec', '~> 3.2'
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spec.add_development_dependency 'yard', '~> 0.8'
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spec.add_development_dependency 'rdoc', '~> 4.2'
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end
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# vim: ts=2 sw=2:
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# encoding: utf-8
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data/bin/bel2rdf
ADDED
@@ -0,0 +1,134 @@
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#!/usr/bin/env ruby
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# bel2rdf: Convert BEL to RDF triples.
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#
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# From BEL file
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# usage: bel2rdf -b file.bel
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#
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# From file
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# usage: bel2rdf --bel [FILE]
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#
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# From standard in
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# usage: echo "<BEL DOCUMENT STRING>" | bel2rdf
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#
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# Format option
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# usage: bel2rdf --bel [FILE] --format [ntriples | nquads | turtle]
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require 'bel'
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require 'optparse'
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require 'set'
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require 'open-uri'
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# setup and parse options
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options = {
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format: 'ntriples',
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schema: false
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}
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OptionParser.new do |opts|
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opts.banner = '''Converts BEL statements to RDF triples.
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Usage: bel2rdf --bel [FILE]'''
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opts.on('-b', '--bel FILE', 'BEL file to convert. STDIN (standard in) can also be used for BEL content.') do |bel|
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options[:bel] = bel
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end
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opts.on('-f', '--format FORMAT', 'RDF file format.') do |format|
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options[:format] = format.downcase
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end
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opts.on('-s', '--[no-]schema', 'Write BEL RDF schema?') do |schema|
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options[:schema] = schema
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end
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end.parse!
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# option guards
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unless options[:bel] or not STDIN.tty?
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$stderr.puts "No bel content provided. Either use --bel option or STDIN (standard in). Use -h / --help for details."
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exit 1
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end
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if options[:bel] and not File.exists? options[:bel]
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$stderr.puts "No file for bel, #{options[:bel]}"
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exit 1
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end
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unless ['ntriples', 'nquads', 'turtle'].include? options[:format]
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$stderr.puts "Format was not one of: ntriples, nquads, or turtle"
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exit 1
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end
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class Main
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include BEL::Language
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def initialize(content, writer)
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BEL::Script.parse(content).find_all { |obj|
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obj.is_a? Statement
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}.each do |stmt|
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triples = stmt.to_rdf[1]
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triples.each do |triple|
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writer << triple
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end
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end
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end
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end
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class Serializer
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attr_reader :writer
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def initialize(stream, format)
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rdf_writer = find_writer(format)
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@writer = rdf_writer.new($stdout, {
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:stream => stream
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}
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)
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end
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def <<(trpl)
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@writer.write_statement(RDF::Statement(*trpl))
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end
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def done
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@writer.write_epilogue
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end
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private
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def find_writer(format)
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case format
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when 'nquads'
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BEL::RDF::RDF::NQuads::Writer
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when 'turtle'
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begin
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require 'rdf/turtle'
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BEL::RDF::RDF::Turtle::Writer
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rescue LoadError
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$stderr.puts """Turtle format not supported.
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Install the 'rdf-turtle' gem."""
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raise
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end
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when 'ntriples'
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BEL::RDF::RDF::NTriples::Writer
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end
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end
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end
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# create writer for format
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rdf_writer = ::Serializer.new(true, options[:format])
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# first write schema if desired
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if options[:schema]
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BEL::RDF::vocabulary_rdf.each do |trpl|
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rdf_writer << trpl
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end
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end
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# read bel content
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content =
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if options[:bel]
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File.open(options[:bel]).read
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else
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$stdin.read
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end
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# parse and write rdf
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Main.new(content, rdf_writer)
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# vim: ts=2 sw=2:
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# encoding: utf-8
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data/bin/bel_compare
ADDED
@@ -0,0 +1,177 @@
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#!/usr/bin/env ruby
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# vim: ts=2 sw=2
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require 'optparse'
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require 'bel'
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include BEL::Language
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include BEL::Namespace
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USAGE = "Usage: #{File.basename(__FILE__)} [options] [file] [file]"
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options = {}
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OptionParser.new do |opts|
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opts.banner = USAGE
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opts.on("-v", "--[no-]verbose", "Run verbosely") do |v|
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options[:verbose] = v
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end
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opts.on_tail("-h", "--help", "Show usage and options") do
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puts opts
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exit
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end
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end.parse!
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if ARGV.length != 2
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$stderr.puts "Need to specify two BEL files."
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$stderr.puts USAGE
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exit 1
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end
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def fetch_groups(bel)
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groups = {}
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active_group = nil
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BEL::Script.parse(bel) do |obj|
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if obj.is_a? BEL::Language::StatementGroup
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active_group = obj
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end
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if obj.is_a? BEL::Language::UnsetStatementGroup
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groups[obj.name] = active_group
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end
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end
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groups
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end
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threads = []
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first_groups = {}
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second_groups = {}
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threads << Thread.new {
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first_groups.update(fetch_groups(File.read(ARGV[0])))
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}
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threads << Thread.new {
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second_groups.update(fetch_groups(File.read(ARGV[1])))
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}
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threads.each { |t| t.join }
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group_diff = second_groups.length - first_groups.length
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if group_diff == 0
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puts "Equal number of statement groups."
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elsif group_diff > 0
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puts "Second file has #{group_diff} more statement groups."
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else
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puts "Second file has #{group_diff.abs} less statement groups."
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end
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first_statements = first_groups.values.
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map {|group| group.statements.map {|s| s.to_bel} }.flatten
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puts "First file has #{first_statements.length} statements."
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second_statements = second_groups.values.
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map {|group| group.statements.map {|s| s.to_bel}}.flatten
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puts "Second file has #{second_statements.length} statements."
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# statement groups in 1st, but not 2nd
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first_groups.each do |name,first|
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second = second_groups[name]
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if not second
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puts "#{name}, in 1st but not 2nd."
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end
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end
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# statement groups in 2nd, but not 1st
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second_groups.each do |name,second|
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first = first_groups[name]
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if not first
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puts "#{name}, in 2nd but not 1st."
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end
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end
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88
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# differences between statement group intersection
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first_groups.each do |name,first|
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second = second_groups[name]
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if second
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first_stmt = first.statements ? first.statements.map {|s| s.to_bel } : []
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second_stmt = second.statements ? second.statements.map {|s| s.to_bel } : []
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if first_stmt == second_stmt
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if options[:verbose]
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puts "#{name}, both contain zero statements" if first_stmt.empty?
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puts "#{name}, both contain #{first_stmt.length} statements"
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end
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else
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puts "#{name}:"
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102
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if options[:verbose]
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puts " 1st contains #{first_stmt.length} statements"
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puts " 2nd contains #{second_stmt.length} statements"
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puts " common to both, #{(first_stmt & second_stmt).length}"
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puts (first_stmt & second_stmt).map {|stmt| stmt.to_s}.join("\n ").prepend(" ")
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end
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108
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ab = first_stmt - second_stmt
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puts " statements only in 1st, #{ab.length} (1st - 2nd)"
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if ab.length > 0
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puts ab.map {|stmt| stmt.to_s}.join("\n ").prepend(" ")
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end
|
114
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|
115
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ba = second_stmt - first_stmt
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116
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puts " statements only in 2nd, #{ba.length} (2nd - 1st)"
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if ba.length > 0
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puts ba.map {|stmt| stmt.to_s}.join("\n ").prepend(" ")
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119
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end
|
120
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end
|
121
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end
|
122
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end
|
123
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|
124
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first_terms = first_groups.values.
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125
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map { |group| group.statements }.flatten.
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126
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map { |stmt|
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127
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l = [stmt.subject.to_bel]
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128
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if stmt.simple?
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129
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l << stmt.object.to_bel
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130
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elsif stmt.nested?
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131
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l << stmt.object.subject.to_bel
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l << stmt.object.object.to_bel
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133
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end
|
134
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l
|
135
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}.flatten.uniq.
|
136
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sort {|term1,term2| term1.to_s <=> term2.to_s}
|
137
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second_terms = second_groups.values.
|
138
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map { |group| group.statements }.flatten.
|
139
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map { |stmt|
|
140
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l = [stmt.subject.to_bel]
|
141
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if stmt.simple?
|
142
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l << stmt.object.to_bel
|
143
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elsif stmt.nested?
|
144
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l << stmt.object.subject.to_bel
|
145
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l << stmt.object.object.to_bel
|
146
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+
end
|
147
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l
|
148
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}.flatten.uniq.
|
149
|
+
sort {|term1,term2| term1.to_s <=> term2.to_s}
|
150
|
+
|
151
|
+
# statements
|
152
|
+
puts "Statements:"
|
153
|
+
ab = first_statements - second_statements
|
154
|
+
puts " only in 1st, #{ab.length} (1st - 2nd)"
|
155
|
+
if ab.length > 0
|
156
|
+
puts ab.map {|t| t.to_s}.join("\n ").prepend(" ")
|
157
|
+
end
|
158
|
+
|
159
|
+
ba = second_statements - first_statements
|
160
|
+
puts " only in 2nd, #{ba.length} (2nd - 1st)"
|
161
|
+
if ba.length > 0
|
162
|
+
puts ba.map {|t| t.to_s}.join("\n ").prepend(" ")
|
163
|
+
end
|
164
|
+
|
165
|
+
# terms
|
166
|
+
puts "Terms:"
|
167
|
+
ab = first_terms - second_terms
|
168
|
+
puts " only in 1st, #{ab.length} (1st - 2nd)"
|
169
|
+
if ab.length > 0
|
170
|
+
puts ab.map {|t| t.to_s}.join("\n ").prepend(" ")
|
171
|
+
end
|
172
|
+
|
173
|
+
ba = second_terms - first_terms
|
174
|
+
puts " only in 2nd, #{ba.length} (2nd - 1st)"
|
175
|
+
if ba.length > 0
|
176
|
+
puts ba.map {|t| t.to_s}.join("\n ").prepend(" ")
|
177
|
+
end
|
data/bin/bel_parse
ADDED
@@ -0,0 +1,60 @@
|
|
1
|
+
#!/usr/bin/env ruby
|
2
|
+
# bel_parse: Show parsed objects from BEL content for debugging purposes.
|
3
|
+
#
|
4
|
+
# From BEL file
|
5
|
+
# usage: bel_parse -b file.bel
|
6
|
+
#
|
7
|
+
# From standard in
|
8
|
+
# usage: echo "<BEL DOCUMENT STRING>" | bel_parse
|
9
|
+
|
10
|
+
require 'bel'
|
11
|
+
require 'optparse'
|
12
|
+
|
13
|
+
# additive String helpers
|
14
|
+
class String
|
15
|
+
def rjust_relative(distance, string)
|
16
|
+
rjust(distance - string.size + size)
|
17
|
+
end
|
18
|
+
end
|
19
|
+
|
20
|
+
# setup and parse options
|
21
|
+
options = {}
|
22
|
+
OptionParser.new do |opts|
|
23
|
+
opts.banner = "Usage: bel_parse [options] [.bel file]"
|
24
|
+
opts.on('-b', '--bel FILE', 'BEL file to parse. STDIN (standard in) can also be used for BEL content.') do |bel|
|
25
|
+
options[:bel] = bel
|
26
|
+
end
|
27
|
+
end.parse!
|
28
|
+
|
29
|
+
# option guards
|
30
|
+
unless options[:bel] or not STDIN.tty?
|
31
|
+
$stderr.puts "No bel content provided. Either use --bel option or STDIN (standard in). Use -h / --help for details."
|
32
|
+
exit 1
|
33
|
+
end
|
34
|
+
|
35
|
+
if options[:bel] and not File.exists? options[:bel]
|
36
|
+
$stderr.puts "No file for bel, #{options[:bel]}"
|
37
|
+
exit 1
|
38
|
+
end
|
39
|
+
|
40
|
+
# read bel content
|
41
|
+
content =
|
42
|
+
if options[:bel]
|
43
|
+
File.open(options[:bel]).read
|
44
|
+
else
|
45
|
+
$stdin.read
|
46
|
+
end
|
47
|
+
|
48
|
+
class Main
|
49
|
+
|
50
|
+
def initialize(content)
|
51
|
+
BEL::Script.parse(content) do |obj|
|
52
|
+
object_desc = obj.class.name.split('::').last
|
53
|
+
object_desc << obj.to_bel.rjust_relative(25, object_desc)
|
54
|
+
puts object_desc
|
55
|
+
end
|
56
|
+
end
|
57
|
+
end
|
58
|
+
Main.new(content)
|
59
|
+
# vim: ts=2 sw=2:
|
60
|
+
# encoding: utf-8
|
data/bin/bel_rdfschema
ADDED
@@ -0,0 +1,72 @@
|
|
1
|
+
#!/usr/bin/env ruby
|
2
|
+
# bel_rdfschema: Dump RDF schema for BEL.
|
3
|
+
# usage: bel_rdfschema --format [ntriples | nquads | turtle]
|
4
|
+
|
5
|
+
require 'bel'
|
6
|
+
require 'optparse'
|
7
|
+
require 'set'
|
8
|
+
require 'open-uri'
|
9
|
+
|
10
|
+
options = {
|
11
|
+
format: 'ntriples'
|
12
|
+
}
|
13
|
+
OptionParser.new do |opts|
|
14
|
+
opts.banner = '''Dumps RDF schema for BEL.
|
15
|
+
Usage: bel_rdfschema'''
|
16
|
+
|
17
|
+
opts.on('-f', '--format FORMAT', 'RDF file format.') do |format|
|
18
|
+
options[:format] = format.downcase
|
19
|
+
end
|
20
|
+
end.parse!
|
21
|
+
|
22
|
+
unless ['ntriples', 'nquads', 'turtle'].include? options[:format]
|
23
|
+
$stderr.puts "Format was not one of: ntriples, nquads, or turtle"
|
24
|
+
exit 1
|
25
|
+
end
|
26
|
+
|
27
|
+
class Serializer
|
28
|
+
attr_reader :writer
|
29
|
+
|
30
|
+
def initialize(stream, format)
|
31
|
+
rdf_writer = find_writer(format)
|
32
|
+
@writer = rdf_writer.new($stdout, {
|
33
|
+
:stream => stream
|
34
|
+
}
|
35
|
+
)
|
36
|
+
end
|
37
|
+
|
38
|
+
def <<(trpl)
|
39
|
+
@writer.write_statement(RDF::Statement(*trpl))
|
40
|
+
end
|
41
|
+
|
42
|
+
def done
|
43
|
+
@writer.write_epilogue
|
44
|
+
end
|
45
|
+
|
46
|
+
private
|
47
|
+
|
48
|
+
def find_writer(format)
|
49
|
+
case format
|
50
|
+
when 'nquads'
|
51
|
+
BEL::RDF::RDF::NQuads::Writer
|
52
|
+
when 'turtle'
|
53
|
+
begin
|
54
|
+
require 'rdf/turtle'
|
55
|
+
BEL::RDF::RDF::Turtle::Writer
|
56
|
+
rescue LoadError
|
57
|
+
$stderr.puts """Turtle format not supported.
|
58
|
+
Install the 'rdf-turtle' gem."""
|
59
|
+
raise
|
60
|
+
end
|
61
|
+
when 'ntriples'
|
62
|
+
BEL::RDF::RDF::NTriples::Writer
|
63
|
+
end
|
64
|
+
end
|
65
|
+
end
|
66
|
+
|
67
|
+
@rdf_writer = ::Serializer.new(true, options[:format])
|
68
|
+
BEL::RDF::vocabulary_rdf.each do |trpl|
|
69
|
+
@rdf_writer << trpl
|
70
|
+
end
|
71
|
+
# vim: ts=2 sw=2:
|
72
|
+
# encoding: utf-8
|