Module: BioVcf::Turtle

Defined in:
lib/bio-vcf/vcfrdf.rb

Class Method Summary collapse

Class Method Details

.identifier(id) ⇒ Object 



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# File 'lib/bio-vcf/vcfrdf.rb', line 86

def Turtle::identifier(id)
  raise "Illegal identifier #{id}" if id != Turtle::mangle_identifier(id)
end

.mangle_identifier(s) ⇒ Object

Replace letters/symbols that are not allowed in a Turtle identifier (short hand URI). This should be the definite mangler and replace the ones in bioruby-table and bio-exominer. Manglers are useful when using data from other sources and trying to transform them into simple RDF identifiers.



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# File 'lib/bio-vcf/vcfrdf.rb', line 96

def Turtle::mangle_identifier(s)
  id = s.strip.gsub(/[^[:print:]]/, '').gsub(/[#)(,]/,"").gsub(/[%]/,"perc").gsub(/(\s|\.|\$|\/|\\|\>)+/,"_")
  id = id.gsub(/\[|\]/,'')
  # id = URI::escape(id)
  id = id.gsub(/\|/,'_')
  id = id.gsub(/\-|:/,'_')
  if id != s 
    # Don't want Bio depency in templates!
    # logger = Bio::Log::LoggerPlus.new 'bio-rdf'
    # logger.warn "\nWARNING: Changed identifier <#{s}> to <#{id}>"
    # $stderr.print "\nWARNING: Changed identifier <#{s}> to <#{id}>"
  end
  if not RDF::valid_uri?(id)
    raise "Invalid URI after mangling <#{s}> to <#{id}>!"
  end
  valid_id = if id =~ /^\d/
               'r' + id
             else
               id
             end
  valid_id  # we certainly hope so!
end

.stringify_literal(literal) ⇒ Object 



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# File 'lib/bio-vcf/vcfrdf.rb', line 82

def Turtle::stringify_literal(literal)
  RDF::stringify_literal(literal)
end