Module: BioExominer::RDF

Defined in:
lib/bio-exominer/rdf.rb

Overview

FIXME: use bioruby-rdf modules instead! It is all there now.

Class Method Summary collapse

Class Method Details

.make_identifier(s) ⇒ Object

An identifier is used for the subject and predicate in RDF. This is a case-sensitive (shortened) URI. You can change default behaviour for identifiers using the options –transform-ids (i.e. in the input side, rather than the output side)



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# File 'lib/bio-exominer/rdf.rb', line 16

def RDF::make_identifier(s)
  id = s.strip.gsub(/[^[:print:]]/, '').gsub(/[#)(,]/,"").gsub(/[%]/,"perc").gsub(/(\s|\.|\$|\/|\\)+/,"_")
  # id = URI::escape(id)
  id = id.gsub(/\|/,'_')
  id = id.gsub(/\-|:/,'_')
  if id != s 
    # logger = Bio::Log::LoggerPlus['bio-table']
    $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
end

.valid_uri?(uri) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/bio-exominer/rdf.rb', line 8

def RDF::valid_uri? uri
  uri =~ /^([!#$&-;=?_a-z~]|%[0-9a-f]{2})+$/i
end