Module: OpenTox::Parser::Owl

Included in:
Dataset, Generic
Defined in:
lib/parser.rb

Overview

OWL-DL parser

Defined Under Namespace

Classes: Dataset, Generic

Class Method Summary collapse

Instance Method Summary collapse

Class Method Details

.from_rdf(rdf, type, allow_multiple = false) ⇒ Owl

creates owl object from rdf-data

Parameters:

  • rdf (String)
  • type (String) —

    of the info (e.g. OT.Task, OT.ErrorReport) needed to get the subject-uri

Returns:

  • (Owl) —

    with uri and metadata set



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# File 'lib/parser.rb', line 89

def self.from_rdf( rdf, type, allow_multiple = false )

  uris = Array.new
  owls = Array.new

  # write to file and read convert with rapper into tripples
  file = Tempfile.new("ot-rdfxml")
  file.puts rdf
  file.close
  #puts "cmd: rapper -i rdfxml -o ntriples #{file} 2>/dev/null"
  triples = `rapper -i rdfxml -o ntriples #{file.path} 2>/dev/null`
  
  # load uri via type
  uri = nil
  triples.each_line do |line|
    triple = line.to_triple
    if triple[1] == RDF['type'] and triple[2]==type
       if !allow_multiple
         raise "uri already set, two uris found with type: "+type.to_s if uri
       end
       uri = triple[0]
       uris << uri
    end
  end
  File.delete(file.path)

  # load metadata
  uris.each { |uri|
    metadata = {}
    triples.each_line do |line|
      triple = line.to_triple
      metadata[triple[1]] = triple[2].split('^^').first if triple[0] == uri and triple[1] != RDF['type']
    end
    owl = Owl::Generic.new(uri)
    owl.metadata = metadata
    owls << owl
  }
  allow_multiple ? owls : owls[0]
end

Instance Method Details

#initialize(uri) ⇒ OpenTox::Parser::Owl

Create a new OWL-DL parser

Parameters:

  • uri —

    URI of OpenTox object

Returns:



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# File 'lib/parser.rb', line 25

def initialize(uri)
  @uri = uri
  @metadata = {}
end

#load_metadata(subjectid = nil) ⇒ Hash

Read metadata from opentox service

Returns:

  • (Hash) —

    Object metadata



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# File 'lib/parser.rb', line 32

def load_metadata(subjectid=nil)
  # avoid using rapper directly because of 2 reasons:
  # * http errors wont be noticed
  # * subjectid cannot be sent as header
  ##uri += "?subjectid=#{CGI.escape(subjectid)}" if subjectid 
  ## `rapper -i rdfxml -o ntriples #{uri} 2>/dev/null`.each_line do |line|
  if File.exist?(@uri)
    file = File.new(@uri)
  else
    file = Tempfile.new("ot-rdfxml")
    if @dataset
      uri = URI::parse(@uri)
      #remove params like dataset/<id>?max=3 from uri, not needed for metadata
      uri.query = nil 
      uri.path = File.join(uri.path,"metadata")
      uri = uri.to_s
    else
      uri = @uri
    end
    file.puts OpenTox::RestClientWrapper.get uri,{:subjectid => subjectid,:accept => "application/rdf+xml"},nil,false
    file.close
    to_delete = file.path
  end
  statements = []
  parameter_ids = []
  `rapper -i rdfxml -o ntriples #{file.path} 2>/dev/null`.each_line do |line|
    triple = line.to_triple
    if triple[0] == @uri
      if triple[1] == RDF.type || triple[1]==OT.predictedVariables || triple[1]==OT.independentVariables # allow multiple types
        @metadata[triple[1]] = [] unless @metadata[triple[1]]
        @metadata[triple[1]] << triple[2].split('^^').first
      else
        @metadata[triple[1]] = triple[2].split('^^').first
      end
    end
    statements << triple 
    parameter_ids << triple[2] if triple[1] == OT.parameters
  end
  File.delete(to_delete) if to_delete
  unless parameter_ids.empty?
    @metadata[OT.parameters] = []
    parameter_ids.each do |p|
      parameter = {}
      statements.each{ |t| parameter[t[1]] = t[2] if t[0] == p and t[1] != RDF['type']}
      @metadata[OT.parameters] << parameter
    end
  end
  #@metadata.each do |k,v|
    #v = v.first if v and v.size == 1
  #end
  @metadata
end