diff options
Diffstat (limited to 'lib/parser.rb')
| -rw-r--r-- | lib/parser.rb | 41 |
1 files changed, 27 insertions, 14 deletions
diff --git a/lib/parser.rb b/lib/parser.rb index 27dfeee..2f59d15 100644 --- a/lib/parser.rb +++ b/lib/parser.rb @@ -41,17 +41,17 @@ module OpenTox ##uri += "?subjectid=#{CGI.escape(subjectid)}" if subjectid ## `rapper -i rdfxml -o ntriples #{uri} 2>/dev/null`.each_line do |line| file = Tempfile.new("ot-rdfxml") - file.puts OpenTox::RestClientWrapper.get @uri,{:subjectid => subjectid,:accept => "application/rdf+xml"} + file.puts OpenTox::RestClientWrapper.get @uri,{:subjectid => subjectid,:accept => "application/rdf+xml"},nil,false file.close - file = "file://"+file.path statements = [] parameter_ids = [] - `rapper -i rdfxml -o ntriples #{file} 2>/dev/null`.each_line do |line| + `rapper -i rdfxml -o ntriples file://#{file.path} 2>/dev/null`.each_line do |line| triple = line.to_triple @metadata[triple[1]] = triple[2].split('^^').first if triple[0] == @uri and triple[1] != RDF['type'] statements << triple parameter_ids << triple[2] if triple[1] == OT.parameters end + File.delete(file.path) unless parameter_ids.empty? @metadata[OT.parameters] = [] parameter_ids.each do |p| @@ -63,18 +63,17 @@ module OpenTox @metadata end - # loads metadata from rdf-data + # creates owl object from rdf-data # @param [String] rdf # @param [String] type of the info (e.g. OT.Task, OT.ErrorReport) needed to get the subject-uri - # @return [Hash] metadata - def self.metadata_from_rdf( rdf, type ) + # @return [Owl] with uri and metadata set + def self.from_rdf( rdf, type ) # write to file and read convert with rapper into tripples file = Tempfile.new("ot-rdfxml") file.puts rdf file.close - file = "file://"+file.path #puts "cmd: rapper -i rdfxml -o ntriples #{file} 2>/dev/null" - triples = `rapper -i rdfxml -o ntriples #{file} 2>/dev/null` + triples = `rapper -i rdfxml -o ntriples file://#{file.path} 2>/dev/null` # load uri via type uri = nil @@ -85,19 +84,23 @@ module OpenTox uri = triple[0] end end - + File.delete(file) # load metadata 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 - metadata + owl = Owl::Generic.new(uri) + owl.metadata = metadata + owl end - + # Generic parser for all OpenTox classes class Generic include Owl + + attr_accessor :uri, :metadata end # OWL-DL parser for datasets @@ -128,12 +131,21 @@ module OpenTox # @return [Hash] Internal dataset representation def load_uri(subjectid=nil) uri = @uri - uri += "?subjectid=#{CGI.escape(subjectid)}" if subjectid + + # 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 #{file} 2>/dev/null`.each_line do |line| + file = Tempfile.new("ot-rdfxml") + file.puts OpenTox::RestClientWrapper.get @uri,{:subjectid => subjectid,:accept => "application/rdf+xml"},nil,false + file.close + data = {} feature_values = {} feature = {} other_statements = {} - `rapper -i rdfxml -o ntriples #{uri} 2>/dev/null`.each_line do |line| + `rapper -i rdfxml -o ntriples file://#{file.path} 2>/dev/null`.each_line do |line| triple = line.chomp.split(' ',3) triple = triple[0..2].collect{|i| i.sub(/\s+.$/,'').gsub(/[<>"]/,'')} case triple[1] @@ -150,6 +162,7 @@ module OpenTox else end end + File.delete(file.path) data.each do |id,entry| entry[:values].each do |value_id| value = feature_values[value_id].split(/\^\^/).first # remove XSD.type @@ -157,7 +170,7 @@ module OpenTox end end load_features - @dataset.metadata = load_metadata + @dataset.metadata = load_metadata(subjectid) @dataset end |