diff options
Diffstat (limited to 'lib/serializer.rb')
| -rw-r--r-- | lib/serializer.rb | 69 |
1 files changed, 35 insertions, 34 deletions
diff --git a/lib/serializer.rb b/lib/serializer.rb index 3def252..3a9cb60 100644 --- a/lib/serializer.rb +++ b/lib/serializer.rb @@ -30,7 +30,6 @@ module OpenTox OT.dataEntry => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } , OT.acceptValue => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } , OT.values => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } , - #XSD.anyUri => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } , OT.algorithm => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } , OT.parameters => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } , @@ -38,14 +37,15 @@ module OpenTox DC.identifier => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } , DC.contributor => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } , DC.creator => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } , + DC.description => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } , OT.isA => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } , + OT.Warnings => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } , + XSD.anyURI => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } , OT.hasSource => { RDF["type"] => [{ "type" => "uri", "value" => OWL.DatatypeProperty }] } , OT.value => { RDF["type"] => [{ "type" => "uri", "value" => OWL.DatatypeProperty }] } , OT.paramScope => { RDF["type"] => [{ "type" => "uri", "value" => OWL.DatatypeProperty }] } , OT.paramValue => { RDF["type"] => [{ "type" => "uri", "value" => OWL.DatatypeProperty }] } , - - #Untyped Individual: http://localhost/algorithm } @data_entries = {} @@ -61,15 +61,10 @@ module OpenTox end def add_compound(uri) - #@classes << OT.Compound unless @classes.include? OT.Compound @object[uri] = { RDF["type"] => [{ "type" => "uri", "value" => OT.Compound }] } end def add_feature(uri,metadata) - #@classes << OT.Feature unless @classes.include? OT.Feature - #@classes << OT.NominalFeature unless @classes.include? OT.NominalFeature - #@classes << OT.NumericFeature unless @classes.include? OT.NumericFeature - #@classes << OT.StringFeature unless @classes.include? OT.StringFeature @object[uri] = { RDF["type"] => [{ "type" => "uri", "value" => OT.Feature }] } add_metadata uri, metadata end @@ -94,32 +89,37 @@ module OpenTox end - def add_algorithm(uri,metadata,parameters) + def add_algorithm(uri,metadata) @object[uri] = { RDF["type"] => [{ "type" => "uri", "value" => OT.Algorithm }] } + LOGGER.debug @object[uri] add_metadata uri, metadata - add_parameters uri, parameters - #metadata.each { |u,v| @object[uri][u] = [{"type" => type(v), "value" => v }] } + LOGGER.debug @object[uri] end - def add_model(uri,metadata) + def add_model(uri,metadata,parameters) + @object[uri] = { RDF["type"] => [{ "type" => "uri", "value" => OT.Model }] } + add_metadata uri, metadata + add_parameters uri, parameters end def add_metadata(uri,metadata) - #@object[uri] = { RDF["type"] => [{ "type" => "uri", "value" => OT[type] }] } + id = 0 metadata.each do |u,v| - @object[uri][u] = [{"type" => type(v), "value" => v }] - end - end - - def add_parameters(uri,parameters) - #@object[uri] = { RDF["type"] => [{ "type" => "uri", "value" => OT[type] }] } - @object[uri][OT.parameters] = [] unless @object[uri][OT.parameters] - parameters.each do |p| - parameter = "_:parameter#{@parameter_id}" - @parameter_id += 1 - @object[uri][OT.parameters] << {"type" => "bnode", "value" => parameter} - @object[parameter] = { RDF["type"] => [{ "type" => "uri", "value" => OT.Parameter }] } - add_metadata parameter, p + if v.is_a? String + @object[uri] = {} unless @object[uri] + @object[uri][u] = [{"type" => type(v), "value" => v }] + elsif v.is_a? Array and u == OT.parameters + @object[uri][u] = [] unless @object[uri][u] + v.each do |value| + id+=1 + genid = "_:genid#{id}" + @object[uri][u] << {"type" => "bnode", "value" => genid} + @object[genid] = { RDF["type"] => [{ "type" => "uri", "value" => OT.Parameter}] } + value.each do |name,entry| + @object[genid][name] = [{"type" => type(entry), "value" => entry }] + end + end + end end end @@ -158,10 +158,11 @@ module OpenTox # Serializers - def ntriples + def to_ntriples #rdf_types @triples = Set.new + #LOGGER.debug @object.to_yaml @object.each do |s,entry| s = url(s) if type(s) == "uri" entry.each do |p,objects| @@ -182,12 +183,12 @@ module OpenTox @triples.sort.collect{ |s| s.join(' ').concat(" .") }.join("\n")+"\n" end - def rdfxml - Tempfile.open("owl-serializer"){|f| f.write(ntriples); @path = f.path} - `rapper -i ntriples -o rdfxml #{@path}` + def to_rdfxml + Tempfile.open("owl-serializer"){|f| f.write(self.to_ntriples); @path = f.path} + `rapper -i ntriples -o rdfxml #{@path} 2>/dev/null` end - def json + def to_json #rdf_types Yajl::Encoder.encode(@object) end @@ -258,7 +259,7 @@ module OpenTox @rows.first << features @rows.first.flatten! dataset.data_entries.each do |compound,entries| - smiles = Compound.new(compound).smiles + smiles = Compound.new(compound).to_smiles row = Array.new(@rows.first.size) row[0] = smiles entries.each do |feature, values| @@ -271,11 +272,11 @@ module OpenTox end end - def csv + def to_csv @rows.collect{|r| r.join(", ")}.join("\n") end - def excel + def to_xls Spreadsheet.client_encoding = 'UTF-8' book = Spreadsheet::Workbook.new sheet = book.create_worksheet(:name => '') |