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Diffstat (limited to 'lib/serializer.rb')
| -rw-r--r-- | lib/serializer.rb | 469 |
1 files changed, 469 insertions, 0 deletions
diff --git a/lib/serializer.rb b/lib/serializer.rb new file mode 100644 index 0000000..44b4414 --- /dev/null +++ b/lib/serializer.rb @@ -0,0 +1,469 @@ +require 'spreadsheet' +require 'yajl' + +module OpenTox + + # Serialzer for various oputput formats + module Serializer + + # OWL-DL Serializer, modelled according to to http://n2.talis.com/wiki/RDF_JSON_Specification + class Owl + + attr_accessor :object + + def initialize + + @object = { + # this should come from opentox.owl + OT.Compound => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } , + OT.Feature => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } , + OT.NominalFeature => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } , + OT.NumericFeature => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } , + OT.StringFeature => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } , + OT.Dataset => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } , + OT.DataEntry => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } , + OT.FeatureValue => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } , + OT.Algorithm => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } , + OT.Parameter => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } , + OT.Task => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } , + #classes for validation + OT.Validation => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } , + OT.ClassificationStatistics => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } , + OT.ConfusionMatrix => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } , + OT.ConfusionMatrixCell => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } , + OT.ClassValueStatistics => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } , + OT.RegressionStatistics => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } , + OT.Crossvalidation => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } , + OT.CrossvalidationInfo => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } , + OT.ErrorReport => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } , + + OT.compound => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } , + OT.feature => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } , + 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 }] } , + OT.algorithm => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } , + OT.parameters => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } , + #object props for validation# + OT.model => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } , + OT.trainingDataset => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } , + OT.predictionFeature => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } , + OT.predictionDataset => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } , + OT.crossvalidation => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } , + OT.testTargetDataset => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } , + OT.testDataset => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } , + OT.classificationStatistics => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } , + OT.confusionMatrix => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } , + OT.confusionMatrixCell => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } , + OT.classValueStatistics => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } , + OT.regressionStatistics => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } , + OT.validation => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } , + OT.crossvalidationInfo => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } , + OT.dataset => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } , + + DC.title => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } , + 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 }] } , + DC.date => { 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.hasStatus => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } , + OT.resultURI => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } , + OT.percentageCompleted => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } , + # annotation props for validation + OT.numUnpredicted => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } , + OT.crossvalidationFold => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } , + OT.numInstances => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } , + OT.numWithoutClass => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } , + OT.percentWithoutClass => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } , + OT.percentUnpredicted => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } , + OT.confusionMatrixActual => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } , + OT.confusionMatrixPredicted => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } , + OT.confusionMatrixValue => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } , + OT.numIncorrect => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } , + OT.percentCorrect => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } , + OT.numCorrect => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } , + OT.accuracy => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } , + OT.trueNegativeRate => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } , + OT.truePositiveRate => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } , + OT.falseNegativeRate => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } , + OT.falsePositiveRate => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } , + OT.numTrueNegatives => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } , + OT.numTruePositives => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } , + OT.numFalseNegatives => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } , + OT.numFalsePositives => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } , + OT.classValue => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } , + OT.precision => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } , + OT.areaUnderRoc => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } , + OT.weightedAreaUnderRoc => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } , + OT.fMeasure => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } , + OT.percentIncorrect => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } , + OT.validationType => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } , + OT.realRuntime => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } , + OT.sampleCorrelationCoefficient => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } , + OT.targetVarianceActual => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } , + OT.targetVariancePredicted => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } , + OT.meanAbsoluteError => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } , + OT.sumSquaredError => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } , + OT.rootMeanSquaredError => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } , + OT.rSquare => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } , + OT.stratified => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } , + OT.numFolds => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } , + OT.randomSeed => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } , + OT.reportType => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } , + OT.message => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } , + OT.statusCode => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } , + OT.actor => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } , + OT.errorCode => { 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 }] } , + } + + @data_entries = {} + @values_id = 0 + @parameter_id = 0 + + @classes = Set.new + @object_properties = Set.new + @annotation_properties = Set.new + @datatype_properties = Set.new + + @objects = Set.new + end + + # Add a compound + # @param [String] uri Compound URI + def add_compound(uri) + @object[uri] = { RDF["type"] => [{ "type" => "uri", "value" => OT.Compound }] } + end + + # Add a feature + # @param [String] uri Feature URI + def add_feature(uri,metadata) + @object[uri] = { RDF["type"] => [{ "type" => "uri", "value" => OT.Feature }] } + add_metadata uri, metadata + end + + # Add a dataset + # @param [String] uri Dataset URI + def add_dataset(dataset) + + @dataset = dataset.uri + + @object[dataset.uri] = { RDF["type"] => [{ "type" => "uri", "value" => OT.Dataset }] } + + add_metadata dataset.uri, dataset.metadata + + dataset.compounds.each { |compound| add_compound compound } + + dataset.features.each { |feature,metadata| add_feature feature,metadata } + + dataset.data_entries.each do |compound,entry| + entry.each do |feature,values| + values.each { |value| add_data_entry compound,feature,value } + end + end + + end + + # Add a algorithm + # @param [String] uri Algorithm URI + def add_algorithm(uri,metadata) + @object[uri] = { RDF["type"] => [{ "type" => "uri", "value" => OT.Algorithm }] } + add_metadata uri, metadata + end + + # Add a model + # @param [String] uri Model URI + def add_model(uri,metadata) + @object[uri] = { RDF["type"] => [{ "type" => "uri", "value" => OT.Model }] } + add_metadata uri, metadata + end + + # Add a task + # @param [String] uri Model URI + def add_task(uri,metadata) + @object[uri] = { RDF["type"] => [{ "type" => "uri", "value" => OT.Task }] } + add_metadata uri, metadata + end + + # Add a resource defined by resource_class and content + # (see documentation of add_content for example) + # @param [String] uri of resource + # @param [String] resource class, e.g. OT.Validation + # @param [Hash] content as hash + def add_resource(uri, resource_class, content) + @object[uri] = { RDF["type"] => [{ "type" => "uri", "value" => resource_class }] } + @@content_id = 1 + add_content uri, content + end + + private + @@content_id = 1 + + # Recursiv function to add content + # @example + # { DC.description => "bla", + # OT.similar_resources => [ "http://uri1", "http://uri2" ], + # OT.matrixCells => + # [ { RDF.type => OT.MatrixCell, OT.cellIndex=1 OT.cellValue => "xy" }, + # { RDF.type => OT.MatrixCell, OT.cellIndex=2 OT.cellValue => "z" } ], + # OT.info => { RDF.type => OT.ImportantInfo, + # DC.description => "blub" } + # } + # @param [String] uri + # @param [Hash] content as hash, uri must already have been added to @object + def add_content(uri, hash) + raise "content is no hash: "+hash.class.to_s unless hash.is_a?(Hash) + hash.each do |u,v| + if v.is_a? Hash + # value is again a hash, i.e. a new owl class is added + # first make sure type (==class) is set + type = v[RDF.type] + raise "type missing for "+u.to_s+" content:\n"+v.inspect unless type + raise "class unknown "+type.to_s+" (for "+u.to_s+")" unless @object.has_key?(type) + # create new node and add to current uri + genid = "_:#{type.split('#')[-1]}#{@@content_id}" + @@content_id += 1 + @object[uri] = {} unless @object[uri] + @object[uri][u] = [{ "type" => "bnode", "value" => genid }] + # add content to new class + add_content(genid,v) + elsif v.is_a? Array + # value is an array, i.e. a list of values with property is added + v.each{ |vv| add_content( uri, { u => vv } ) } + else # v.is_a? String + # simple string value + @object[uri] = {} unless @object[uri] + @object[uri][u] = [] unless @object[uri][u] + raise "property unknown "+u.to_s if !@object.has_key?(u) and u!=RDF.type + # use << to allow different values for one property + @object[uri][u] << {"type" => type(v), "value" => v } + end + end + end + + public + + # Add metadata + # @param [Hash] metadata + def add_metadata(uri,metadata) + id = 0 + metadata.each do |u,v| + if 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 + else # v.is_a? String + @object[uri] = {} unless @object[uri] + @object[uri][u] = [{"type" => type(v), "value" => v }] + end + end + end + + # Add a data entry + # @param [String] compound Compound URI + # @param [String] feature Feature URI + # @param [Boolead,Float] value Feature value + def add_data_entry(compound,feature,value) + add_compound(compound) unless @object[compound] + add_feature(feature,{}) unless @object[feature] + unless data_entry = @data_entries[compound] + data_entry = "_:dataentry#{@data_entries.size}" + @data_entries[compound] = data_entry + @object[@dataset][OT.dataEntry] = [] unless @object[@dataset][OT.dataEntry] + @object[@dataset][OT.dataEntry] << {"type" => "bnode", "value" => data_entry} + @object[data_entry] = { + RDF["type"] => [{ "type" => "uri", "value" => OT.DataEntry }], + OT.compound => [{ "type" => "uri", "value" => compound }], + OT.values => [], + } + end + values = "_:values#{@values_id}" + @values_id += 1 + @object[data_entry][OT.values] << {"type" => "bnode", "value" => values} + case type(value) + when "uri" + v = [{ "type" => "uri", "value" => value}] + when "literal" + v = [{ "type" => "literal", "value" => value, "datatype" => datatype(value) }] + else + raise "Illegal type #{type(value)} for #{value}." + end + @object[values] = { + RDF["type"] => [{ "type" => "uri", "value" => OT.FeatureValue }], + OT.feature => [{ "type" => "uri", "value" => feature }], + OT.value => v + } + @object[feature][RDF["type"]] << { "type" => "uri", "value" => featuretype(value) } + end + + # Serializers + + # Convert to N-Triples + # @return [text/plain] Object OWL-DL in N-Triples format + def to_ntriples + + @triples = Set.new + @object.each do |s,entry| + s = url(s) if type(s) == "uri" + entry.each do |p,objects| + p = url(p) + objects.each do |o| + case o["type"] + when "uri" + o = url(o["value"]) + when "literal" + o = literal(o["value"],datatype(o["value"])) + when "bnode" + o = o["value"] + end + @triples << [s,p,o] + end + end + end + @triples.sort.collect{ |s| s.join(' ').concat(" .") }.join("\n")+"\n" + end + + # Convert to RDF/XML + # @return [text/plain] Object OWL-DL in RDF/XML format + def to_rdfxml + Tempfile.open("owl-serializer"){|f| f.write(self.to_ntriples); @path = f.path} + `rapper -i ntriples -f 'xmlns:ot="#{OT.uri}"' -f 'xmlns:dc="#{DC.uri}"' -f 'xmlns:rdf="#{RDF.uri}"' -f 'xmlns:owl="#{OWL.uri}"' -o rdfxml #{@path} 2>/dev/null` + end + + # Convert to JSON as specified in http://n2.talis.com/wiki/RDF_JSON_Specification + # (Ambit services use a different JSON representation) + # @return [text/plain] Object OWL-DL in JSON format + def to_json + #rdf_types + Yajl::Encoder.encode(@object) + end + + # Helpers for type detection + private + + def datatype(value) + if value.is_a? TrueClass or value.is_a? FalseClass + XSD.boolean + elsif value.is_a? Float + XSD.float + else + XSD.string + end + end + + def featuretype(value) + if value.is_a? TrueClass or value.is_a? FalseClass + datatype = OT.NominalFeature + elsif value.is_a? Float + datatype = OT.NumericFeature + else + datatype = OT.StringFeature + end + end + + def type(value) + begin + uri = URI.parse(value) + if uri.class == URI::HTTP or uri.class == URI::HTTPS + "uri" + elsif value.match(/^_/) + "bnode" + else + "literal" + end + rescue + "literal" + end + end + + def literal(value,type) + # concat and << are faster string concatination operators than + + '"'.concat(value.to_s).concat('"^^<').concat(type).concat('>') + end + + def url(uri) + # concat and << are faster string concatination operators than + + '<'.concat(uri).concat('>') + end + + def rdf_types + @classes.each { |c| @object[c] = { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } } + @object_properties.each { |p| @object[p] = { RDF["type"] => [{ "type" => "uri", "value" => OWL['ObjectProperty'] }] } } + @annotation_properties.each { |a| @object[a] = { RDF["type"] => [{ "type" => "uri", "value" => OWL['AnnotationProperty'] }] } } + @datatype_properties.each { |d| @object[d] = { RDF["type"] => [{ "type" => "uri", "value" => OWL['DatatypeProperty'] }] } } + end + + end + + # Serializer for spreadsheet formats + class Spreadsheets # to avoid nameclash with Spreadsheet gem + + # Create a new spreadsheet serializer + # @param [OpenTox::Dataset] dataset Dataset object + def initialize(dataset) + @rows = [] + @rows << ["SMILES"] + features = dataset.features.keys + @rows.first << features + @rows.first.flatten! + dataset.data_entries.each do |compound,entries| + smiles = Compound.new(compound).to_smiles + row = Array.new(@rows.first.size) + row[0] = smiles + entries.each do |feature, values| + i = features.index(feature)+1 + values.each do |value| + if row[i] + row[i] = "#{row[i]} #{value}" # multiple values + else + row[i] = value + end + end + end + @rows << row + end + end + + # Convert to CSV string + # @return [String] CSV string + def to_csv + @rows.collect{|r| r.join(", ")}.join("\n") + end + + # Convert to spreadsheet workbook + # @return [Spreadsheet::Workbook] Workbook object (use the spreadsheet gemc to write a file) + def to_spreadsheet + Spreadsheet.client_encoding = 'UTF-8' + book = Spreadsheet::Workbook.new + sheet = book.create_worksheet(:name => '') + sheet.column(0).width = 100 + i = 0 + @rows.each do |row| + row.each do |c| + sheet.row(i).push c + end + i+=1 + end + book + end + + end + + + end +end |