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Diffstat (limited to 'lib/serializer.rb')
| -rw-r--r-- | lib/serializer.rb | 491 |
1 files changed, 0 insertions, 491 deletions
diff --git a/lib/serializer.rb b/lib/serializer.rb deleted file mode 100644 index 5a9fd0a..0000000 --- a/lib/serializer.rb +++ /dev/null @@ -1,491 +0,0 @@ -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.Model => { 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'] }] } , - OTA.PatternMiningSupervised => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } , - OTA.ClassificationLazySingleTarget => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } , - OTA.RegressionLazySingleTarget => { 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.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 }] } , - OT.featureDataset => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } , - OT.dependentVariables => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } , - OT.predictedVariables => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } , - OT.paramValue => { 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 }] } , - OT.acceptValue => { 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.weightedAccuracy => { 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 - @object[metadata[OT.featureDataset]] = { RDF["type"] => [{ "type" => "uri", "value" => OT.Dataset }] } - @object[metadata[OT.trainingDataset]] = { RDF["type"] => [{ "type" => "uri", "value" => OT.Dataset }] } - @object[metadata[OT.dependentVariables]] = { RDF["type"] => [{ "type" => "uri", "value" => OT.Feature }] } - metadata[OT.predictedVariables].each{|feature| @object[feature] = { RDF["type"] => [{ "type" => "uri", "value" => OT.Feature }] }} - # TODO: add algorithms from parameters - @object["http://ot-dev.in-silico.ch/algorithm/fminer/bbrc"] = { RDF["type"] => [{ "type" => "uri", "value" => OT.Algorithm }] } - @object["http://ot-dev.in-silico.ch/algorithm/fminer/last"] = { RDF["type"] => [{ "type" => "uri", "value" => OT.Algorithm }] } - @object["http://ot-dev.in-silico.ch/algorithm/lazar"] = { RDF["type"] => [{ "type" => "uri", "value" => OT.Algorithm }] } - 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 or u == RDF.type) - if v.is_a? Array and u == OT.parameters#or u == RDF.type) - @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 - elsif v.is_a? Array #and u == RDF.type - @object[uri] = {} unless @object[uri] - v.each do |value| - @object[uri][u] = [] unless @object[uri][u] - @object[uri][u] << {"type" => type(value), "value" => value } - end - elsif 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) } - #@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} - # TODO: add base uri for ist services - `rapper -i ntriples -f 'xmlns:ot="#{OT.uri}"' -f 'xmlns:ota="#{OTA.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 |