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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
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