diff options
Diffstat (limited to 'lib/dataset.rb')
| -rw-r--r-- | lib/dataset.rb | 239 |
1 files changed, 225 insertions, 14 deletions
diff --git a/lib/dataset.rb b/lib/dataset.rb index fe49622..fad6baa 100644 --- a/lib/dataset.rb +++ b/lib/dataset.rb @@ -1,23 +1,184 @@ module OpenTox - class Dataset < OpenTox + class Dataset + include Owl - # Initialize with <tt>:uri => uri</tt> or <tt>:name => name</tt> (creates a new dataset) - def initialize(uri) - super(uri) + #attr_accessor :model + + def initialize + super + end + + # find or create a new compound and return the resource + def find_or_create_compound(uri) + compound = @model.subject(DC["identifier"], uri) + if compound.nil? + compound = @model.create_resource + @model.add compound, RDF['type'], OT["Compound"] + @model.add compound, DC["identifier"], uri + end + compound + end + + # find or create a new feature and return the resource + def find_or_create_feature(f) + feature = @model.subject(DC["title"], f[:name].to_s) + if feature.nil? + feature = @model.create_resource + @model.add feature, RDF['type'], OT["Feature"] + @model.add feature, DC["identifier"], File.join("feature",feature.to_s.gsub(/[()]/,'')) # relative uri as we don know the final uri + @model.add feature, DC["title"], f[:name].to_s + @model.add feature, OT['hasSource'], f[:source].to_s if f[:source] + end + feature + end + + # find or create a new value and return the resource + def find_or_create_value(v) + value = @model.subject OT["value"], v.to_s + if value.nil? + value = @model.create_resource + @model.add value, RDF['type'], OT["FeatureValue"] + @model.add value, OT["value"], v.to_s + end + value + end + + def tuple?(t) + statements = [] + has_tuple = true + t.each do |name,v| + feature = self.find_or_create_feature(:name => name) + value = self.find_or_create_value(v) + tuple = @model.subject(feature,value) + has_tuple = false if tuple.nil? + statements << [tuple,feature,value] + end + tuples_found = statements.collect{|s| s[0]}.uniq + has_tuple = false unless tuples_found.size == 1 + has_tuple end - def self.create(data) - uri = RestClient.post @@config[:services]["opentox-dataset"], data, :content_type => 'application/rdf+xml' - Dataset.new(uri.to_s) + def create_tuple(t) + tuple = @model.create_resource + @model.add tuple, RDF['type'], OT["Tuple"] + t.each do |name,value| + feature = self.find_or_create_feature(:name => name) + value = self.find_or_create_value(value) + pair = @model.create_resource + @model.add tuple, OT['tuple'], pair + @model.add pair, OT['feature'], feature + @model.add pair, OT['value'], value + end + tuple + end + + def find_or_create_tuple(t) + if self.tuple?(t) + t + else + self.create_tuple(t) + end + end + + def add_data_entry(compound,feature,value) + data_entry = @model.create_resource + @model.add data_entry, RDF['type'], OT["DataEntry"] + @model.add data_entry, OT['compound'], compound + @model.add data_entry, OT['feature'], feature + @model.add data_entry, OT['values'], value + end + + def self.create(data, content_type = 'application/rdf+xml') + uri = RestClient.post @@config[:services]["opentox-dataset"], data, :content_type => content_type + dataset = Dataset.new + dataset.read uri.to_s + dataset end def self.find(uri) - RestClient.get uri # check if the resource is available + begin + RestClient.get uri # check if the resource is available + dataset = Dataset.new + dataset.read uri.to_s + dataset + rescue + nil + end + end + + def features end - def self.base_uri - @@config[:services]["opentox-dataset"] + def feature_values(uri) + features = {} + feature = @model.subject(DC["identifier"],uri) + @model.subjects(RDF['type'], OT["Compound"]).each do |compound_node| + compound = @model.object(compound_node, DC["identifier"]).to_s.sub(/^\[(.*)\]$/,'\1') + features[compound] = [] unless features[compound] + @model.subjects(OT['compound'], compound_node).each do |data_entry| + if feature == @model.object(data_entry, OT['feature']) + values_node = @model.object(data_entry, OT['values']) + @model.find(values_node, OT['value'], nil) do |s,p,value| + case value.to_s + when "true" + features[compound] << true + when "false" + features[compound] << false + else + features[compound] << value.to_s + end + end + end + end + end + features + end + + def tuples + tuples = [] + @model.subjects(RDF['type'], OT["Tuple"]).each do |t| + tuple = {} + compounds = [] + @model.subjects(OT['values'], t).each do |data_entry| + compound_node = @model.object(data_entry,OT['compound']) + compounds << @model.object(compound_node, DC["identifier"]).to_s + end + @model.find(t, OT['tuple'],nil) do |s,p,pair| + feature_node = @model.object(pair, OT['feature']) + feature_name = @model.object(feature_node, DC['title']).to_s + value_node = @model.object(pair, OT['value']) + value = @model.object(value_node, OT['value']).to_s + value = value.to_f if value.match(/^[\d\.]+$/) + tuple[feature_name.to_sym] = value + end + tuple[:compounds] = compounds + tuples << tuple + end + tuples + end + + def tuple(compound_uri) + compound_node = @model.subject(DC["identifier"],compound_uri) + #puts compound_uri + @model.subjects(OT['compound'], compound_node).each do |data_entry| + values_node = @model.object(data_entry, OT['values']) + @model.find(values_node, OT['tuple'], nil) do |s,p,tuple| + @model.find(tuple, OT['feature'], nil) do |s,p,feature| + name = @model.object(feature,DC['title']).to_s + #puts name + end + end + #puts values_node + end + end + + def compounds + compounds = [] + @model.subjects(RDF['type'], OT["Compound"]).each do |compound_node| + compounds << @model.object(compound_node, DC["identifier"])#.to_s.sub(/^\[(.*)\]$/,'\1') + end + compounds end # Delete a dataset @@ -25,6 +186,15 @@ module OpenTox RestClient.delete @uri end + def save + RestClient.post(@@config[:services]["opentox-dataset"], self.rdf, :content_type => "application/rdf+xml").to_s + end + + end + +end + + # def tanimoto(dataset) # RestClient.get(File.join(@uri,'tanimoto',dataset.path)) # end @@ -32,7 +202,48 @@ module OpenTox # def weighted_tanimoto(dataset) # RestClient.get(File.join(@uri,'weighted_tanimoto',dataset.path)) # end - - end - -end +=begin + def data_entries + data = {} + @model.subjects(RDF['type'], OT["Compound"]).each do |compound_node| + compound = @model.object(compound_node, DC["identifier"]).to_s#.sub(/^\[(.*)\]$/,'\1') + #compound = OpenTox::Compound.new(:inchi => compound).smiles + data[compound] = [] unless data[compound] + #puts compound + @model.subjects(OT['compound'], compound_node).each do |data_entry| + feature_node = @model.object(data_entry, OT['feature']) + feature = @model.object(feature_node, DC["identifier"]).to_s + values_node = @model.object(data_entry, OT['values']) + type = @model.object(values_node,RDF['type']).to_s + case type + when /FeatureValue/ + @model.find(values_node, OT['value'], nil) do |s,p,value| + case value.to_s + when "true" + data[compound] << {feature => true} + when "false" + data[compound] << {feature => false} + else + data[compound] << {feature => value.to_s} + end + end + when /Tuple/ # this is really slow + t = {} + @model.find(values_node, OT['tuple'], nil) do |s,p,tuple| + @model.find(tuple, OT['feature'], nil) do |s,p,feature| + @name = @model.object(feature,DC['title']).to_s + end + @model.find(tuple, OT['value'], nil) do |s,p,value| + v = @model.object(value,OT['value']).to_s + t[@name] = v + #print @name + ": " + #puts v + end + end + data[compound] << t + end + end + end + data + end +=end |