diff options
author | Christoph Helma <helma@in-silico.de> | 2009-12-17 13:58:03 +0100 |
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committer | Christoph Helma <helma@in-silico.de> | 2009-12-17 13:58:03 +0100 |
commit | a5789305534c2a622a658e7ef14b016a1bac4bd6 (patch) | |
tree | 76ff10ff5efc9fa278312fbdf7cabfb0dd55a345 /lib/dataset.rb | |
parent | 887a921e25c3d7778e9e5ce998f52fde41d517f8 (diff) |
YAML output for datasets added
Diffstat (limited to 'lib/dataset.rb')
-rw-r--r-- | lib/dataset.rb | 72 |
1 files changed, 63 insertions, 9 deletions
diff --git a/lib/dataset.rb b/lib/dataset.rb index fad6baa..895c9fc 100644 --- a/lib/dataset.rb +++ b/lib/dataset.rb @@ -3,8 +3,6 @@ module OpenTox class Dataset include Owl - #attr_accessor :model - def initialize super end @@ -28,7 +26,7 @@ module OpenTox @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] + @model.add feature, DC['source'], f[:source].to_s if f[:source] end feature end @@ -66,9 +64,12 @@ module OpenTox 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, RDF['type'], OT['FeatureValue'] + @model.add tuple, OT['complexValue'], pair @model.add pair, OT['feature'], feature - @model.add pair, OT['value'], value + @model.add pair, OT['value'], value #FIX + #@model.add tuple, OT['feature'], feature + #@model.add tuple, OT['values'], value end tuple end @@ -98,7 +99,7 @@ module OpenTox def self.find(uri) begin - RestClient.get uri # check if the resource is available + RestClient.get uri, :accept => 'application/rdf+xml' # check if the resource is available dataset = Dataset.new dataset.read uri.to_s dataset @@ -108,11 +109,42 @@ module OpenTox end def features + features = [] + @model.subjects(RDF['type'], OT["Feature"]).each do |feature_node| + features << @model.object(feature_node, DC["identifier"])# + end + features end - def feature_values(uri) + def data_entries + data_entries = {} + self.compounds.each do |compound| + compound_node = @model.subject(DC["identifier"],compound) + compound = compound.to_s.sub(/^\[(.*)\]$/,'\1') + data_entries[compound] = {} unless data_entries[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']) + data_entries[compound][feature] = [] unless data_entries[compound][feature] + @model.find(values_node, OT['value'], nil) do |s,p,value| + case value.to_s + when "true" + data_entries[compound][feature] << true + when "false" + data_entries[compound][feature] << false + else + data_entries[compound][feature] << value.to_s + end + end + end + end + data_entries + end + + def feature_values(feature_uri) features = {} - feature = @model.subject(DC["identifier"],uri) + feature = @model.subject(DC["identifier"],feature_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] @@ -176,7 +208,7 @@ module OpenTox def compounds compounds = [] @model.subjects(RDF['type'], OT["Compound"]).each do |compound_node| - compounds << @model.object(compound_node, DC["identifier"])#.to_s.sub(/^\[(.*)\]$/,'\1') + compounds << @model.object(compound_node, DC["identifier"])# end compounds end @@ -190,6 +222,28 @@ module OpenTox RestClient.post(@@config[:services]["opentox-dataset"], self.rdf, :content_type => "application/rdf+xml").to_s end + def to_yaml + #compounds.each do |c| + #end + { + :uri => self.uri, + :opentox_class => self.owl_class, + :title => self.title, + :source => self.source, + :identifier => self.identifier, + :compounds => self.compounds.collect{|c| c.to_s.to_s.sub(/^\[(.*)\]$/,'\1')}, + :features => self.features.collect{|f| f.to_s }, + :data_entries => self.data_entries, +=begin + :tuples => self.compounds.collect{|c| + compound_uri = c.to_s.to_s.sub(/^\[(.*)\]$/,'\1') + {compound_uri => self.tuple(compound_uri)} + }, +=end + #:feature_values => self.features.collect{|f| { f.to_s => self.feature_values(f.to_s)} } + }.to_yaml + end + end end |