all opentox-client tests pass

1 files changed, 115 insertions, 19 deletions

diff --git a/lib/dataset.rb b/lib/dataset.rb
index 33e1571..ed0ccdd 100644
--- a/lib/dataset.rb
+++ b/lib/dataset.rb
@@ -3,32 +3,128 @@ module OpenTox
   # Ruby wrapper for OpenTox Dataset Webservices (http://opentox.org/dev/apis/api-1.2/dataset).
   class Dataset 
 
-    def data_entries
-      data_entries = []
-      #pull 
-      #@reload = false
-      begin
-        self.[](RDF::OT.dataEntry).collect{|data_entry| data_entries << @rdf.to_hash[data_entry] }
-      rescue
+    attr_accessor :features, :compounds, :data_entries
+
+    def initialize uri=nil, subjectid=nil
+      super uri, subjectid
+      @features = []
+      @compounds = []
+      @data_entries = []
+      append RDF.type, RDF::OT.OrderedDataset
+    end
+
+    def upload filename
+      file = File.new filename
+      RestClientWrapper.put(@uri, {:file => file}, {:subjectid => @subjectid})
+    end
+
+    def get
+      super
+      @features = []
+      @compounds = []
+      @data_entries = []
+      query = RDF::Query.new do
+        pattern [:uri, RDF.type, RDF::OT.OrderedDataset]
       end
-      begin
-      # TODO: remove API 1.1
-        self.[](RDF::OT1.dataEntry).collect{|data_entry| data_entries << @rdf.to_hash[data_entry] }
-      rescue
+      if query.execute(@rdf).first # ordered dataset
+        query = RDF::Query.new do
+          pattern [:uri, RDF.type, RDF::OT.Compound]
+          pattern [:uri, RDF::OLO.index, :idx]
+        end
+        @compounds = query.execute(@rdf).sort_by{|s| s.idx}.collect{|s| OpenTox::Compound.new s.uri.to_s}
+        query = RDF::Query.new do
+          pattern [:uri, RDF.type, RDF::OT.Feature]
+          pattern [:uri, RDF::OLO.index, :idx]
+        end
+        @features = query.execute(@rdf).sort_by{|s| s.idx}.collect{|s| OpenTox::Feature.new(s.uri.to_s)}
+        numeric_features = @features.collect{|f| f.get; f[RDF.type].include? RDF::OT.NumericFeature}
+        @compounds.each_with_index do |compound,i|
+          query = RDF::Query.new do
+            pattern [:data_entry, RDF::OLO.index, i]
+            pattern [:data_entry, RDF::OT.values, :values]
+            pattern [:values, RDF::OT.feature, :feature]
+            pattern [:feature, RDF::OLO.index, :feature_idx]
+            pattern [:values, RDF::OT.value, :value]
+          end
+          values = query.execute(@rdf).sort_by{|s| s.feature_idx}.collect do |s|
+            numeric_features[s.feature_idx] ?  s.value.to_s.to_f : s.value.to_s
+          end
+          @data_entries << values
+        end
+      else
+        query = RDF::Query.new do
+          pattern [:uri, RDF.type, RDF::OT.Feature]
+        end
+        @features = query.execute(@rdf).collect{|s| OpenTox::Feature.new(s.uri.to_s)}
+        query = RDF::Query.new do
+          pattern [:data_entry, RDF::OT.compound, :compound]
+        end
+        @compounds = query.execute(@rdf).sort_by{|s| s.data_entry}.collect{|s| OpenTox::Compound.new s.compound.to_s}
+        numeric_features = @features.collect{|f| f.get; f[RDF.type].include? RDF::OT.NumericFeature}
+        @compounds.each do |compound|
+          values = []
+          @features.each_with_index do |feature,i|
+            query = RDF::Query.new do
+              pattern [:data_entry, RDF::OT.compound, RDF::URI.new(compound.uri)]
+              pattern [:data_entry, RDF::OT.values, :values]
+              pattern [:values, RDF::OT.feature, RDF::URI.new(feature.uri)]
+              pattern [:values, RDF::OT.value, :value]
+            end
+            value = query.execute(@rdf).first.value.to_s
+            value = value.to_f if numeric_features[i]
+            values << value
+          end
+          @data_entries << values
+        end
       end
-      #@reload = true
-      data_entries
     end
 
-    def compounds
-      uri = File.join(@uri,"compounds")
-      RestClientWrapper.get(uri,{},{:accept => "text/uri-list", :subjectid => @subjectid}).split("\n").collect{|uri| OpenTox::Compound.new uri}
+    def get_metadata
+      uri = File.join(@uri,"metadata")
+      begin
+        parse_ntriples RestClientWrapper.get(uri,{},{:accept => "text/plain", :subjectid => @subjectid})
+      rescue # fall back to rdfxml
+        parse_rdfxml RestClientWrapper.get(uri,{},{:accept => "application/rdf+xml", :subjectid => @subjectid})
+      end
+      metadata
     end
 
-    def features
-      uri = File.join(@uri,"features")
-      RestClientWrapper.get(uri,{},{:accept => "text/uri-list", :subjectid => @subjectid}).split("\n").collect{|uri| OpenTox::Feature.new uri}
+    def << data_entry
+      compound = data_entry.shift
+      bad_request_error "Dataset features are empty." unless features
+      bad_request_error "data_entry size does not match features size." unless data_entry.size == features.size
+      bad_request_error "First data_entry is not a OpenTox::Compound" unless compound.class == OpenTox::Compound
+      @compounds << compound
+      @data_entries << data_entry
     end
 
+    RDF_FORMATS.each do |format|
+
+      # redefine rdf serialization methods 
+      send :define_method, "to_#{format}".to_sym do
+        # TODO: check, might affect appending to unordered datasets
+        features.each_with_index do |feature,i|
+          @rdf << [RDF::URI.new(feature.uri), RDF::URI.new(RDF.type), RDF::URI.new(RDF::OT.Feature)] 
+          @rdf << [RDF::URI.new(feature.uri), RDF::URI.new(RDF::OLO.index), RDF::Literal.new(i)] 
+        end
+        compounds.each_with_index do |compound,i|
+          @rdf << [RDF::URI.new(compound.uri), RDF::URI.new(RDF.type), RDF::URI.new(RDF::OT.Compound)]
+          @rdf << [RDF::URI.new(compound.uri), RDF::URI.new(RDF::OLO.index), RDF::Literal.new(i)]
+          data_entry_node = RDF::Node.new
+          @rdf << [RDF::URI.new(@uri), RDF::URI.new(RDF::OT.dataEntry), data_entry_node]
+          @rdf << [data_entry_node, RDF::URI.new(RDF.type), RDF::URI.new(RDF::OT.DataEntry)]
+          @rdf << [data_entry_node, RDF::URI.new(RDF::OLO.index), RDF::Literal.new(i)]
+          @rdf << [data_entry_node, RDF::URI.new(RDF::OT.compound), RDF::URI.new(compound.uri)]
+          data_entries[i].each_with_index do |value,j|
+            value_node = RDF::Node.new
+            @rdf << [data_entry_node, RDF::URI.new(RDF::OT.values), value_node]
+            @rdf << [value_node, RDF::URI.new(RDF::OT.feature), RDF::URI.new(@features[j].uri)]
+            @rdf << [value_node, RDF::URI.new(RDF::OT.value), RDF::Literal.new(value)]
+          end
+        end
+        super()
+      end
+
+    end
   end
 end