1 files changed, 48 insertions, 0 deletions
diff --git a/lib/utils/rdf/dataset.rb b/lib/utils/rdf/dataset.rb
new file mode 100644
index 0000000..5cfb827
--- /dev/null
+++ b/lib/utils/rdf/dataset.rb
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+=begin
+* Name: dataset.rb
+* Description: Dataset RDF tools
+* Author: Andreas Maunz <andreas@maunz.de>
+* Date: 10/2012
+=end
+
+module OpenTox
+  class Dataset
+
+    # Load features via RDF (slow)
+    # @param [String] Dataset URI
+    # @return [Array] Features in order
+    def self.find_features_rdf(rdf)
+      query = RDF::Query.new do
+        pattern [:uri, RDF.type, RDF::OT.Feature]
+        pattern [:uri, RDF::OLO.index, :idx]
+      end
+      query.execute(rdf).sort_by{|s| s.idx}.collect{|s| OpenTox::Feature.new(s.uri.to_s)}
+    end
+
+    # Load compounds via RDF (slow)
+    # @param [String] Dataset URI
+    # @return [Array] Compounds in order
+    def self.find_compounds_rdf(rdf)
+      query = RDF::Query.new do
+        pattern [:uri, RDF.type, RDF::OT.Compound]
+        pattern [:uri, RDF::OLO.index, :idx]
+      end
+      query.execute(rdf).sort_by{|s| s.idx}.collect{|s| OpenTox::Compound.new(s.uri.to_s)}
+    end
+
+    # Load data entries via RDF (slow)
+    # @param [String] Dataset uri
+    # @return [Array] Data entries, ordered primarily over rows and secondarily over cols
+    def self.find_data_entries_rdf(rdf)
+      query = RDF::Query.new do
+        pattern [:data_entry, RDF::OLO.index, :cidx] # compound index: now a free variable
+        pattern [:data_entry, RDF::OT.values, :vals]
+        pattern [:vals, RDF::OT.feature, :f]
+        pattern [:f, RDF::OLO.index, :fidx]
+        pattern [:vals, RDF::OT.value, :val]
+      end
+      query.execute(rdf).order_by(:fidx, :cidx).collect { |s| s.val.to_s }
+    end
+
+  end
+end