Separate libs for sparql and rdf

3 files changed, 97 insertions, 38 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
@@ -0,0 +1,48 @@
+=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
diff --git a/lib/utils/shims/dataset.rb b/lib/utils/shims/dataset.rb
index b5faf18..912510c 100644
--- a/lib/utils/shims/dataset.rb
+++ b/lib/utils/shims/dataset.rb
@@ -23,44 +23,6 @@ module OpenTox
     end
 
 
-    # Load features via SPARQL (fast)
-    # @param [String] Dataset URI
-    # @return [Array] Features in order
-    def self.find_features(uri)
-      sparql = "SELECT DISTINCT ?s FROM <#{uri}> WHERE {
-        ?s <#{RDF.type}> <#{RDF::OT.Feature}> ;
-           <#{RDF::OLO.index}> ?fidx
-        } ORDER BY ?fidx"
-      OpenTox::Backend::FourStore.query(sparql, "text/uri-list").split("\n").collect { |uri| OpenTox::Feature.new uri.strip }
-    end
-
-    # Load compounds via SPARQL (fast)
-    # @param [String] Dataset URI
-    # @return [Array] Compounds in order
-    def self.find_compounds(uri)
-      sparql = "SELECT DISTINCT ?compound FROM <#{uri}> WHERE {
-        ?s <#{RDF.type}> <#{RDF::OT.DataEntry}> ;
-           <#{RDF::OLO.index}> ?cidx;
-           <#{RDF::OT.compound}> ?compound
-        } ORDER BY ?cidx"
-      OpenTox::Backend::FourStore.query(sparql, "text/uri-list").split("\n").collect { |uri| OpenTox::Compound.new uri.strip }
-    end
-
-    # Load data entries via SPARQL (fast)
-    # @param [String] Dataset uri
-    # @return [Array] Data entries, ordered primarily over rows and secondarily over cols
-    def self.find_data_entries(uri)
-      sparql = "SELECT ?value FROM <#{uri}> WHERE {
-        ?data_entry <#{RDF::OLO.index}> ?cidx ;
-                    <#{RDF::OT.values}> ?v .
-        ?v          <#{RDF::OT.feature}> ?f;
-                    <#{RDF::OT.value}> ?value .
-        ?f          <#{RDF::OLO.index}> ?fidx.
-        } ORDER BY ?cidx ?fidx"
-      OpenTox::Backend::FourStore.query(sparql,"text/uri-list").split("\n").collect { |val| val.strip }
-    end
-
-
     ### Index Structures
 
     # Create value map
diff --git a/lib/utils/sparql/dataset.rb b/lib/utils/sparql/dataset.rb
new file mode 100644
index 0000000..e781f08
--- /dev/null
+++ b/lib/utils/sparql/dataset.rb
@@ -0,0 +1,49 @@
+=begin
+* Name: dataset.rb
+* Description: Dataset SPARQL tools
+* Author: Andreas Maunz <andreas@maunz.de>
+* Date: 10/2012
+=end
+
+module OpenTox
+  class Dataset
+
+    # Load features via SPARQL (fast)
+    # @param [String] Dataset URI
+    # @return [Array] Features in order
+    def self.find_features_sparql(uri)
+      sparql = "SELECT DISTINCT ?s FROM <#{uri}> WHERE {
+        ?s <#{RDF.type}> <#{RDF::OT.Feature}> ;
+           <#{RDF::OLO.index}> ?fidx
+        } ORDER BY ?fidx"
+      OpenTox::Backend::FourStore.query(sparql, "text/uri-list").split("\n").collect { |uri| OpenTox::Feature.new uri.strip }
+    end
+
+    # Load compounds via SPARQL (fast)
+    # @param [String] Dataset URI
+    # @return [Array] Compounds in order
+    def self.find_compounds_sparql(uri)
+      sparql = "SELECT DISTINCT ?compound FROM <#{uri}> WHERE {
+        ?s <#{RDF.type}> <#{RDF::OT.DataEntry}> ;
+           <#{RDF::OLO.index}> ?cidx;
+           <#{RDF::OT.compound}> ?compound
+        } ORDER BY ?cidx"
+      OpenTox::Backend::FourStore.query(sparql, "text/uri-list").split("\n").collect { |uri| OpenTox::Compound.new uri.strip }
+    end
+
+    # Load data entries via SPARQL (fast)
+    # @param [String] Dataset uri
+    # @return [Array] Data entries, ordered primarily over rows and secondarily over cols
+    def self.find_data_entries_sparql(uri)
+      sparql = "SELECT ?value FROM <#{uri}> WHERE {
+        ?data_entry <#{RDF::OLO.index}> ?cidx ;
+                    <#{RDF::OT.values}> ?v .
+        ?v          <#{RDF::OT.feature}> ?f;
+                    <#{RDF::OT.value}> ?value .
+        ?f          <#{RDF::OLO.index}> ?fidx.
+        } ORDER BY ?cidx ?fidx"
+      OpenTox::Backend::FourStore.query(sparql,"text/uri-list").split("\n").collect { |val| val.strip }
+    end
+
+  end
+end