Added shims for SPARQL retrieval

1 files changed, 37 insertions, 0 deletions

diff --git a/lib/utils/shims/dataset.rb b/lib/utils/shims/dataset.rb
index 75948e0..b5faf18 100644
--- a/lib/utils/shims/dataset.rb
+++ b/lib/utils/shims/dataset.rb
@@ -23,6 +23,43 @@ 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