sparql property request function

2 files changed, 39 insertions, 12 deletions

diff --git a/lib/utils/rdf/dataset.rb b/lib/utils/rdf/dataset.rb
index 5cfb827..b2deeb8 100644
--- a/lib/utils/rdf/dataset.rb
+++ b/lib/utils/rdf/dataset.rb
@@ -9,8 +9,8 @@ module OpenTox
   class Dataset
 
     # Load features via RDF (slow)
-    # @param [String] Dataset URI
-    # @return [Array] Features in order
+    # @param [String] uri Dataset URI
+    # @return [Array] features Features in order
     def self.find_features_rdf(rdf)
       query = RDF::Query.new do
         pattern [:uri, RDF.type, RDF::OT.Feature]
@@ -20,8 +20,8 @@ module OpenTox
     end
 
     # Load compounds via RDF (slow)
-    # @param [String] Dataset URI
-    # @return [Array] Compounds in order
+    # @param [String] uri Dataset URI
+    # @return [Array] compounds Compounds in order
     def self.find_compounds_rdf(rdf)
       query = RDF::Query.new do
         pattern [:uri, RDF.type, RDF::OT.Compound]
@@ -31,8 +31,8 @@ module OpenTox
     end
 
     # Load data entries via RDF (slow)
-    # @param [String] Dataset uri
-    # @return [Array] Data entries, ordered primarily over rows and secondarily over cols
+    # @param [String] uri Dataset uri
+    # @return [Array] entries 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
diff --git a/lib/utils/sparql/dataset.rb b/lib/utils/sparql/dataset.rb
index e781f08..ecc0321 100644
--- a/lib/utils/sparql/dataset.rb
+++ b/lib/utils/sparql/dataset.rb
@@ -9,8 +9,8 @@ module OpenTox
   class Dataset
 
     # Load features via SPARQL (fast)
-    # @param [String] Dataset URI
-    # @return [Array] Features in order
+    # @param [String] uri Dataset URI
+    # @return [Array] features OpenTox::Features in order
     def self.find_features_sparql(uri)
       sparql = "SELECT DISTINCT ?s FROM <#{uri}> WHERE {
         ?s <#{RDF.type}> <#{RDF::OT.Feature}> ;
@@ -19,9 +19,36 @@ module OpenTox
       OpenTox::Backend::FourStore.query(sparql, "text/uri-list").split("\n").collect { |uri| OpenTox::Feature.new uri.strip }
     end
 
+    # Load properties via SPARQL (fast)
+    # @param [Array] uris URIs (assumed ordered)
+    # @param [Hash] properties Properties (keys: user-defined identifier, values: rdf identifier as strings)
+    # @return [Array] types Properties in order of URIs
+    def self.find_props_sparql(uris, props)
+      selects = props.keys
+      conditions = selects.collect{ |k|
+        "<#{props[k]}> ?#{k.to_s}"
+      }
+      h={}
+      uris.each{ |uri|
+        sparql = "SELECT ?id #{selects.collect{|k| "?#{k.to_s}"}.join(" ")} FROM <#{uri}> WHERE { ?id #{conditions.join(";")} }"
+        res = OpenTox::Backend::FourStore.query(sparql, "text/uri-list")
+        res.split("\n").inject(h){ |h,row| 
+          values = row.split("\t")
+          id=values.shift
+          h[id] = {}
+          values.each_with_index { |val,idx|
+            h[id][selects[idx]] = [] unless h[id][selects[idx]]
+            h[id][selects[idx]] << val.to_s
+          }
+          h
+        }
+      }
+      h
+    end
+
     # Load compounds via SPARQL (fast)
-    # @param [String] Dataset URI
-    # @return [Array] Compounds in order
+    # @param [String] uri Dataset URI
+    # @return [Array] compounds Compounds in order
     def self.find_compounds_sparql(uri)
       sparql = "SELECT DISTINCT ?compound FROM <#{uri}> WHERE {
         ?s <#{RDF.type}> <#{RDF::OT.DataEntry}> ;
@@ -32,8 +59,8 @@ module OpenTox
     end
 
     # Load data entries via SPARQL (fast)
-    # @param [String] Dataset uri
-    # @return [Array] Data entries, ordered primarily over rows and secondarily over cols
+    # @param [String] uri Dataset uri
+    # @return [Array] entries 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 ;