From 8a2b749ccef94b229a32ec716c93388f5c7495d7 Mon Sep 17 00:00:00 2001
From: Andreas Maunz <andreas@maunz.de>
Date: Wed, 31 Oct 2012 15:35:34 +0100
Subject: Fixed get for dataset from RDF

---
 lib/dataset.rb           | 12 ++++++++----
 lib/opentox.rb           |  4 ++--
 lib/utils/rdf/dataset.rb | 14 +++++++++++++-
 3 files changed, 23 insertions(+), 7 deletions(-)

(limited to 'lib')

diff --git a/lib/dataset.rb b/lib/dataset.rb
index 4351dc5..288e4d3 100644
--- a/lib/dataset.rb
+++ b/lib/dataset.rb
@@ -29,17 +29,21 @@ module OpenTox
 
     def get(force_no_backend_query=false)
       have_rdf = (force_no_backend_query and @rdf.size>0)
-      super() unless have_rdf
       ordered = (have_rdf or OpenTox::Dataset.ordered?(@uri))
+      super() if (!have_rdf and !ordered)
       @features = []
       @compounds = []
       @data_entries = []
 
       # AM: read ordered dataset from RDF
       if ordered
-        @uri = s[0].uri.to_s if have_rdf # AM: must rewrite URI
-        @compounds = find_compounds_rdf
-        @features = find_features_rdf
+        # Read only some data as rdf
+        unless have_rdf
+          self.parse_rdfxml( RestClient.get([@uri,"allnde"].join("/"),{:accept => "application/rdf+xml"}), true )
+        end
+        @compounds = self.find_compounds_rdf
+        @features = self.find_features_rdf
+
         numeric_features = @features.collect{|f| 
           f.get
           f[RDF.type].include?(RDF::OT.NumericFeature) or f[RDF.type].include?(RDF::OT.Substructure)
diff --git a/lib/opentox.rb b/lib/opentox.rb
index faa7b58..0f29c30 100644
--- a/lib/opentox.rb
+++ b/lib/opentox.rb
@@ -130,8 +130,8 @@ module OpenTox
   RDF_FORMATS.each do |format|
 
     # rdf parse methods for all formats e.g. parse_rdfxml
-    send :define_method, "parse_#{format}".to_sym do |rdf|
-      @rdf = RDF::Graph.new
+    send :define_method, "parse_#{format}".to_sym do |rdf,init=true|
+      @rdf = RDF::Graph.new if init
       RDF::Reader.for(format).new(rdf) do |reader|
         reader.each_statement{ |statement| @rdf << statement }
       end
diff --git a/lib/utils/rdf/dataset.rb b/lib/utils/rdf/dataset.rb
index e101b67..2cb32a9 100644
--- a/lib/utils/rdf/dataset.rb
+++ b/lib/utils/rdf/dataset.rb
@@ -47,7 +47,7 @@ module OpenTox
     # Query a dataset URI for ordered status 
     # by loading its metadata (OpenTox compliant)
     # @param [String] uri Dataset uri
-    # @return [TrueClass,FalseClass] status Whether the dataset is ordered
+    # @return [TrueClass, FalseClass] status Whether the dataset is ordered
     def self.ordered?(uri)
       ds = OpenTox::Dataset.new # dummy 
       ds.parse_rdfxml(RestClient.get([uri,"metadata"].join("/"),{:accept => "application/rdf+xml"}))
@@ -57,5 +57,17 @@ module OpenTox
       query.execute(ds.rdf).size>0
     end
 
+    # Load dataset URI from given RDF (slow)
+    # @param [String] rdf RDF
+    # @return [String] uri URI
+    def self.uri_from_rdf(rdf)
+      ds = OpenTox::Dataset.new # dummy 
+      ds.parse_rdfxml(rdf)
+      query = RDF::Query.new do
+        pattern [:dataset, RDF.type, RDF::OT.Dataset]
+      end
+      query.execute(ds.rdf).collect { |s| s.dataset.to_s }[0]
+    end
+
   end
 end
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