From e1ab21b21e88254b796c47c83f44d406e37f06a8 Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Wed, 17 Jul 2013 14:50:35 +0200
Subject: uri objects fixed in ntriples serialsiation

---
 lib/dataset.rb | 12 +++++++-----
 lib/opentox.rb | 13 +++++++++++--
 2 files changed, 18 insertions(+), 7 deletions(-)

diff --git a/lib/dataset.rb b/lib/dataset.rb
index 2d3c533..153cdce 100644
--- a/lib/dataset.rb
+++ b/lib/dataset.rb
@@ -254,13 +254,15 @@ module OpenTox
 
       ntriples = ""
       @metadata[RDF.type] = [ RDF::OT.Dataset, RDF::OT.OrderedDataset ]
-      @metadata[RDF.type] ||= eval("RDF::OT."+self.class.to_s.split('::').last)
-      @metadata[RDF::DC.date] ||= DateTime.now
+
       @metadata.each do |predicate,values|
-        [values].flatten.each { |value| ntriples << "<#{@uri}> <#{predicate}> '#{value}' .\n" }
+        [values].flatten.each do |value|
+          URI.valid?(value) ? value = "<#{value}>" : value = "'#{value}'"
+          ntriples << "<#{@uri}> <#{predicate}> #{value} .\n" 
+        end
       end
-      @parameters.each do |parameter|
-        p_node = RDF::Node.new.to_s
+      @parameters.each_with_index do |parameter,i|
+        p_node = "_:parameter"+ i.to_s
         ntriples <<  "<#{@uri}> <#{RDF::OT.parameters}> #{p_node} .\n"
         ntriples <<  "#{p_node} <#{RDF.type}> <#{RDF::OT.Parameter}> .\n"
         parameter.each { |k,v| ntriples <<  "#{p_node} <#{k}> '#{v}' .\n" }
diff --git a/lib/opentox.rb b/lib/opentox.rb
index 87b241a..5e0bc29 100644
--- a/lib/opentox.rb
+++ b/lib/opentox.rb
@@ -233,6 +233,7 @@ module OpenTox
       end
 
       def self.find_or_create metadata
+        t = Time.now
         sparql = "SELECT DISTINCT ?s WHERE { "
         metadata.each do |predicate,objects|
           unless [RDF::DC.date,RDF::DC.modified,RDF::DC.description].include? predicate # remove dates and description (strange characters in description may lead to SPARQL errors)
@@ -248,11 +249,19 @@ module OpenTox
           end
         end
         sparql <<  "}"
+        puts "Create SPARQL: #{Time.now-t}"
+        t = Time.new
         uris = RestClientWrapper.get(service_uri,{:query => sparql},{:accept => "text/uri-list"}).split("\n")
+        puts "Query: #{Time.now-t}"
+        t = Time.new
         if uris.empty?
-          self.create metadata
+          f=self.create metadata
+          puts "Create: #{Time.now-t}"
+          f
         else
-          self.new uris.first
+          f=self.new uris.first
+          puts "Found: #{Time.now-t}"
+          f
         end
       end
     end
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