From 34c6eb7840464d3d2b30982f4d51109faa1e8a3e Mon Sep 17 00:00:00 2001
From: Andreas Maunz <andreas@maunz.de>
Date: Mon, 1 Oct 2012 17:35:21 +0200
Subject: Fixed row parsing

---
 lib/parser.rb | 3 ++-
 lib/utils.rb  | 3 ++-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/lib/parser.rb b/lib/parser.rb
index 257d250..5ac934c 100644
--- a/lib/parser.rb
+++ b/lib/parser.rb
@@ -525,7 +525,8 @@ module OpenTox
       end
 
       def split_row(row)
-        row.chomp.gsub(/["']/,'').split(/\s*[,;\t]\s*/,-1) # -1: do not skip empty cells
+        CSV.parse(row)[0]
+        #row.chomp.gsub(/["']/,'').split(/\s*[,;\t]\s*/,-1) # -1: do not skip empty cells
       end
 
     end
diff --git a/lib/utils.rb b/lib/utils.rb
index 555ac17..d34081b 100644
--- a/lib/utils.rb
+++ b/lib/utils.rb
@@ -312,7 +312,8 @@ module OpenTox
             sdf_data = []
             params[:compounds].each_with_index { |c_uri, c_idx| 
               cmpd = OpenTox::Compound.new(c_uri)
-              LOGGER.debug "3D for #{cmpd.to_smiles}"
+              #LOGGER.debug "3D for #{cmpd.to_smiles}"
+              LOGGER.debug "3D for #{c_idx}"
               obconv = OpenBabel::OBConversion.new
               obmol = OpenBabel::OBMol.new
               obconv.set_in_format("smi") 
-- 
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