Revert "fix storing feature datasets for dataset with duplicate compounds, preserve feature order"

This reverts commit 02e63dd161f07b9ec750af61b933ce60c34be42c.

1 files changed, 14 insertions, 33 deletions

diff --git a/lib/descriptor.rb b/lib/descriptor.rb
index 7403ebf..36fb1a5 100644
--- a/lib/descriptor.rb
+++ b/lib/descriptor.rb
@@ -1,8 +1,5 @@
 require 'digest/md5'
 ENV["JAVA_HOME"] ||= "/usr/lib/jvm/java-7-openjdk" 
-
-BABEL_3D_CACHE_DIR = File.join(Dir.pwd,'/babel_3d_cache')
-
 module OpenTox
 
   module Algorithm 
@@ -121,7 +118,7 @@ module OpenTox
             $logger.debug "> #{line.chomp}"
           end
           io.close
-          raise "external cmd failed '#{cmd}' (see log file for error msg)" unless $?.to_i == 0
+          raise "external cmd failed '#{cmd}' (error should be logged)" unless $?.to_i == 0
         end
       end
 
@@ -175,7 +172,7 @@ module OpenTox
         obconversion.set_out_format 'sdf'
 
         digest = Digest::MD5.hexdigest compounds.collect{|c| c.uri}.inspect
-        sdf_file = File.join(BABEL_3D_CACHE_DIR,"#{digest}.sdf")
+        sdf_file = "/tmp/#{digest}.sdf"
         if File.exists? sdf_file # do not recreate existing 3d sdfs
           $logger.debug "re-using cached 3d structures from #{sdf_file}"
         else
@@ -188,36 +185,20 @@ module OpenTox
           c = 0
           compounds.each do |compound|
             c += 1
-            cmp_file = File.join(BABEL_3D_CACHE_DIR,Digest::MD5.hexdigest(compound.inchi)+".sdf")
-            cmp_sdf = nil
-            if File.exists? cmp_file
-              $logger.debug "read cached 3d structure for compound #{c}/#{compounds.size}"
-              cmp_sdf = File.read(cmp_file)
+            $logger.debug "compute 3d structures for compound #{c}/#{compounds.size}"
+            obconversion.read_string obmol, compound.inchi
+            sdf_2d = obconversion.write_string(obmol)  
+            OpenBabel::OBOp.find_type("Gen3D").do(obmol) 
+            sdf_3d = obconversion.write_string(obmol)  
+            if sdf_3d.match(/.nan/)
+              warning = "3D generation failed for compound #{compound.uri}, trying to calculate descriptors from 2D structure."
+              $logger.warn warning
+              # TODO
+              #@feature_dataset[RDF::OT.Warnings] ? @feature_dataset[RDF::OT.Warnings] << warning : @feature_dataset[RDF::OT.Warnings] = warning
+              tmp_file.write sdf_2d
             else
-              $logger.debug "compute 3d structure for compound #{c}/#{compounds.size}"
-              obconversion.read_string obmol, compound.inchi
-              sdf_2d = obconversion.write_string(obmol)  
-              error = nil
-              if compound.inchi.include?(";") # component includes multiple compounds (; in inchi, . in smiles)
-                error = "OpenBabel 3D generation failed for multi-compound #{compound.uri}, trying to calculate descriptors from 2D structure."
-              else
-                OpenBabel::OBOp.find_type("Gen3D").do(obmol) 
-                sdf_3d = obconversion.write_string(obmol)  
-                error = "3D generation failed for compound #{compound.uri}, trying to calculate descriptors from 2D structure." if sdf_3d.match(/.nan/)
-              end
-              if error
-                $logger.warn error
-                # TODO
-                # @feature_dataset[RDF::OT.Warnings] ? @feature_dataset[RDF::OT.Warnings] << error : @feature_dataset[RDF::OT.Warnings] = error
-                cmp_sdf = sdf_2d
-              else
-                cmp_sdf = sdf_3d
-              end
-              File.open(cmp_file,"w") do |f|
-                f.write(cmp_sdf)
-              end
+              tmp_file.write sdf_3d
             end
-            tmp_file.write cmp_sdf
           end
           tmp_file.close
           File.rename(tmp_file, sdf_file)