From 791398c12af4f8290095425dac87e3c852905ab6 Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Sat, 7 Sep 2019 18:20:10 +0200
Subject: obsolete data and java directories deleted

---
 lib/dataset.rb | 55 +------------------------------------------------------
 1 file changed, 1 insertion(+), 54 deletions(-)

(limited to 'lib/dataset.rb')

diff --git a/lib/dataset.rb b/lib/dataset.rb
index 8cb343f..87e7fef 100644
--- a/lib/dataset.rb
+++ b/lib/dataset.rb
@@ -68,63 +68,10 @@ class Dataset
     @independent_variable_names = ["Canonical Smiles"] + fingerprints.flatten.sort.uniq
     print_variables
   end
+
 end
 
 =begin
-    # Create a dataset from SDF file 
-    #   files with a single data field are read as BioActivities (i.e. dependent variable)
-    #   files with multiple data fields are read as SubstanceProperties (i.e. independent variable)
-    # @param [File] 
-    # @return [OpenTox::Dataset]
-    def self.from_sdf_file file
-      md5 = Digest::MD5.hexdigest(File.read(file)) # use hash to identify identical files
-      dataset = self.find_by(:md5 => md5)
-      if dataset
-        $logger.debug "Found #{file} in the database (id: #{dataset.id}, md5: #{dataset.md5}), skipping import."
-      else
-        $logger.debug "Parsing #{file}."
-
-        dataset = self.new(:source => file, :name => File.basename(file,".*"), :md5 => md5)
-        original_id = OriginalId.find_or_create_by(:dataset_id => dataset.id,:name => dataset.name+".ID")
-
-        read_result = false
-        sdf = ""
-        feature_name = ""
-        compound = nil
-        features = {}
-        table = [["ID","SMILES"]]
-
-        File.readlines(file).each do |line|
-          if line.match %r{\$\$\$\$}
-            sdf << line
-            id = sdf.split("\n").first.chomp
-            compound = Compound.from_sdf sdf
-            row = [id,compound.smiles]
-            features.each do |f,v|
-              table[0] << f unless table[0].include? f
-              row[table[0].index(f)] = v
-            end
-            table << row
-            sdf = ""
-            features = {}
-          elsif line.match /^>\s+</
-            feature_name = line.match(/^>\s+<(.*)>/)[1]
-            read_result = true
-          else
-            if read_result
-              value = line.chomp
-              features[feature_name] = value
-              read_result = false
-            else
-              sdf << line
-            end
-          end
-        end
-        dataset.parse_table table
-      end
-      dataset
-    end
-
     # Create a dataset from PubChem Assay
     # @param [Integer] PubChem AssayID (AID)
     # @return [OpenTox::Dataset]
-- 
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