opentox-ruby 2.0.0 → 2.0.1

data/VERSION

@@ -1 +1 @@
-2.0.0
+2.0.1

data/lib/compound.rb

@@ -159,9 +159,9 @@ module OpenTox
     # @param [Array] deactivating Array with deactivating Smarts strings
     # @return [String] URI for compound image with highlighted fragments
     def matching_smarts_image_uri(activating, deactivating)
-      activating_smarts = URI.encode "\"#{activating.join("\"/\"")}\""
-      deactivating_smarts = URI.encode "\"#{deactivating.join("\"/\"")}\""
-      File.join @uri, "smarts/activating", URI.encode(activating_smarts),"deactivating", URI.encode(deactivating_smarts)
+      activating_smarts = "\"#{activating.collect{|smarts| CGI.escape(smarts)}.join("\"/\"")}\""
+      deactivating_smarts = "\"#{deactivating.collect{|smarts| CGI.escape(smarts)}.join("\"/\"")}\""
+      File.join @uri, "smarts/activating", activating_smarts, "deactivating", deactivating_smarts
     end
 
 

data/lib/helper.rb

@@ -44,8 +44,9 @@ helpers do
 
   def uri_available?(urlStr)
     url = URI.parse(urlStr)
+    subjectidstr = @subjectid ? "?subjectid=#{CGI.escape @subjectid}" : ""
     Net::HTTP.start(url.host, url.port) do |http|
-      return http.head("#{url.request_uri}?subjectid=#{CGI.escape @subjectid}").code == "200"
+      return http.head("#{url.request_uri}#{subjectidstr}").code == "200"
     end
   end
 

data/lib/parser.rb

@@ -277,7 +277,16 @@ module OpenTox
       def load_spreadsheet(book)
         book.default_sheet = 0
         add_features book.row(1)
-        2.upto(book.last_row) { |i| add_values book.row(i) }
+
+        # AM: fix mixed read in
+        regression_features=false
+        2.upto(book.last_row) { |i| 
+          row = book.row(i)
+          regression_features = detect_regression_features row
+          break if regression_features==true
+        }
+        
+        2.upto(book.last_row) { |i| add_values book.row(i),regression_features }
         warnings
         @dataset
       end
@@ -289,11 +298,21 @@ module OpenTox
         row = 0
         input = csv.split("\n")
         add_features split_row(input.shift)
-        input.each { |row| add_values split_row(row) }
+
+
+        # AM: fix mixed read in
+        regression_features=false
+        input.each { |row| 
+          row = split_row(row)
+          regression_features = detect_regression_features row
+          break if regression_features==true
+        }
+        input.each { |row| add_values split_row(row),regression_features }
         warnings
         @dataset
       end
 
+
       private
 
       def warnings
@@ -335,7 +354,20 @@ module OpenTox
         end
       end
 
-      def add_values(row)
+      def detect_regression_features row
+        row.shift
+        regression_features=false
+        row.each_index do |i|
+          value = row[i]
+          type = feature_type(value)
+          if type == OT.NumericFeature
+            regression_features=true
+          end
+        end
+        regression_features
+      end
+
+      def add_values(row, regression_features=false)
 
         smiles = row.shift
         compound = Compound.from_smiles(smiles)
@@ -353,19 +385,23 @@ module OpenTox
 
           @feature_types[feature] << type 
 
-          case type
-          when OT.NominalFeature
-            case value.to_s
-            when TRUE_REGEXP
-              val = true
-            when FALSE_REGEXP
-              val = false
-            end
-          when OT.NumericFeature
+          if (regression_features)
             val = value.to_f
-          when OT.StringFeature
-            val = value.to_s
-            @activity_errors << smiles+", "+row.join(", ")
+          else
+            case type
+            when OT.NominalFeature
+              case value.to_s
+              when TRUE_REGEXP
+                val = true
+              when FALSE_REGEXP
+                val = false
+              end
+            when OT.NumericFeature
+              val = value.to_f
+            when OT.StringFeature
+              val = value.to_s
+              @activity_errors << smiles+", "+row.join(", ")
+            end
           end
           if val!=nil
             @dataset.add(compound.uri, feature, val)

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: opentox-ruby
 version: !ruby/object:Gem::Version 
-  hash: 15
+  hash: 13
   prerelease: 
   segments: 
   - 2
   - 0
-  - 0
-  version: 2.0.0
+  - 1
+  version: 2.0.1
 platform: ruby
 authors: 
 - Christoph Helma, Martin Guetlein, Andreas Maunz, Micha Rautenberg, David Vorgrimmler
@@ -15,7 +15,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-05-23 00:00:00 +02:00
+date: 2011-06-15 00:00:00 +02:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency