Merge branch 'hotfix/uri_available' into development

4 files changed, 91 insertions, 24 deletions

diff --git a/lib/dataset.rb b/lib/dataset.rb
index 2b5759e..4005c1c 100644
--- a/lib/dataset.rb
+++ b/lib/dataset.rb
@@ -74,7 +74,7 @@ module OpenTox
     # @param [optional,String] uri URI of the dataset service, defaults to service specified in configuration
     # @return [Array] Array of dataset object without data (use one of the load_* methods to pull data from the server)
     def self.all(uri=CONFIG[:services]["opentox-dataset"], subjectid=nil)
-      RestClientWrapper.get(uri,{:accept => "text/uri-list",:subjectid => subjectid}).to_s.each_line.collect{|u| Dataset.new(u, subjectid)}
+      RestClientWrapper.get(uri,{:accept => "text/uri-list",:subjectid => subjectid}).to_s.each_line.collect{|u| Dataset.new(u.chomp, subjectid)}
     end
 
     # Load YAML representation into the dataset
@@ -158,8 +158,12 @@ module OpenTox
     # Load and return only features from the dataset service
     # @return [Hash]  Features of the dataset
     def load_features(subjectid=nil)
-      parser = Parser::Owl::Dataset.new(@uri, subjectid)
-      @features = parser.load_features(subjectid)
+      if (CONFIG[:yaml_hosts].include?(URI.parse(@uri).host))
+        @features = YAML.load(RestClientWrapper.get(File.join(@uri,"features"), {:accept => "application/x-yaml", :subjectid => subjectid}))
+      else
+        parser = Parser::Owl::Dataset.new(@uri, subjectid)
+        @features = parser.load_features(subjectid)
+      end
       @features
     end
 
diff --git a/lib/helper.rb b/lib/helper.rb
index 3a6126a..995f3e9 100644
--- a/lib/helper.rb
+++ b/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
 
diff --git a/lib/parser.rb b/lib/parser.rb
index 7bdee95..5f847c3 100644
--- a/lib/parser.rb
+++ b/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)
diff --git a/opentox-ruby.gemspec b/opentox-ruby.gemspec
index 289dacd..e62eec5 100644
--- a/opentox-ruby.gemspec
+++ b/opentox-ruby.gemspec
@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = %q{opentox-ruby}
-  s.version = "1.0.2"
+  s.version = "2.0.0"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Christoph Helma, Martin Guetlein, Andreas Maunz, Micha Rautenberg, David Vorgrimmler"]
-  s.date = %q{2011-03-16}
+  s.date = %q{2011-05-23}
   s.description = %q{Ruby wrapper for the OpenTox REST API (http://www.opentox.org)}
   s.email = %q{helma@in-silico.ch}
   s.executables = ["opentox-install-debian.sh", "opentox-install-ubuntu.sh"]
@@ -34,7 +34,7 @@ Gem::Specification.new do |s|
     "lib/feature.rb",
     "lib/helper.rb",
     "lib/model.rb",
-    "lib/ontology_service.rb",
+    "lib/ontology.rb",
     "lib/opentox-ruby.rb",
     "lib/opentox.owl",
     "lib/opentox.rb",
@@ -45,7 +45,6 @@ Gem::Specification.new do |s|
     "lib/serializer.rb",
     "lib/spork.rb",
     "lib/task.rb",
-    "lib/templates/config.yaml",
     "lib/templates/default_guest_policy.xml",
     "lib/templates/default_policy.xml",
     "lib/to-html.rb",
@@ -53,7 +52,7 @@ Gem::Specification.new do |s|
   ]
   s.homepage = %q{http://github.com/helma/opentox-ruby}
   s.require_paths = ["lib"]
-  s.rubygems_version = %q{1.4.2}
+  s.rubygems_version = %q{1.5.2}
   s.summary = %q{Ruby wrapper for the OpenTox REST API}
 
   if s.respond_to? :specification_version then
@@ -77,9 +76,18 @@ Gem::Specification.new do |s|
       s.add_runtime_dependency(%q<tmail>, [">= 0"])
       s.add_runtime_dependency(%q<rinruby>, [">= 0"])
       s.add_runtime_dependency(%q<ohm>, [">= 0"])
+      s.add_runtime_dependency(%q<ohm-contrib>, [">= 0"])
       s.add_runtime_dependency(%q<SystemTimer>, [">= 0"])
       s.add_runtime_dependency(%q<rjb>, [">= 0"])
+      s.add_runtime_dependency(%q<dm-core>, [">= 0"])
+      s.add_runtime_dependency(%q<dm-serializer>, [">= 0"])
+      s.add_runtime_dependency(%q<dm-timestamps>, [">= 0"])
+      s.add_runtime_dependency(%q<dm-types>, [">= 0"])
+      s.add_runtime_dependency(%q<dm-migrations>, [">= 0"])
+      s.add_runtime_dependency(%q<dm-validations>, [">= 0"])
+      s.add_runtime_dependency(%q<dm-sqlite-adapter>, [">= 0"])
       s.add_runtime_dependency(%q<haml>, [">= 3"])
+      s.add_runtime_dependency(%q<ruby-plot>, ["~> 0.4.0"])
       s.add_development_dependency(%q<jeweler>, [">= 0"])
     else
       s.add_dependency(%q<sinatra>, [">= 0"])
@@ -99,9 +107,18 @@ Gem::Specification.new do |s|
       s.add_dependency(%q<tmail>, [">= 0"])
       s.add_dependency(%q<rinruby>, [">= 0"])
       s.add_dependency(%q<ohm>, [">= 0"])
+      s.add_dependency(%q<ohm-contrib>, [">= 0"])
       s.add_dependency(%q<SystemTimer>, [">= 0"])
       s.add_dependency(%q<rjb>, [">= 0"])
+      s.add_dependency(%q<dm-core>, [">= 0"])
+      s.add_dependency(%q<dm-serializer>, [">= 0"])
+      s.add_dependency(%q<dm-timestamps>, [">= 0"])
+      s.add_dependency(%q<dm-types>, [">= 0"])
+      s.add_dependency(%q<dm-migrations>, [">= 0"])
+      s.add_dependency(%q<dm-validations>, [">= 0"])
+      s.add_dependency(%q<dm-sqlite-adapter>, [">= 0"])
       s.add_dependency(%q<haml>, [">= 3"])
+      s.add_dependency(%q<ruby-plot>, ["~> 0.4.0"])
       s.add_dependency(%q<jeweler>, [">= 0"])
     end
   else
@@ -122,9 +139,18 @@ Gem::Specification.new do |s|
     s.add_dependency(%q<tmail>, [">= 0"])
     s.add_dependency(%q<rinruby>, [">= 0"])
     s.add_dependency(%q<ohm>, [">= 0"])
+    s.add_dependency(%q<ohm-contrib>, [">= 0"])
     s.add_dependency(%q<SystemTimer>, [">= 0"])
     s.add_dependency(%q<rjb>, [">= 0"])
+    s.add_dependency(%q<dm-core>, [">= 0"])
+    s.add_dependency(%q<dm-serializer>, [">= 0"])
+    s.add_dependency(%q<dm-timestamps>, [">= 0"])
+    s.add_dependency(%q<dm-types>, [">= 0"])
+    s.add_dependency(%q<dm-migrations>, [">= 0"])
+    s.add_dependency(%q<dm-validations>, [">= 0"])
+    s.add_dependency(%q<dm-sqlite-adapter>, [">= 0"])
     s.add_dependency(%q<haml>, [">= 3"])
+    s.add_dependency(%q<ruby-plot>, ["~> 0.4.0"])
     s.add_dependency(%q<jeweler>, [">= 0"])
   end
 end