resolved conflicts, replace text/x-yaml with application/x-yaml, acceess classification values w/o confidence

1 files changed, 18 insertions, 127 deletions

diff --git a/lib/dataset.rb b/lib/dataset.rb
index e506305..1254992 100644
--- a/lib/dataset.rb
+++ b/lib/dataset.rb
@@ -15,15 +15,16 @@ module OpenTox
 		def self.find(uri, accept_header=nil) 
     
       unless accept_header
-        if uri.match(@@config[:services]["opentox-dataset"]) || uri=~ /188.40.32.88/ || uri =~ /in-silico.ch/
-          accept_header = 'text/x-yaml'
+        #if uri.match(@@config[:services]["opentox-dataset"]) || uri=~ /188.40.32.88/ || uri =~ /informatik/
+        if !@@config[:accept_headers]["opentox-dataset"].grep(/yaml/).empty?
+          accept_header = 'application/x-yaml'
         else
           accept_header = "application/rdf+xml"
         end
       end
       case accept_header
-      when "text/x-yaml"
-				d = YAML.load RestClientWrapper.get(uri.to_s.strip, :accept => 'text/x-yaml').to_s 
+      when "application/x-yaml"
+				d = YAML.load RestClientWrapper.get(uri.to_s.strip, :accept => 'application/x-yaml').to_s 
         d.uri = uri unless d.uri
 			when "application/rdf+xml"
 				owl = OpenTox::Owl.from_uri(uri.to_s.strip, "Dataset")
@@ -90,15 +91,16 @@ module OpenTox
         else
           return "no classification key"
         end
-      else
-        raise "predicted class value is not a hash\n"+
+      elsif v.is_a?(Array)
+        raise "predicted class value is an array\n"+
           "value "+v.to_s+"\n"+
           "value-class "+v.class.to_s+"\n"+
           "dataset "+@uri.to_s+"\n"+
           "compound "+compound.to_s+"\n"+
           "feature "+feature.to_s+"\n"
+      else
+        return v
       end
-      
     end
     
     # returns prediction confidence if available
@@ -112,12 +114,14 @@ module OpenTox
           raise "no confidence key"
         end
       else
-        raise "prediction confidence value is not a hash value\n"+
-          "value "+v.to_s+"\n"+
-          "value-class "+v.class.to_s+"\n"+
-          "dataset "+@uri.to_s+"\n"+
-          "compound "+compound.to_s+"\n"+
-          "feature "+feature.to_s+"\n"
+        LOGGER.warn "no confidence for compound: "+compound.to_s+", feature: "+feature.to_s
+        return 1
+#        raise "prediction confidence value is not a hash value\n"+
+#          "value "+v.to_s+"\n"+
+#          "value-class "+v.class.to_s+"\n"+
+#          "dataset "+@uri.to_s+"\n"+
+#          "compound "+compound.to_s+"\n"+
+#          "feature "+feature.to_s+"\n"
       end
     end
     
@@ -172,122 +176,9 @@ module OpenTox
     
 			@features.uniq!
 			@compounds.uniq!
-      OpenTox::RestClientWrapper.post(@@config[:services]["opentox-dataset"],{:content_type =>  "text/x-yaml"},self.to_yaml).strip.to_s
-		end
-
-=begin
-		# create/add to entry from uris or Redland::Resources
-		def add(compound,feature,value)
-			compound = self.find_or_create_compound compound unless compound.class == Redland::Resource
-			feature = self.find_or_create_feature feature unless feature.class == Redland::Resource
-			data_entry = @model.subject OT['compound'], compound
-			if data_entry.nil?
-				data_entry = @model.create_resource
-				dataset = @model.subject(RDF['type'],OT[self.owl_class])
-				@model.add dataset, OT['dataEntry'], data_entry
-				@model.add data_entry, RDF['type'], OT["DataEntry"]
-				@model.add data_entry, OT['compound'], compound
-			end
-			values = @model.create_resource
-			@model.add data_entry, OT['values'], values
-			@model.add values, RDF['type'], OT['FeatureValue']
-			@model.add values, OT['feature'], feature
-			@model.add values, OT['value'], value.to_s
-		end
-
-		def add_tuple(compound,tuple)
-			compound = self.find_or_create_compound compound unless compound.class == Redland::Resource
-			data_entry = @model.subject OT['compound'], compound
-			if data_entry.nil?
-				data_entry = @model.create_resource
-				dataset = @model.subject(RDF['type'],OT[self.owl_class])
-				@model.add dataset, OT['dataEntry'], data_entry
-				@model.add data_entry, RDF['type'], OT["DataEntry"]
-				@model.add data_entry, OT['compound'], compound
-			end
-			@model.add data_entry, OT['values'], tuple
-		end
-
-		def create_tuple(feature,t)
-			feature = self.find_or_create_feature feature unless feature.class == Redland::Resource
-			tuple = @model.create_resource
-			@model.add tuple, RDF['type'], OT["Tuple"]
-			@model.add tuple, OT['feature'], feature
-			t.each do |name,value|
-				f = self.find_or_create_feature name unless name.class == Redland::Resource
-				complex_value = @model.create_resource
-				feature = self.find_or_create_feature(name) 
-				@model.add tuple, OT['complexValue'], complex_value
-				@model.add complex_value, RDF['type'], OT["FeatureValue"]
-				@model.add complex_value, OT['feature'], f
-				@model.add complex_value, OT['value'], value.to_s
-      end
-  	
-			tuple
-		end
-
-		# find or create a new compound and return the resource
-		def find_or_create_compound(uri)
-			compound = @model.subject(DC["identifier"], uri)
-			if compound.nil?
-				compound = @model.create_resource(uri)
-				@model.add compound, RDF['type'], OT["Compound"]
-				@model.add compound, DC["identifier"], uri
-			end
-			compound
-		end
-
-		# find or create a new feature and return the resource
-		def find_or_create_feature(uri)
-			feature = @model.subject(DC["identifier"], uri)
-			if feature.nil?
-				feature = @model.create_resource(uri)
-				@model.add feature, RDF['type'], OT["Feature"]
-				@model.add feature, DC["identifier"], uri
-				@model.add feature, DC["title"], File.basename(uri).split(/#/)[1]
-				@model.add feature, DC['source'], uri
-			end
-			feature
-		end
-
-		def self.create(data, content_type = 'application/rdf+xml')
-      resource = RestClient::Resource.new(@@config[:services]["opentox-dataset"], :user => @@users[:users].keys[0], :password => @@users[:users].values[0])		  
-		  uri = resource.post data, :content_type => content_type
-			dataset = Dataset.new
-			dataset.read uri.chomp.to_s
-			dataset
-		end
-
-		def features
-			features = []
-			@model.subjects(RDF['type'], OT["Feature"]).each do |feature_node|
-				features << @model.object(feature_node,  DC["identifier"])#
-			end
-			features
-		end
-
-		def compounds
-			compounds = []
-			@model.subjects(RDF['type'], OT["Compound"]).each do |compound_node|
-				compounds << @model.object(compound_node,  DC["identifier"]).to_s
-			end
-			compounds
-		end
-
-		# Delete a dataset
-		def delete
-  		resource = RestClient::Resource.new(@uri, :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
-      resource.delete
-    end
-
-		def to_owl
-		end
-
-		def from_owl
+        OpenTox::RestClientWrapper.post(@@config[:services]["opentox-dataset"],{:content_type =>  "application/x-yaml"},self.to_yaml).strip 	
 		end
 
-=end
-
     def init_dirty_features(owl)
       @dirty_features = @features
       @owl = owl