added amit dataset parsing, static lazar feature modifier

4 files changed, 22 insertions, 7 deletions

diff --git a/lib/dataset.rb b/lib/dataset.rb
index bbadd2d..2d49829 100644
--- a/lib/dataset.rb
+++ b/lib/dataset.rb
@@ -123,6 +123,16 @@ module OpenTox
 							value = true
 						when FALSE_REGEXP # defined in environment.rb
 							value = false
+				  	when /.*\^\^<.*XMLSchema#.*>/
+              case value.to_s
+              when /XMLSchema#string/
+                value = value.to_s[0..(value.to_s.index("^^")-1)]
+              when /XMLSchema#double/
+                value = value.to_s[0..(value.to_s.index("^^")-1)].to_f
+              else
+                LOGGER.warn " ILLEGAL TYPE "+compound_uri + " has value '" + value.to_s + "' for feature " + feature_uri
+                value = nil
+              end
 						else
 							LOGGER.warn compound_uri + " has value '" + value.to_s + "' for feature " + feature_uri
 							value = nil
diff --git a/lib/environment.rb b/lib/environment.rb
index 27da072..4c501b4 100644
--- a/lib/environment.rb
+++ b/lib/environment.rb
@@ -113,8 +113,7 @@ end
 begin
   0 < @@users[:users].keys.length
 rescue
-  puts "Please edit #{user_file} and restart your application. Create at least one user with password."
-  exit
+  raise "Please edit #{user_file} and restart your application. Create at least one user with password."
 end
 
 # RDF namespaces
diff --git a/lib/model.rb b/lib/model.rb
index 6c48734..b4ef86c 100644
--- a/lib/model.rb
+++ b/lib/model.rb
@@ -2,7 +2,9 @@ module OpenTox
 	module Model
    
 		class Lazar
-			include Owl
+    	include Owl
+      
+      PREDICTION_FEATURE_MODIFIER = "_lazar_prediction"
 
 			# Create a new prediction model from a dataset
 			def initialize
@@ -24,7 +26,7 @@ module OpenTox
 				lazar.algorithm = File.join(@@config[:services]["opentox-algorithm"],"lazar")
 				lazar.trainingDataset = yaml[:activity_dataset]
 				lazar.dependentVariables = yaml[:endpoint]
-				lazar.predictedVariables = yaml[:endpoint] + "_lazar_prediction"
+				lazar.predictedVariables = yaml[:endpoint] + PREDICTION_FEATURE_MODIFIER
 				lazar
 			end
 
@@ -35,7 +37,8 @@ module OpenTox
 			def self.find(uri)
 				yaml = RestClient.get(uri, :accept => "application/x-yaml")
 				OpenTox::Model::Lazar.from_yaml(yaml)
-			end
+  		end
+    
 			
 			# Predict a compound
 			def predict(compound)
@@ -80,7 +83,7 @@ module OpenTox
 
 			def trainingDataset=(trainingDataset)
 				me = @model.subject(RDF['type'],OT[self.owl_class])
-				@model.add me, OT['trainingDataset'], Redland::Uri.new(trainingDataset) # untyped individual comes from this line, why??
+        @model.add me, OT['trainingDataset'], Redland::Uri.new(trainingDataset) # untyped individual comes from this line, why??
 				@model.add Redland::Uri.new(trainingDataset), RDF['type'], OT['Dataset']
 			end
 
@@ -100,7 +103,8 @@ module OpenTox
 				me = @model.subject(RDF['type'],OT[self.owl_class])
 				@model.add me, OT['predictedVariables'], Redland::Uri.new(predictedVariables) # untyped individual comes from this line, why??
 				@model.add Redland::Uri.new(predictedVariables), RDF['type'], OT['Feature']
-			end
+		  end
+    
 		end
 	end
 end
diff --git a/lib/spork.rb b/lib/spork.rb
index 5b43281..e8cf37f 100644
--- a/lib/spork.rb
+++ b/lib/spork.rb
@@ -37,6 +37,7 @@ module Spork
   def self.spork(options={})
     logger = options[:logger]
     logger.debug "spork> parent PID = #{Process.pid}" if logger
+    
     child = fork do
       begin
         start = Time.now
@@ -52,6 +53,7 @@ module Spork
         yield
 
       rescue => ex
+        raise ex
         logger.error "spork> Exception in child[#{Process.pid}] - #{ex.class}: #{ex.message}" if logger
       ensure
         logger.info "spork> child[#{Process.pid}] took #{Time.now - start} sec" if logger