Michas changes merged

3 files changed, 19 insertions, 11 deletions

diff --git a/features/compound.feature b/features/compound.feature
index 7ee2c03..f628f4b 100644
--- a/features/compound.feature
+++ b/features/compound.feature
@@ -11,8 +11,8 @@ Feature: Create compound URI
 	Examples:
 		|descriptor                        |mime-type                 |inchi                                                         |cansmi                     |
 		|F[B-](F)(F)F.[Na+]                |chemical/x-daylight-smiles|InChI=1S/BF4.Na/c2-1(3,4)5;/q-1;+1                            |[Na+].F[B-](F)(F)F         |
-	#|CC(=O)CC(C)C#N                    |chemical/x-daylight-smiles|InChI=1S/C6H9NO/c1-5(4-7)3-6(2)8/h5H,3H2,1-2H3                |CC(CC(=O)C)C#N             |
-		#|Benzene                           |text/plain                |InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H                            |c1ccccc1                   |
-		#|N#[N+]C1=CC=CC=C1.F[B-](F)(F)F    |chemical/x-daylight-smiles|InChI=1S/C6H5N2.BF4/c7-8-6-4-2-1-3-5-6;2-1(3,4)5/h1-5H;/q+1;-1|N#[N+]c1ccccc1.F[B-](F)(F)F|
-		#|InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H|chemical/x-inchi          |InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H                            |c1ccccc1                   |
+		|CC(=O)CC(C)C#N                    |chemical/x-daylight-smiles|InChI=1S/C6H9NO/c1-5(4-7)3-6(2)8/h5H,3H2,1-2H3                |CC(CC(=O)C)C#N             |
+		|Benzene                           |text/plain                |InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H                            |c1ccccc1                   |
+		|N#[N+]C1=CC=CC=C1.F[B-](F)(F)F    |chemical/x-daylight-smiles|InChI=1S/C6H5N2.BF4/c7-8-6-4-2-1-3-5-6;2-1(3,4)5/h1-5H;/q+1;-1|N#[N+]c1ccccc1.F[B-](F)(F)F|
+		|InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H|chemical/x-inchi          |InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H                            |c1ccccc1                   |
 
diff --git a/features/step_definitions/common_steps.rb b/features/step_definitions/common_steps.rb
index e0d31e5..c912cee 100644
--- a/features/step_definitions/common_steps.rb
+++ b/features/step_definitions/common_steps.rb
@@ -11,6 +11,7 @@ When /^I post (.*) to the (.*) webservice$/ do |data,component|
 		@data = data
 	end
 	@uri = RestClient::Resource.new(@@config[:services]["opentox-#{component}"], :user => @@users[:users].keys[0], :password => @@users[:users].values[0]).post data, :content_type => @content_type
+	puts @uri
 	@resources << @uri unless /compound|feature/ =~ component
 end
 
@@ -27,7 +28,7 @@ When /^the task is completed$/ do
 end
 
 Then /^I should receive a valid URI$/ do
-	puts @uri
+	#puts @uri
 	@response = RestClient.get @uri, :accept => '*/*'
 	#puts @response.to_yaml
 end
@@ -43,8 +44,8 @@ Then /^the URI response should be (.+)$/ do |data|
 	when /^file:/
 		data = @data
 	end
-	puts data
-	puts @response
+	#puts data
+	#puts @response
 	assert data == @response, true
 end
 
diff --git a/features/step_definitions/lazar_steps.rb b/features/step_definitions/lazar_steps.rb
index ae8c6b2..a049153 100644
--- a/features/step_definitions/lazar_steps.rb
+++ b/features/step_definitions/lazar_steps.rb
@@ -13,18 +13,25 @@ Then /^the model should predict (.*) for (.*)$/ do |activity,smiles|
 	#puts @uri
 	#puts compound_uri
   resource = RestClient::Resource.new(@uri, :user => @@users[:users].keys[0], :password => @@users[:users].values[0])	
-	prediction = resource.post :compound_uri => compound_uri, :accept => "application/x-yaml"
+	prediction_rdf = resource.post :compound_uri => compound_uri#, :accept => "application/x-yaml"
 	model = Redland::Model.new Redland::MemoryStore.new
 	parser = Redland::Parser.new
-	parser.parse_string_into_model(model,prediction,'/')
+	parser.parse_string_into_model(model,prediction_rdf,'/')
 
-	#puts prediction
+	puts prediction_rdf
 	model.subjects(RDF['type'], OT['FeatureValue']).each do |v|
 		feature = model.object(v,OT['feature'])
 		feature_name = model.object(feature,DC['title']).to_s
 		prediction = model.object(v,OT['value']).to_s if feature_name.match(/classification/)
 	end
-	#puts values.to_yaml
+=begin
+	model.subjects(RDF['type'], OT['FeatureValue']).each do |v|
+		feature = model.object(v,OT['feature'])
+		feature_name = model.object(feature,DC['title']).to_s
+		prediction = model.object(v,OT['value']).to_s if feature_name.match(/classification/)
+	end
+=end
+	puts prediction
 	assert_equal activity.to_s, prediction
 end