owl-dl (temporarily) removed, switched to YAML representation

1 files changed, 35 insertions, 29 deletions

diff --git a/fminer.rb b/fminer.rb
index 86f6876..944a308 100644
--- a/fminer.rb
+++ b/fminer.rb
@@ -1,11 +1,7 @@
-LOGGER.progname = File.expand_path(__FILE__)
-
 ENV['FMINER_SMARTS'] = 'true'
 ENV['FMINER_PVALUES'] = 'true'
 @@fminer = Fminer::Fminer.new
 @@fminer.SetAromatic(true)
-#@@fminer.SetConsoleOut(false)
-#@@fminer.SetChisqSig(0.95)
 
 get '/fminer/?' do
 	response['Content-Type'] = 'application/rdf+xml'
@@ -19,8 +15,10 @@ post '/fminer/?' do
 	feature_uri = params[:feature_uri]
 	halt 404, "Please submit a feature_uri parameter." if feature_uri.nil?
 	begin
-		LOGGER.debug "Retrieving #{params[:dataset_uri]}?feature_uris\\[\\]=#{CGI.escape(feature_uri)}"
-		training_dataset = OpenTox::Dataset.find "#{params[:dataset_uri]}?feature_uris\\[\\]=#{CGI.escape(feature_uri)}"
+		#LOGGER.debug "Retrieving #{params[:dataset_uri]}?feature_uris\\[\\]=#{CGI.escape(feature_uri)}"
+		#training_dataset = OpenTox::Dataset.find "#{params[:dataset_uri]}?feature_uris\\[\\]=#{CGI.escape(feature_uri)}"
+		LOGGER.debug "Retrieving #{params[:dataset_uri]}"
+		training_dataset = OpenTox::Dataset.find "#{params[:dataset_uri]}"
 	rescue
 		LOGGER.error "Dataset #{params[:dataset_uri]} not found" 
 		halt 404, "Dataset #{params[:dataset_uri]} not found." if training_dataset.nil? 
@@ -38,13 +36,16 @@ post '/fminer/?' do
 		feature_dataset.title = title
 		feature_dataset.source = url_for('/fminer',:full)
 		bbrc_uri = url_for("/fminer#BBRC_representative",:full)
-		bbrc_feature = feature_dataset.find_or_create_feature bbrc_uri
+		feature_dataset.features << bbrc_uri
+		#bbrc_feature = feature_dataset.find_or_create_feature bbrc_uri
 
 		id = 1 # fminer start id is not 0
 		compounds = []
 		@@fminer.Reset
 		LOGGER.debug "Fminer: initialising ..."
 		training_dataset.data.each do |c,features|
+			LOGGER.debug c
+			LOGGER.debug features
 			begin
 				smiles = OpenTox::Compound.new(:uri => c.to_s).smiles
 			rescue
@@ -54,26 +55,29 @@ post '/fminer/?' do
 			if smiles == '' or smiles.nil?
 				LOGGER.warn "Cannot find smiles for #{c.to_s}."
 			else
-				compound = feature_dataset.find_or_create_compound(c.to_s)
-				LOGGER.warn "No #{feature_uri} for #{c.to_s}." if features[feature_uri].size == 0
-				features[feature_uri].each do |act|
-					if act.nil? 
-						LOGGER.warn "No #{feature_uri} activiity for #{c.to_s}."
-					else
-						case act.to_s
-						when "true"
-							LOGGER.debug id.to_s + ' "' + smiles +'"' +  "\t" + true.to_s
-							activity = 1
-						when "false"
-							LOGGER.debug id.to_s + ' "' + smiles +'"' +  "\t" + false.to_s
-							activity = 0
-						end
-						compounds[id] = compound
-						begin
-							@@fminer.AddCompound(smiles,id)
-							@@fminer.AddActivity(activity, id)
-						rescue
-							LOGGER.warn "Could not add " + smiles + "\t" + activity + " to fminer"
+				feature_dataset.compounds << c.to_s
+				if !features[feature_uri] or features[feature_uri].size == 0
+					LOGGER.warn "No #{feature_uri} for #{c.to_s}."
+				else
+					features[feature_uri].each do |act|
+						if act.nil? 
+							LOGGER.warn "No #{feature_uri} activiity for #{c.to_s}."
+						else
+							case act.to_s
+							when "true"
+								LOGGER.debug id.to_s + ' "' + smiles +'"' +  "\t" + true.to_s
+								activity = 1
+							when "false"
+								LOGGER.debug id.to_s + ' "' + smiles +'"' +  "\t" + false.to_s
+								activity = 0
+							end
+							compounds[id] = c.to_s
+							begin
+								@@fminer.AddCompound(smiles,id)
+								@@fminer.AddActivity(activity, id)
+							rescue
+								LOGGER.warn "Could not add " + smiles + "\t" + activity + " to fminer"
+							end
 						end
 					end
 				end
@@ -97,10 +101,12 @@ post '/fminer/?' do
 				else
 					effect = 'deactivating'
 				end
-				tuple = feature_dataset.create_tuple(bbrc_feature,{ url_for('/fminer#smarts',:full) => smarts, url_for('/fminer#p_value',:full) => p_value.to_f, url_for('/fminer#effect',:full) => effect })
+				tuple = { url_for('/fminer#smarts',:full) => smarts, url_for('/fminer#p_value',:full) => p_value.to_f, url_for('/fminer#effect',:full) => effect }
+				#tuple = feature_dataset.create_tuple(bbrc_feature,{ url_for('/fminer#smarts',:full) => smarts, url_for('/fminer#p_value',:full) => p_value.to_f, url_for('/fminer#effect',:full) => effect })
 				LOGGER.debug "#{f[0]}\t#{f[1]}\t#{effect}"
 				ids.each do |id|
-					feature_dataset.add_tuple compounds[id], tuple
+					feature_dataset.data[compounds[id]] = {} unless feature_dataset.data[compounds[id]]
+					feature_dataset.data[compounds[id]][bbrc_uri] = tuple
 				end
 			end
 		end