Prediction calculation fixed

1 files changed, 52 insertions, 99 deletions

diff --git a/lazar.rb b/lazar.rb
index 8ec4db8..16cb69b 100644
--- a/lazar.rb
+++ b/lazar.rb
@@ -1,11 +1,3 @@
-require 'redland'
-require 'rdf/redland'
-require 'rdf/redland/util'
-
-@@storage = Redland::MemoryStore.new
-@@parser = Redland::Parser.new
-@@serializer = Redland::Serializer.new
-
 get '/?' do # get index of models
 	Dir["models/*"].collect{|model|  url_for("/", :full) + File.basename(model,".yaml")}.sort.join("\n")
 end
@@ -31,81 +23,34 @@ delete '/:id/?' do
 	end
 end
 
-post '/lazar/?' do # create model
-	halt 404, "Dataset #{params[:activity_dataset_uri]} not found" unless  OpenTox::Dataset.find(params[:activity_dataset_uri])
-	halt 404, "Dataset #{params[:feature_dataset_uri]} not found" unless OpenTox::Dataset.find(params[:feature_dataset_uri])
-	activities = Redland::Model.new @storage
-	features = Redland::Model.new @storage
-	training_activities = OpenTox::Dataset.find params[:activity_dataset_uri]
-	training_features = OpenTox::Dataset.find params[:feature_dataset_uri]
-	@@parser.parse_string_into_model(activities,training_activities,'/')
-	@@parser.parse_string_into_model(features,training_features,'/')
-	feature = Redland::Node.new(Redland::Uri.new(File.join(@@config[:services]["opentox-algorithm"],'fminer')))
-	p_value = Redland::Node.new(Redland::Uri.new(File.join(@@config[:services]["opentox-algorithm"],'fminer/p_value')))
-	effect = Redland::Node.new(Redland::Uri.new(File.join(@@config[:services]["opentox-algorithm"],'fminer/effect')))
-
-	smarts = []
-	p_vals = {}
-	effects = {}
-	fingerprints = {}
-	features.triples do |s,p,o|
-		s = s.uri.to_s.sub(/^\//,'') 
-		case p
-		when feature
-			fingerprints[s] = [] unless fingerprints[s]
-			fingerprints[s] << o.uri.to_s.sub(/^\//,'') 
-		when p_value
-			sma = s.to_s
-			smarts << sma
-			p_vals[sma] = o.to_s.to_f
-		when effect
-			sma = s.to_s
-			effects[sma] = o.to_s
-		end
-	end
+post '/?' do # create model
 
-	activity_uris = []
-	act = {}
-	activities.triples do |s,p,o|
-		activity_uris << p.uri.to_s
-		s = s.uri.to_s
-		case o.to_s
-		when "true"
-			act[s] = true
-		when "false"
-			act[s] = false
+	case request.content_type
+	when /application\/x-yaml|text\/yaml/
+		input =	request.env["rack.input"].read
+		id = Dir["models/*"].collect{|model|  File.basename(model,".yaml").to_i}.sort.last
+		if id.nil?
+			id = 1
+		else
+			id += 1
 		end
-	end
-
-	activity_uris.uniq!
-	if activity_uris.size != 1
-		halt 400
-		"Dataset #{params[:activity_dataset_uri]} has not exactly one feature."
-	end
-
-	id = Dir["models/*"].collect{|models|  File.basename(models,".yaml").to_i}.sort.last
-	if id.nil?
-		id = 1
+		File.open(File.join("models",id.to_s + ".yaml"),"w+") { |f| f.write input }
+		url_for("/#{id}", :full)
 	else
-		id += 1
+		halt 400, "MIME type \"#{request.content_type}\" not supported."
 	end
 
-	File.open(File.join("models",id.to_s + ".yaml"),"w") do |f|
-		f.write({
-			:endpoint => activity_uris[0],
-			:features => smarts,
-			:p_values => p_vals,
-			:effects => effects,
-			:fingerprints => fingerprints,
-			:activities => act
-		}.to_yaml)
-	end
 	url_for("/#{id}", :full)
 
 end
 
 # PREDICTIONS
 post '/:id/?' do # create prediction
+
+  storage = Redland::MemoryStore.new
+  parser = Redland::Parser.new
+  serializer = Redland::Serializer.new
+
 	path = File.join("models",params[:id] + ".yaml")
 	if !File.exists? path
 		status 404
@@ -118,48 +63,56 @@ post '/:id/?' do # create prediction
 
 	# find database activities
 	if data[:activities][compound.uri]
-		output = Redland::Model.new @storage
+		output = Redland::Model.new storage
 		output.add Redland::Uri.new(compound.uri), Redland::Uri.new(data[:endpoint]), Redland::Literal.new(data[:activities][compound.uri].to_s)
-		halt 200, @@serializer.model_to_string(Redland::Uri.new(url_for("/",:full)), output)
-	end
+		response = serializer.model_to_string(Redland::Uri.new(url_for("/",:full)), output)
+	else
+		compound_matches = compound.match data[:features]
 
-	compound_matches = compound.match data[:features]
+		conf = 0.0
+		neighbors = []
+		classification = nil
 
-	conf = 0.0
-	neighbors = []
-	classification = nil
+		data[:fingerprints].each do |uri,matches|
 
-	data[:fingerprints].each do |uri,matches|
-		sim = weighted_tanimoto(compound_matches,matches,data[:p_values])
-		if sim > 0.3
+			sim = weighted_tanimoto(compound_matches,matches,data[:p_values])
+			if sim > 0.3
 
-			neighbors << uri
-			case data[:activities][uri].to_s
-			when 'true'
-				conf += OpenTox::Utils.gauss(sim) 
-			when 'false'
-				conf -= OpenTox::Utils.gauss(sim)
+				neighbors << uri
+				case data[:activities][uri].to_s
+				when 'true'
+					puts "t: #{sim}"
+					conf += OpenTox::Utils.gauss(sim)
+				when 'false'
+					conf -= OpenTox::Utils.gauss(sim)
+				end
 			end
 		end
+
 		conf = conf/neighbors.size
 		if conf > 0.0
 			classification = true
 		elsif conf < 0.0
 			classification = false
 		end
-	end
-
-	output = Redland::Model.new @storage
 
-	output.add Redland::Uri.new(compound.uri), Redland::Uri.new(url_for("/#{params[:id]}/classification",:full)), classification.to_s
-	output.add Redland::Uri.new(compound.uri), Redland::Uri.new(url_for("/#{params[:id]}/confidence",:full)), conf.to_s
-	@@serializer.model_to_string(Redland::Uri.new(url_for("/",:full)), output)
+		output = Redland::Model.new storage
+		output.add Redland::Uri.new(compound.uri), Redland::Uri.new(url_for("/#{params[:id]}/classification",:full)), classification.to_s
+		output.add Redland::Uri.new(compound.uri), Redland::Uri.new(url_for("/#{params[:id]}/confidence",:full)), conf.to_s
+		neighbors.each do |neighbor|
+			output.add Redland::Uri.new(compound.uri), Redland::Uri.new(url_for("/#{params[:id]}/neighbor",:full)), Redland::Uri.new(neighbor)
+		end
+		response =serializer.model_to_string(Redland::Uri.new(url_for("/",:full)), output)
+	end
 	
-#	{ :classification => classification,
-#		:confidence => conf,
-#		:neighbors => neighbors,
-#		:features => compound_matches
-#	}.to_yaml
+	m = { :classification => classification,
+		:confidence => conf,
+		:neighbors => neighbors,
+		:features => compound_matches
+	}
+	puts m.to_yaml
+
+	response
 end