Passes tests in opentox-test

1 files changed, 134 insertions, 0 deletions

diff --git a/lazar.rb b/lazar.rb
new file mode 100644
index 0000000..2b23495
--- /dev/null
+++ b/lazar.rb
@@ -0,0 +1,134 @@
+require 'datamapper'
+
+DataMapper::setup(:default, "sqlite3://#{Dir.pwd}/db/#{ENV['RACK_ENV']}.db")
+
+class LazarModel
+	include DataMapper::Resource
+	property :id, Serial
+	property :activity_dataset_uri, String, :length => 256 # default is too short for URIs
+	property :feature_dataset_uri, String, :length => 256 # default is too short for URIs
+	property :created_at, DateTime
+
+	def uri
+		File.join(OpenTox::Model::LazarClassification.base_uri,"lazar_classification", self.id.to_s)
+	end
+
+	def predict(compound)
+
+		training_activities = OpenTox::Dataset.find :uri => @activity_dataset_uri
+		# TODO: find database activities
+		# TODO: find prediction
+		training_features = OpenTox::Dataset.find :uri => @feature_dataset_uri
+
+		prediction_dataset = OpenTox::Dataset.find_or_create(:name => training_activities.name + '_predictions')
+		prediction_neighbors = OpenTox::Dataset.find_or_create(:name => training_activities.name + '_neighbors')
+		prediction_features = OpenTox::Dataset.find_or_create(:name => training_activities.name + '_prediction_features')
+
+		feature_uris = compound.match(training_features)
+		prediction_features.add({compound.uri => feature_uris}.to_yaml)
+
+		conf = 0.0
+		neighbors = []
+
+		training_features.compounds.each do |neighbor|
+			sim = OpenTox::Algorithm::Similarity.weighted_tanimoto(training_features,neighbor,prediction_features,compound).to_f
+			if sim > 0.3
+				neighbors << neighbor.uri
+				training_activities.features(neighbor).each do |a|
+					case OpenTox::Feature.new(:uri => a.uri).value('classification').to_s
+					when 'true'
+						conf += OpenTox::Utils.gauss(sim) 
+					when 'false'
+						conf -= OpenTox::Utils.gauss(sim)
+					end
+				end
+			end
+		end
+		conf = conf/neighbors.size
+		if conf > 0.0
+			classification = true
+		elsif conf < 0.0
+			classification = false
+		end
+
+		prediction = OpenTox::Feature.new(:name => training_activities.name + " prediction", :classification => classification, :confidence => conf)
+		prediction_neighbors.add({compound.uri => neighbors}.to_yaml)
+		prediction_dataset.add({compound.uri => [prediction.uri]}.to_yaml)
+
+		prediction.uri
+
+	end
+end
+
+# automatically create the post table
+LazarModel.auto_migrate! #unless LazarModel.table_exists?
+LazarModel.auto_migrate! if ENV['RACK_ENV'] == 'test'
+
+get '/lazar_classification/?' do # get index of models
+	LazarModel.all.collect{|m| m.uri}.join("\n")
+end
+
+get '/lazar_classification/:id/?' do
+	halt 404, "Model #{params[:id]} not found." unless @model = LazarModel.get(params[:id])
+	@model.to_yaml
+end
+
+delete '/lazar_classification/:id/?' do
+	halt 404, "Model #{params[:id]} not found." unless @model = LazarModel.get(params[:id])
+	@model.destroy
+	"Model #{params[:id]} succesfully deleted."
+end
+
+post '/lazar_classification/?' do # create model
+	halt 404, "Dataset #{params[:activity_dataset_uri]} not found" unless  OpenTox::Dataset.find(:uri => params[:activity_dataset_uri])
+	halt 404, "Dataset #{params[:feature_dataset_uri]} not found" unless OpenTox::Dataset.find(:uri => params[:feature_dataset_uri])
+	model = LazarModel.new(params)
+	model.save
+	model.uri
+end
+
+# PREDICTIONS
+post '/lazar_classification/:id/?' do # create prediction
+	halt 404, "Model #{params[:id]} not found." unless @model = LazarModel.get(params[:id])
+	compound = OpenTox::Compound.new :uri => params[:compound_uri]
+	@model.predict(compound)
+end
+
+get '/lazar_classification/*/predictions?' do # get dataset URI
+	name = params[:splat].first
+	halt 404, "Model #{name} not found." unless @model = LazarModel.get(request.url)
+	# Dataset.find
+end
+
+get '/lazar_classification/*/prediction/*' do	# display prediction for a compound
+	name = params[:splat].first
+	compound_uri = params[:splat][1]
+	halt 404, "Model #{name} not found." unless @model = LazarModel.get(request.url)
+	# prediction not found
+	#prediction.to_yaml
+	#xml prediction
+end
+
+get '/lazar_classification/*/prediction/*/neighbors' do	
+	name = params[:splat].first
+	compound_uri = params[:splat][1]
+	halt 404, "Model #{name} not found." unless @model = LazarModel.get(request.url)
+	# prediction not found
+	# prediction.neighbors
+end
+
+get '/lazar_classification/*/prediction/*/features' do	
+	name = params[:splat].first
+	compound_uri = params[:splat][1]
+	halt 404, "Model #{name} not found." unless @model = LazarModel.get(request.url)
+	# prediction not found
+	# prediction not found
+	# prediction.features
+end
+
+delete '/lazar_classification/*/prediction/*' do	# display prediction for a compound
+	name = params[:splat].first
+	halt 404, "Model #{name} not found." unless @model = LazarModel.get(request.url)
+	# Prediction.destroy
+end
+