Initial stub for OpenTox validation webservice

1 files changed, 87 insertions, 0 deletions

diff --git a/application.rb b/application.rb
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+## SETUP
+[ 'rubygems', 'sinatra', 'sinatra/url_for', 'dm-core', 'dm-more', 'builder', 'opentox-ruby-api-wrapper' ].each do |lib|
+	require lib
+end
+
+## MODELS
+
+class CrossValidation
+	include DataMapper::Resource
+	property :id, Serial
+	property :uri, String, :size => 255
+	property :algorithm_uri, String, :size => 255
+	property :dataset_uri, String, :size => 255
+	has n, :validations
+
+	def validation_folds
+		# create folds from dataset_uri, return an array of validation objects with initialized training/test datasets
+	end
+
+end
+
+class Validation
+	include DataMapper::Resource
+	property :id, Serial
+	property :uri, String, :size => 255
+	property :model_uri, String, :size => 255
+	property :training_dataset_uri, String, :size => 255
+	property :test_dataset_uri, String, :size => 255
+	property :prediction_dataset_uri, String, :size => 255
+	property :finished, Boolean, :default => false
+	belongs_to :crossvalidation
+end
+
+sqlite = "#{File.expand_path(File.dirname(__FILE__))}/#{Sinatra::Base.environment}.sqlite3"
+DataMapper.setup(:default, "sqlite3:///#{sqlite}")
+DataMapper::Logger.new(STDOUT, 0)
+
+unless FileTest.exists?("#{sqlite}")
+	[CrossValidation, Validation].each do |model|
+		model.auto_migrate!
+	end
+end
+
+## REST API
+
+get '/crossvalidations/?' do
+	CrossValidation.all.collect{ |d| url_for("/", :full) + d.id.to_s }.join("\n")
+end
+
+get '/crossvalidation/:id' do
+	halt 404, "CrossValidation #{params[:id]} not found." unless validation = CrossValidation.get(params[:id])
+	halt 202, crossvalidation.to_yaml  unless crossvalidation.finished
+	crossvalidation.to_yaml
+end
+
+post '/crossvalidation/?' do
+	#protected!
+	cv = CrossValidation.new( :algorithm_uri => params[:algorithm_uri], :dataset_uri => params[:dataset_uri] )
+	Spork.spork do
+		cv.validation_folds.each do |validation|
+			model = OpenTox::Model.new(:algorithm_uri => cv.algorithm_uri, :dataset_uri => validation.training_dataset_uri)
+			# wait until model is finished
+			prediction_dataset = OpenTox::Dataset.new :name => "Validation #{validation.id} predictions"
+			validation.training_set.compounds.each do |compound|
+				prediction = model.predict compound
+				# wait until prediction is finished
+				feature = OpenTox::Feature.new :name => model.name, :values => {:prediction => prediction.classification, :confidence => prediction.confidence}
+				prediction_dataset.add(:compound_uri => compound.uri, :feature_uri => feature.uri)
+			end
+			prediction_dataset.close
+		end
+	end
+	cv.uri
+end
+
+get '/validations/?' do
+	Validation.all.collect{ |d| url_for("/", :full) + d.id.to_s }.join("\n")
+end
+
+get '/validation/:id' do
+	halt 404, "Validation #{params[:id]} not found." unless validation = Validation.get(params[:id])
+	halt 202, validation.to_yaml  unless validation.finished
+	validation.to_yaml
+end
+
+post '/validation/?' do
+end