initial commit of devel version

1 files changed, 96 insertions, 61 deletions

diff --git a/application.rb b/application.rb
index 18c980f..88a2852 100644
--- a/application.rb
+++ b/application.rb
@@ -1,87 +1,122 @@
-## SETUP
-[ 'rubygems', 'sinatra', 'sinatra/url_for', 'dm-core', 'dm-more', 'builder', 'opentox-ruby-api-wrapper' ].each do |lib|
-	require lib
-end
 
-## MODELS
+[ 'rubygems', 'sinatra', 'sinatra/url_for', 'dm-core', 'opentox-ruby-api-wrapper', 'datamapper', 'logger', 'opentox-validation-lib' ].each do |lib|
+  require lib
+end
 
-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
+load 'validation_service.rb'
 
-	def validation_folds
-		# create folds from dataset_uri, return an array of validation objects with initialized training/test datasets
-	end
 
-end
+# hack: store self in $sinatra to make url_for method accessible in validation_service
+# (before is executed in every rest call, problem is that the request object is not set, until the first rest-call )
+before {$sinatra = self unless $sinatra}
+LOGGER = Logger.new(STDOUT)
+LOGGER.datetime_format = "%Y-%m-%d %H:%M:%S "
 
-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
+class Sinatra::Base
+  # logging halts (!= 202)
+  def halt(status,msg)
+    LOGGER.error "halt "+status.to_s+" "+msg.to_s if (status != 202)
+    throw :halt, [status, msg] 
+  end
 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")
+  LOGGER.info "list all crossvalidations"
+  Crossvalidation.all.collect{ |d| url_for("/crossvalidation/", :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
+  LOGGER.info "get crossvalidation with id "+params[:id].to_s
+  halt 404, "Crossvalidation #{params[:id]} not found." unless crossvalidation = Crossvalidation.get(params[:id])
+  halt 202, crossvalidation.to_yaml  unless crossvalidation.finished
+  crossvalidation.to_yaml
+end
+
+delete '/crossvalidation/:id/?' do
+  LOGGER.info "delete crossvalidation with id "+params[:id].to_s
+  halt 404, "Crossvalidation #{params[:id]} not found." unless crossvalidation = Crossvalidation.get(params[:id])
+  crossvalidation.delete
+end
+
+get '/crossvalidation/:id/validations' do
+  LOGGER.info "get all validations for crossvalidation with id "+params[:id].to_s
+  halt 404, "Crossvalidation #{params[:id]} not found." unless crossvalidation = Crossvalidation.get(params[:id])
+  Validation.all(:crossvalidation_id => params[:id]).collect{ |v| v.uri.to_s }.join("\n")+"\n"
 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
+  LOGGER.info "creating crossvalidation "+params.inspect
+  halt 400, "alogrithm_uri and/or dataset_uri missing: "+params.inspect unless params[:dataset_uri] and params[:algorithm_uri]
+  cv_params = { :dataset_uri => params[:dataset_uri],  
+                :algorithm_uri => params[:algorithm_uri] }
+  [ :num_folds, :random_seed, :stratified ].each{ |sym| cv_params[sym] = params[sym] if params[sym] }
+  cv = Crossvalidation.new cv_params
+  cv.create_cv_datasets
+  cv.perform_cv params[:feature_service_uri]
+  cv.uri
 end
 
 get '/validations/?' do
-	Validation.all.collect{ |d| url_for("/", :full) + d.id.to_s }.join("\n")
+  LOGGER.info "list all validations"
+  Validation.all.collect{ |d| url_for("/validation/", :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
+  LOGGER.info "get validation with id "+params[:id].to_s
+  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
+  LOGGER.info "creating validation "+params.inspect
+  if params[:model_uri] and params[:test_dataset_uri] and !params[:training_dataset_uri] and !params[:algorithm_uri]
+    v = Validation.new :model_uri => params[:model_uri], 
+                     :test_dataset_uri => params[:test_dataset_uri]
+    v.validate_model
+  elsif params[:algorithm_uri] and params[:training_dataset_uri] and params[:test_dataset_uri] and !params[:model_uri]
+   v = Validation.new :training_dataset_uri => params[:training_dataset_uri], 
+                     :test_dataset_uri => params[:test_dataset_uri]
+   v.validate_algorithm( params[:algorithm_uri], params[:feature_service_uri]) 
+  else
+    halt 400, "illegal param combination, use either (model_uri and test_dataset_uri) OR (algorithm_uri and training_dataset_uri and test_dataset_uri): "+params.inspect
+  end
+  
+  v.uri
 end
+
+post '/validation/training_test_split' do
+  LOGGER.info "creating training test split "+params.inspect
+  halt 400, "dataset_uri missing" unless params[:dataset_uri]
+  params.merge!(ValidationUtil.train_test_dataset_split(params[:dataset_uri], params[:split_ratio], params[:random_seed]))
+  if (params[:algorithm_uri])
+     v = Validation.new :training_dataset_uri => params[:training_dataset_uri], 
+                     :test_dataset_uri => params[:test_dataset_uri]
+     v.validate_algorithm( params[:algorithm_uri], params[:feature_service_uri]) 
+  else
+    v = Validation.new :training_dataset_uri => params[:training_dataset_uri], :test_dataset_uri => params[:test_dataset_uri] 
+  end
+  v.uri
+end
+
+get '/validation/:id/:attribute' do
+  LOGGER.info "access validation attribute "+params.inspect
+  halt 404, "Validation #{params[:id]} not found." unless validation = Validation.get(params[:id])
+  begin
+    raise unless validation.attribute_loaded?(params[:attribute])
+  rescue
+    halt 400, "Not a validation attribute: "+params[:attribute].to_s
+  end
+  return validation.send(params[:attribute])
+end
+
+delete '/validation/:id' do
+  LOGGER.info "delete validation with id "+params[:id].to_s
+  halt 404, "Validation #{params[:id]} not found." unless validation = Validation.get(params[:id])
+  validation.delete
+end
+
+
+