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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
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