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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
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