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|
get '/lazar/?' do
owl = OpenTox::Owl.create 'Algorithm', url_for('/lazar',:full)
owl.set 'title',"lazar"
owl.set 'creator',"http://github.com/helma/opentox-algorithm"
owl.parameters = {
"Dataset URI" =>
{ :scope => "mandatory", :value => "dataset_uri" },
"Feature URI for dependent variable" =>
{ :scope => "mandatory", :value => "prediction_feature" },
"Feature generation URI" =>
{ :scope => "mandatory", :value => "feature_generation_uri" }
}
rdf = owl.rdf
File.open('public/lazar.owl', 'w') {|f| f.print rdf}
response['Content-Type'] = 'application/rdf+xml'
rdf
end
post '/lazar/?' do # create a model
LOGGER.debug "Dataset: '" + params[:dataset_uri].to_s + "'"
LOGGER.debug "Endpoint: '" + params[:prediction_feature].to_s + "'"
LOGGER.debug "Feature generation: '" + params[:feature_generation_uri].to_s + "'"
LOGGER.debug "Token ID: #{params[:token_id]}"
dataset_uri = "#{params[:dataset_uri]}"
begin
training_activities = OpenTox::Dataset.find(dataset_uri)
rescue
halt 404, "Dataset #{dataset_uri} not found"
end
halt 404, "No prediction_feature parameter." unless params[:prediction_feature]
halt 404, "No feature_generation_uri parameter." unless params[:feature_generation_uri]
halt 404, "No feature #{params[:prediction_feature]} in dataset #{params[:dataset_uri]}. (features: "+
training_activities.features.inspect+")" unless training_activities.features and training_activities.features.include?(params[:prediction_feature])
response['Content-Type'] = 'text/uri-list'
task_uri = OpenTox::Task.as_task("Create lazar model",url_for('/lazar',:full)) do |task|
# create features
LOGGER.debug "Starting fminer"
params[:feature_uri] = params[:prediction_feature]
fminer_task_uri = OpenTox::Algorithm::Fminer.create_feature_dataset(params)
fminer_task = OpenTox::Task.find(fminer_task_uri)
fminer_task.wait_for_completion
raise "fminer failed" unless fminer_task.completed?
LOGGER.debug "Fminer finished #{Time.now}"
feature_dataset_uri = fminer_task.resultURI.to_s
training_features = OpenTox::Dataset.find(feature_dataset_uri)
halt 404, "Dataset #{feature_dataset_uri} not found." if training_features.nil?
lazar = OpenTox::Model::Lazar.new
lazar.token_id = params[:token_id] if params[:token_id]
lazar.token_id = request.env["HTTP_TOKEN_ID"] if !lazar.token_id and request.env["HTTP_TOKEN_ID"]
lazar.trainingDataset = dataset_uri
lazar.feature_dataset_uri = feature_dataset_uri
halt 404, "More than one descriptor type" unless training_features.features.size == 1
bbrc = training_features.features.first
training_features.data.each do |compound,features|
lazar.fingerprints[compound] = [] unless lazar.fingerprints[compound]
features.each do |feature|
tuple = feature[bbrc]
if tuple
smarts =nil; p_value = nil; effect = nil
tuple.each do |k,v|
case k
when /fminer#smarts/
smarts = v
lazar.features << smarts
lazar.fingerprints[compound] << smarts
when /fminer#p_value/
p_value = v
when /fminer#effect/
effect = v
end
end
lazar.p_values[smarts] = p_value
lazar.effects[smarts] = effect
end
end
end
activities = {}
classification = true
training_activities.data.each do |compound,features|
lazar.activities[compound] = [] unless lazar.activities[compound]
features.each do |feature|
case feature[params[:prediction_feature]].to_s
when "true"
lazar.activities[compound] << true
when "false"
lazar.activities[compound] << false
# AM: handle quantitative activity values of features
else
lazar.activities[compound] << feature[params[:prediction_feature]].to_f
classification = false
end
end
end
# TODO: insert regression
if classification
lazar.dependentVariables = params[:prediction_feature]+"_lazar_classification"
else
lazar.dependentVariables = params[:prediction_feature]+"_lazar_regression"
end
model_uri = lazar.save
LOGGER.info model_uri + " created #{Time.now}"
model_uri
end
halt 202,task_uri
end
post '/property_lazar/?' do # create a model
LOGGER.debug "Dataset: '" + params[:dataset_uri].to_s + "'"
LOGGER.debug "Endpoint: '" + params[:prediction_feature].to_s + "'"
LOGGER.debug "Feature dataset: '" + params[:feature_dataset_uri].to_s + "'"
dataset_uri = "#{params[:dataset_uri]}"
begin
training_activities = OpenTox::Dataset.find(dataset_uri)
rescue
halt 404, "Dataset #{dataset_uri} not found"
end
halt 404, "No prediction_feature parameter." unless params[:prediction_feature]
halt 404, "No feature_dataset_uri parameter." unless params[:feature_dataset_uri]
halt 404, "No feature #{params[:prediction_feature]} in dataset #{params[:dataset_uri]}. (features: "+
training_activities.features.inspect+")" unless training_activities.features and training_activities.features.include?(params[:prediction_feature])
response['Content-Type'] = 'text/uri-list'
task_uri = OpenTox::Task.as_task("Create lazar model",url_for('/property_lazar',:full)) do |task|
# create features
#LOGGER.debug "Starting fminer"
#params[:feature_uri] = params[:prediction_feature]
#fminer_task_uri = OpenTox::Algorithm::Fminer.create_feature_dataset(params)
#fminer_task = OpenTox::Task.find(fminer_task_uri)
#fminer_task.wait_for_completion
#raise "fminer failed" unless fminer_task.completed?
#LOGGER.debug "Fminer finished #{Time.now}"
feature_dataset_uri = params[:feature_dataset_uri]
training_features = OpenTox::Dataset.find(feature_dataset_uri)
halt 404, "Dataset #{feature_dataset_uri} not found." if training_features.nil?
lazar = OpenTox::Model::PropertyLazar.new
lazar.trainingDataset = dataset_uri
lazar.feature_dataset_uri = feature_dataset_uri
#halt 404, "More than one descriptor type" unless training_features.features.size == 1
lazar.features = training_features.features
training_features.data.each do |compound,features|
lazar.properties[compound] = {} unless lazar.properties[compound]
LOGGER.debug features.inspect
if features
features.each do |f|
f.each do |name,value|
#lazar.features.each do |feature|
lazar.properties[compound][name] = value
#lazar.properties[compound] = features
end
end
end
end
activities = {}
classification = true
training_activities.data.each do |compound,features|
lazar.activities[compound] = [] unless lazar.activities[compound]
features.each do |feature|
case feature[params[:prediction_feature]].to_s
when "true"
lazar.activities[compound] << true
when "false"
lazar.activities[compound] << false
else
lazar.activities[compound] << feature[params[:prediction_feature]].to_f
classification = false
end
end
end
if classification
lazar.dependentVariables = params[:prediction_feature]+"_lazar_classification"
else
lazar.dependentVariables = params[:prediction_feature]+"_lazar_regression"
end
model_uri = lazar.save
LOGGER.info model_uri + " created #{Time.now}"
model_uri
end
halt 202,task_uri
end
|
