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|
load 'environment.rb'
# MODELS
get '/models/?' do # get index of models
Model.all.collect{ |m| m.uri }.join("\n")
end
get '/model/:id' do
begin
model = Model.get(params[:id])
rescue
status 404
"Model #{params[:id]} not found"
end
if model.finished
xml model
else
status 202
"Model #{params[:id]} under construction"
end
end
post '/models' do # create a model
if params[:dataset_uri]
training_dataset = OpenTox::Dataset.new :uri => params[:dataset_uri]
else
training_dataset = OpenTox::Dataset.new :name => params[:name]
end
model = Model.create(:name => params[:name], :training_dataset_uri => training_dataset.uri)
model.update_attributes(:uri => url_for("/model/", :full) + model.id.to_s)
pid = fork do #Spork.spork do
unless params[:dataset_uri] # create model from a tab delimited file
File.open(params[:file][:tempfile].path).each_line do |line|
items = line.chomp.split(/\s+/)
compound = OpenTox::Compound.new :smiles => items[0]
feature = OpenTox::Feature.new :name => params[:name], :values => { 'classification' => items[1] }
training_dataset.add(compound, feature)
end
end
feature_generation = OpenTox::Fminer.new(training_dataset)
feature_dataset = feature_generation.dataset
model.feature_dataset_uri = feature_dataset.uri.chomp
model.finished = true
model.save
end
Process.detach(pid)
model.uri.to_s
end
delete '/model/:id' do
begin
model = Model.get params[:id]
rescue
status 404
"Model #{params[:id]} not found"
end
model.predictions.each do |p|
p.neighbors.each { |n| n.destroy }
p.features.each { |n| f.destroy }
p.destroy
end
model.destroy
"Model #{params[:id]} succesfully deleted."
# TODO: what happens with datasets, avoid stale datasets, but other components might need them
end
post '/model/:id' do # create prediction
begin
model = Model.get params[:id]
rescue
status 404
"Model #{params[:id]} not found"
end
query_compound = OpenTox::Compound.new :uri => params[:compound_uri]
activity_dataset = OpenTox::Dataset.new :uri => model.training_dataset_uri
database_activities = activity_dataset.features(query_compound)
if database_activities.size > 0 # return database values
database_activities.collect{ |f| f.uri }.join('\n')
else # make prediction
prediction = Prediction.find_or_create(:model_uri => model.uri, :compound_uri => params[:compound_uri])
unless prediction.finished # present cached prediction if finished
#Spork.spork do
pid = fork do
prediction.update_attributes(:uri => url_for("/prediction/", :full) + prediction.id.to_s)
feature_dataset = OpenTox::Dataset.new :uri => model.feature_dataset_uri
compound_descriptors = feature_dataset.all_compounds_and_features
training_features = feature_dataset.all_features
compound_activities = activity_dataset.all_compounds_and_features
query_features = query_compound.match(training_features)
query_features.each do |f|
puts f.uri
Feature.find_or_create(:feature_uri => f.uri, :prediction_uri => prediction.uri)
end
conf = 0.0
compound_descriptors.each do |compound_uri,features|
sim = similarity(features,query_features,model)
if sim > 0.0
Neighbor.find_or_create(:compound_uri => compound_uri, :similarity => sim, :prediction_uri => prediction.uri)
compound_activities[compound_uri].each do |a|
case a.value('classification').to_s
when 'true'
conf += sim #TODO gaussian
when 'false'
conf -= sim #TODO gaussian
end
end
end
end
if conf > 0.0
classification = true
elsif conf < 0.0
classification = false
end
prediction.update_attributes(:confidence => conf, :classification => classification, :finished => true)
prediction.save!
puts prediction.to_yaml
end
Process.detach(pid)
end
prediction.uri
end
end
# PREDICTIONS
get '/predictions?' do # get index of predictions
Prediction.all.collect{ |p| p.uri }.join("\n")
end
get '/prediction/:id' do # display prediction
begin
prediction = Prediction.get(params[:id])
rescue
status 404
"Prediction #{params[:id]} not found."
end
if prediction.finished
xml prediction
else
status 202
"Prediction #{params[:id]} not yet finished."
end
end
get '/prediction/:id/neighbors' do
begin
prediction = Prediction.get(params[:id])
rescue
status 404
"Prediction #{params[:id]} not found."
end
xml Neighbor.all(:prediction_uri => prediction.uri)
end
get '/prediction/:id/features' do
begin
prediction = Prediction.get(params[:id])
rescue
status 404
"Prediction #{params[:id]} not found."
end
xml Feature.all(:prediction_uri => prediction.uri)
end
delete '/prediction/:id' do
begin
p = Prediction.get(params[:id])
rescue
status 404
"Prediction #{params[:id]} not found."
end
p.neighbors.each { |n| n.destroy }
p.features.each { |f| f.destroy }
p.destroy
"Prediction #{params[:id]} succesfully deleted."
end
# Utility functions
def similarity(neighbor_features, query_features, model)
nf = neighbor_features.collect{|f| f.uri }
qf = query_features.collect{|f| f.uri }
#common_features = neighbor_features & query_features
#all_features = neighbor_features | query_features
common_features = nf & qf
all_features = nf | qf
sum_p_common = 0.0
sum_p_all = 0.0
#all_features.each { |f| sum_p_all += f.value.to_f }
#common_features.each { |f| sum_p_common += f.value.to_f }
#sum_p_common/sum_p_all
common_features.size.to_f/all_features.size.to_f
end
def xml(object)
builder do |xml|
xml.instruct!
object.to_xml
end
end
|
