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['rubygems', "haml", "sass"].each do |lib|
require lib
end
require 'rack-flash'
#require 'benchmark'
gem 'opentox-ruby-api-wrapper', '= 1.2.6'
require 'opentox-ruby-api-wrapper'
gem 'sinatra-static-assets'
require 'sinatra/static_assets'
use Rack::Flash
set :sessions, true
get '/?' do
redirect url_for('/create')
end
get '/predict/?' do
@models = OpenTox::Model::Lazar.find_all
haml :predict
end
get '/create' do
haml :create
end
get '/about' do
haml :about
end
get '/csv_format' do
haml :csv_format
end
get '/tasks' do
@tasks = OpenTox::Task.all
haml :tasks
end
get '/task' do
@task = OpenTox::Task.find(session[:task_uri])
haml :task
end
post '/upload' do # create a new model
dataset = OpenTox::Dataset.new
title = params[:endpoint].sub(/\s+/,'_')
dataset.title = title
feature_uri = url_for("/feature#"+title, :full)
feature = dataset.find_or_create_feature(feature_uri)
params[:file][:tempfile].each_line do |line|
items = line.chomp.split(/\s*,\s*/)
smiles = items[0]
compound_uri = OpenTox::Compound.new(:smiles => smiles).uri
compound = dataset.find_or_create_compound(compound_uri)
case items[1].to_s
when '1'
dataset.add(compound,feature,true)
when '0'
dataset.add(compound,feature,false)
else
flash[:notice] = "Irregular activity '#{items[1]}' for SMILES #{smiles}. Please use 1 for active and 0 for inactive compounds"
end
end
dataset_uri = dataset.save
task_uri = OpenTox::Algorithm::Lazar.create_model(:dataset_uri => dataset_uri, :feature_uri => feature_uri)
flash[:notice] = "Model creation started - this may take some time. You can view and manage the status of current tasks at the #{link_to("Tasks page", "/tasks")}. #{link_to("Reload this page", "/predict")} to use the new model."
session[:task_uri] = task_uri
redirect url_for('/predict')
end
post '/predict/?' do # post chemical name to model
@identifier = params[:identifier]
begin
@compound = OpenTox::Compound.new(:name => params[:identifier])
rescue
flash[:notice] = "Could not find a structure for #{@identifier}. Please try again."
redirect '/predict'
end
@predictions = []
params[:selection].keys.each do |uri|
prediction = nil
confidence = nil
title = nil
prediction = RestClient.post uri, :compound_uri => @compound.uri, :accept => "application/x-yaml"
model = Redland::Model.new Redland::MemoryStore.new
parser = Redland::Parser.new
parser.parse_string_into_model(model,prediction,'/')
f = model.subject(RDF['type'],OT['Feature']) # this can be dangerous if OWL is not properly sorted
title = model.object(f,DC['title']).to_s
model.subjects(RDF['type'], OT['FeatureValue']).each do |v|
feature = model.object(v,OT['feature'])
feature_name = model.object(feature,DC['title']).to_s
prediction = model.object(v,OT['value']).to_s if feature_name.match(/classification/)
confidence = model.object(v,OT['value']).to_s if feature_name.match(/confidence/)
end
case prediction.to_s
when "true"
prediction = "active"
when "false"
prediction = "inactive"
else
prediction = "not available"
end
@predictions << {:title => title, :prediction => prediction, :confidence => confidence}
end
haml :prediction
#@predictions.to_yaml
end
post '/task/cancel' do
puts params[:task_uri]
task = OpenTox::Task.find(params[:task_uri])
task.cancel
redirect url_for('/tasks')
end
delete '/:id' do
#begin
OpenTox::Model::LazarClassification.delete(params[:id])
haml :index
#rescue
#"Deletion of model with ID #{params[:id]} failed. Please check your username and password."
#end
end
# SASS stylesheet
get '/stylesheets/style.css' do
headers 'Content-Type' => 'text/css; charset=utf-8'
sass :style
end
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