1 files changed, 0 insertions, 132 deletions
diff --git a/application.rb b/application.rb
deleted file mode 100644
index 11115ff..0000000
--- a/application.rb
+++ /dev/null
@@ -1,132 +0,0 @@
-['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