Initial import of opentox-lazar

1 files changed, 92 insertions, 0 deletions

diff --git a/lazar.rb b/lazar.rb
new file mode 100644
index 0000000..fc69573
--- /dev/null
+++ b/lazar.rb
@@ -0,0 +1,92 @@
+#['rubygems', 'sinatra', 'rest_client', 'sinatra/url_for', 'crack/xml', 'dm-core', 'spork'].each do |lib|
+['rubygems', 'sinatra', 'rest_client', 'sinatra/url_for', 'crack/xml', 'dm-core', 'builder', 'logger'].each do |lib|
+	require lib
+end
+
+DataMapper.setup(:default, "sqlite3://#{Dir.pwd}/lazar.sqlite3")
+
+class Model
+	include DataMapper::Resource
+	property :id, Serial
+	property :name, String
+	property :feature_dataset_uri, String
+	property :training_dataset_uri, String
+end
+
+Model.auto_migrate! unless File.exists?("lazar.sqlite3")
+
+COMPOUNDS_URI = 'http://webservices.in-silico.ch/compounds/'
+FEATURES_URI  = 'http://webservices.in-silico.ch/features/'
+DATASET_URI   = 'http://localhost:4567/'
+FEATURE_GENERATION_URI = 'http://localhost:9394/'
+@similarity_prediction = RestClient::Resource.new 'http://webservices.in-silico.ch/weighted_similarity_classification'
+
+get '/?' do # get index of models
+	Model.all.collect{ |m| url_for("/", :full) + m.id.to_s }.join("\n")
+end
+
+get '/:id' do
+	@model = Model.get(params[:id])
+	builder :model
+end
+
+get '/:id/:inchikey' do # show prediction
+	@prediction = Prediction.first(:model_id => params[:id], :compound_uri => params[:compound_uri])
+	builder :prediction
+end
+
+post '/:id' do # create prediction
+	unless prediction = Prediction.first(:model_id => params[:id], :compound_uri => params[:compound_uri])
+		Spork.spork do
+			Prediction.create(@similarity_prediction.post, :compound_uri => params[:compound_uri], :feature_dataset_uri => Model.get(params[:id]).feature_dataset_uri)
+		end
+	end
+	inchikey = @compounds.get "#{params[:compound_uri]}.inchikey"
+	# or redirect?
+	url_for("/#{params[:id]}/#{inchikey}", :full)
+end
+
+post '/' do # create model
+
+	training_dataset_uri = RestClient.post DATASET_URI, :name => params[:name]
+	dataset = RestClient::Resource.new training_dataset_uri
+	model = Model.create(:name => params[:name], :training_dataset_uri => training_dataset_uri)
+
+	#Spork.spork do
+	pid = fork do
+	
+		# create model from a tab delimited file
+		File.open(params[:file][:tempfile].path).each_line do |line|
+			items = line.split(/\s+/)
+			begin
+				compound_uri = COMPOUNDS_URI + URI.encode(items[0])
+				#compound_uri = RestClient.post COMPOUNDS_URI, :smiles => items[0]
+			rescue
+				puts "Failed to get InChI key for #{items[0]}"
+			end
+				feature_uri = RestClient.post FEATURES_URI, :name => params[:name], :value => items[1]
+				dataset.put :compound_uri => compound_uri, :feature_uri => feature_uri
+				model.training_dataset_uri = training_dataset_uri
+				model.save
+			#rescue
+				#puts "Creation of feature #{params[:name]}:#{items[1]} for compound #{items[0]} failed."
+			#end
+		end
+
+
+		feature_dataset_uri = RestClient.post FEATURE_GENERATION_URI, :dataset_uri => training_dataset_uri
+		model.feature_dataset_uri = feature_dataset_uri.chomp 
+		model.save
+
+		# create features
+		#feature_dataset_uri = @feature_generation.post :dataset_uri => params[:dataset_uri]
+		#model = Model.create(:name => params[:name], :training_dataset_uri => training_dataset_uri, :feature_dataset_uri => feature_dataset_uri)
+		#model.save
+		# validate
+		# or redirect?
+
+	end
+
+	Process.detach(pid)
+	url_for("/", :full) + model.id.to_s 
+end