From 7d19f5562f3f59f7a14a4d6f7d8da6f24fdabd8c Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.de>
Date: Fri, 14 Aug 2009 10:33:51 +0200
Subject: Initial version of opentox-lazar

---
 lazar.rb | 92 ----------------------------------------------------------------
 1 file changed, 92 deletions(-)
 delete mode 100644 lazar.rb

(limited to 'lazar.rb')

diff --git a/lazar.rb b/lazar.rb
deleted file mode 100644
index fc69573..0000000
--- a/lazar.rb
+++ /dev/null
@@ -1,92 +0,0 @@
-#['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
-- 
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