Passes tests in opentox-test

4 files changed, 31 insertions, 81 deletions

diff --git a/Rakefile b/Rakefile
index e8ed9f4..b804237 100644
--- a/Rakefile
+++ b/Rakefile
@@ -1,5 +1,7 @@
 require 'rubygems'
 require 'rake'
+require 'opentox-ruby-api-wrapper'
+require 'tasks/opentox'
 
 @gems = "sinatra rest-client emk-sinatra-url-for cehoffman-sinatra-respond_to"
 
@@ -36,6 +38,6 @@ end
 
 desc "Run tests"
 task :test do
-	load 'test.rb'
+	load 'test/test.rb'
 end
 
diff --git a/application.rb b/application.rb
index 7920b92..eb927e0 100644
--- a/application.rb
+++ b/application.rb
@@ -1,60 +1,32 @@
-[ 'rubygems', 'sinatra', 'rest_client', 'sinatra/url_for', 'sinatra/respond_to', 'openbabel' ].each do |lib|
-	require lib
-end
+require 'rubygems'
+require 'opentox-ruby-api-wrapper'
+require 'sinatra/respond_to'
 
-mime :uid, "text/plain"
 mime :smiles, "chemical/x-daylight-smiles"
 mime :inchi, "chemical/x-inchi"
 mime :sdf, "chemical/x-mdl-sdfile"
 mime :image, "image/gif"
 mime :names, "text/plain"
 
-CACTUS_URI="http://cactus.nci.nih.gov/chemical/structure/"
-
 set :default_content, :smiles
 
-get '/*/match/*' do
-	smiles = URI.decode(params[:splat][0])
-	smarts = URI.decode(params[:splat][1])
-	smi2mol = OpenBabel::OBConversion.new
-	smi2mol.set_in_format('smi')
-	obmol = OpenBabel::OBMol.new
-	smi2mol.read_string(obmol,smiles) 
-	obmol.add_hydrogens
-	smarts_pattern = OpenBabel::OBSmartsPattern.new
-	smarts_pattern.init(smarts)
-	if smarts_pattern.match(obmol)
-		'true'
-	else
-		'false'
-	end
-end
-
-get %r{/(.+)} do |cansmi| # catches all remaining get requests
+get %r{/(.+)} do |inchi| # catches all remaining get requests
+	inchi = URI.unescape request.env['REQUEST_URI'].sub(/^\//,'') # hack to avoid sinatra's URI/CGI unescaping, splitting, ...
 	respond_to do |format|
-		format.uid   { URI.escape(cansmi, /[^#{URI::PATTERN::UNRESERVED}]/) }
-		format.smiles { URI.unescape(cansmi).chomp }
-		format.names  { RestClient.get "#{CACTUS_URI}#{cansmi}/names" }
-		format.inchi  { RestClient.get "#{CACTUS_URI}#{cansmi}/stdinchi" }
-		format.sdf    { RestClient.get "#{CACTUS_URI}#{cansmi}/sdf" }
-		format.image  { "#{CACTUS_URI}#{cansmi}/image" }
+		format.smiles { OpenTox::Compound.new(:inchi => inchi).smiles }
+		format.names  { RestClient.get "#{CACTUS_URI}#{inchi}/names" }
+		format.inchi  { inchi }
+		format.sdf    { RestClient.get "#{CACTUS_URI}#{inchi}/sdf" }
+		format.image  { "#{CACTUS_URI}#{inchi}/image" }
 	end
 end
 
 post '/?' do 
 	if params[:smiles]
-		cansmi = canonical_smiles(URI.unescape(params[:smiles]),'smi')
+		OpenTox::Compound.new(:smiles => params[:smiles]).uri
+	elsif params[:inchi]
+		OpenTox::Compound.new(:inchi => params[:inchi]).uri
 	elsif params[:name]
-		cansmi = RestClient.get "#{CACTUS_URI}#{params[:name]}/smiles"
+		OpenTox::Compound.new(:name => params[:name]).uri
 	end
-	url_for("/", :full) + URI.escape(cansmi.gsub(/\s+/,''), /[^#{URI::PATTERN::UNRESERVED}]/)
-end
-
-def canonical_smiles(identifier,format)
-	conversion = OpenBabel::OBConversion.new
-	conversion.set_in_and_out_formats format, 'can'
-	mol = OpenBabel::OBMol.new
-	conversion.read_string mol, identifier
-	conversion.write_string mol
 end
-
diff --git a/config.ru b/config.ru
index 0ca30c5..63dd2ce 100644
--- a/config.ru
+++ b/config.ru
@@ -1,10 +1,23 @@
 require 'rubygems'
 require 'sinatra'
 require 'application.rb'
+require 'rack'
+require 'rack/contrib'
 
 FileUtils.mkdir_p 'log' unless File.exists?('log')
-log = File.new("log/sinatra.log", "a")
+log = File.new("log/#{ENV["RACK_ENV"]}.log", "a")
 $stdout.reopen(log)
 $stderr.reopen(log)
+ 
+if ENV['RACK_ENV'] == 'production'
+	use Rack::MailExceptions do |mail|
+		mail.to 'helma@in-silico.ch'
+		mail.subject '[ERROR] %s'
+	end 
+elsif ENV['RACK_ENV'] == 'development'
+  use Rack::Reloader 
+  use Rack::ShowExceptions
+end
 
 run Sinatra::Application
+
diff --git a/test.rb b/test.rb
deleted file mode 100644
index 9a84276..0000000
--- a/test.rb
+++ /dev/null
@@ -1,37 +0,0 @@
-require 'application'
-require 'test/unit'
-require 'rack/test'
-
-
-class CompoundsTest < Test::Unit::TestCase
-  include Rack::Test::Methods
-
-  def app
-    Sinatra::Application
-  end
-
-  def test_uri_generation_from_smiles
-    post '/', :smiles => 'CC(=O)CC(C)C#N'
-		assert last_response.body.include?('CC%28CC%28%3DO%29C%29C%23N')
-  end
-
-  def test_uri_generation_from_name
-    post '/', :name => 'Benzene'
-		assert last_response.body.include?('c1ccccc1')
-  end
-
-  def test_smiles
-    get '/CC%28CC%28%3DO%29C%29C%23N'
-    assert last_response.body.include?('CC(CC(=O)C)C#N')
-  end
-
-	def test_smarts_match_true
-    get '/CC%28CC%28%3DO%29C%29C%23N/match/CC'
-    assert last_response.body.include?('true')
-	end
-
-	def test_smarts_match_false
-    get '/CC%28CC%28%3DO%29C%29C%23N/match/Cl'
-    assert last_response.body.include?('false')
-	end
-end