1 files changed, 14 insertions, 42 deletions
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
-