From 76948b1a6ac9f48edb783c8cb1126dbeed3df4b4 Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.de>
Date: Tue, 25 Aug 2009 20:52:16 +0200
Subject: modified smiles escaping, uid supported

---
 Rakefile       |  4 +++-
 application.rb |  8 +++++---
 config.ru      | 10 ++++------
 3 files changed, 12 insertions(+), 10 deletions(-)

diff --git a/Rakefile b/Rakefile
index 6ba8585..e8ed9f4 100644
--- a/Rakefile
+++ b/Rakefile
@@ -1,10 +1,12 @@
 require 'rubygems'
 require 'rake'
 
+@gems = "sinatra rest-client emk-sinatra-url-for cehoffman-sinatra-respond_to"
+
 desc "Install required gems and openbabel"
 task :install do
 	puts `sudo gem sources -a http://gems.github.com`
-	puts `sudo gem install sinatra rest-client emk-sinatra-url-for cehoffman-sinatra-respond_to`
+	puts `sudo gem install #{@gems}`
 	begin
 		require 'openbabel'
 		puts "Openbabel is already installed"
diff --git a/application.rb b/application.rb
index 1ff8e16..7920b92 100644
--- a/application.rb
+++ b/application.rb
@@ -2,6 +2,7 @@
 	require lib
 end
 
+mime :uid, "text/plain"
 mime :smiles, "chemical/x-daylight-smiles"
 mime :inchi, "chemical/x-inchi"
 mime :sdf, "chemical/x-mdl-sdfile"
@@ -10,6 +11,8 @@ 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])
@@ -29,8 +32,7 @@ end
 
 get %r{/(.+)} do |cansmi| # catches all remaining get requests
 	respond_to do |format|
-		format.html   { URI.unescape(cansmi).chomp }
-		format.text   { URI.unescape(cansmi).chomp }
+		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" }
@@ -45,7 +47,7 @@ post '/?' do
 	elsif params[:name]
 		cansmi = RestClient.get "#{CACTUS_URI}#{params[:name]}/smiles"
 	end
-	url_for("/", :full) + URI.escape(cansmi.gsub(/\s+/,''), /[^\w]/)
+	url_for("/", :full) + URI.escape(cansmi.gsub(/\s+/,''), /[^#{URI::PATTERN::UNRESERVED}]/)
 end
 
 def canonical_smiles(identifier,format)
diff --git a/config.ru b/config.ru
index 95e58ae..0ca30c5 100644
--- a/config.ru
+++ b/config.ru
@@ -2,11 +2,9 @@ require 'rubygems'
 require 'sinatra'
 require 'application.rb'
 
-if ENV["RACK_ENV"] == 'production'
-	FileUtils.mkdir_p 'log' unless File.exists?('log')
-	log = File.new("log/sinatra.log", "a")
-	$stdout.reopen(log)
-	$stderr.reopen(log)
-end
+FileUtils.mkdir_p 'log' unless File.exists?('log')
+log = File.new("log/sinatra.log", "a")
+$stdout.reopen(log)
+$stderr.reopen(log)
 
 run Sinatra::Application
-- 
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