central config.ru, generic compound API

5 files changed, 21 insertions, 20 deletions

diff --git a/Rakefile b/Rakefile
index 5974a9c..b8bf71c 100644
--- a/Rakefile
+++ b/Rakefile
@@ -10,7 +10,7 @@ begin
     gem.email = "helma@in-silico.ch"
     gem.homepage = "http://github.com/helma/opentox-ruby-api-wrapper"
     gem.authors = ["Christoph Helma"]
-		["sinatra", "rest-client", "rack", "rack-contrib", "thin", "emk-sinatra-url-for", "cehoffman-sinatra-respond_to", "dm-more", "dm-core"].each do |dep|
+		["sinatra", "rest-client", "rack", "rack-contrib", "rack-flash", "thin", "emk-sinatra-url-for", "cehoffman-sinatra-respond_to", "dm-more", "dm-core"].each do |dep|
 			gem.add_dependency dep
 		end
 		gem.add_development_dependency "cucumber"
diff --git a/lib/compound.rb b/lib/compound.rb
index 4385a7d..0a90663 100644
--- a/lib/compound.rb
+++ b/lib/compound.rb
@@ -20,14 +20,19 @@ module OpenTox
 				@inchi = RestClient.get("#{@@cactus_uri}#{params[:name]}/stdinchi").chomp
 				@uri = File.join(@@config[:services]["opentox-compound"],URI.escape(@inchi))
 			elsif params[:uri]
-				@inchi = params[:uri].sub(/^.*InChI/, 'InChI')
+				if params[:uri].match(/InChI/) # shortcut for IST services
+					@inchi = params[:uri].sub(/^.*InChI/, 'InChI')
+				else
+					@inchi = RestClient.get @uri, :accept => 'chemical/x-inchi'
+				end
 				@uri = params[:uri]
 			end
 		end
 
 		# Get the (canonical) smiles
 		def smiles
-			obconversion(@inchi,'inchi','can')
+			RestClient.get(@uri, :accept => 'chemical/x-daylight-smiles').split(/\s+/).first # fix ambit output
+			#obconversion(@inchi,'inchi','can')
 		end
 
 		def sdf
diff --git a/lib/model.rb b/lib/model.rb
index 24f6e52..c4041f2 100644
--- a/lib/model.rb
+++ b/lib/model.rb
@@ -31,6 +31,12 @@ module OpenTox
 			def self.find_all
 				RestClient.get(@@config[:services]["opentox-model"]).split("\n")
 			end
+
+			def self.find(uri)
+				puts uri
+				yaml = RestClient.get(uri, :accept => "application/x-yaml")
+				OpenTox::Model::Lazar.from_yaml(yaml)
+			end
 			
 			# Predict a compound
 			def predict(compound)
@@ -46,7 +52,7 @@ module OpenTox
 			end
 
 			def endpoint
-				YAML.load(RestClient.get uri)[:endpoint]
+				YAML.load(RestClient.get(uri))[:endpoint]
 			end
 
 			def algorithm=(algorithm)
diff --git a/lib/templates/config.ru b/lib/templates/config.ru
index 63dd2ce..81cea9d 100644
--- a/lib/templates/config.ru
+++ b/lib/templates/config.ru
@@ -1,23 +1,13 @@
 require 'rubygems'
-require 'sinatra'
+require 'opentox-ruby-api-wrapper'
 require 'application.rb'
 require 'rack'
 require 'rack/contrib'
 
-FileUtils.mkdir_p 'log' unless File.exists?('log')
-log = File.new("log/#{ENV["RACK_ENV"]}.log", "a")
+FileUtils.mkdir_p @@tmp_dir
+log = File.new("#{@@tmp_dir}/#{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
-
+use Rack::ShowExceptions
 run Sinatra::Application
-
diff --git a/opentox-ruby-api-wrapper.gemspec b/opentox-ruby-api-wrapper.gemspec
index 88bed8f..21879b3 100644
--- a/opentox-ruby-api-wrapper.gemspec
+++ b/opentox-ruby-api-wrapper.gemspec
@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = %q{opentox-ruby-api-wrapper}
-  s.version = "1.2.4"
+  s.version = "1.2.5"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Christoph Helma"]
-  s.date = %q{2010-01-09}
+  s.date = %q{2010-01-11}
   s.description = %q{Ruby wrapper for the OpenTox REST API (http://www.opentox.org)}
   s.email = %q{helma@in-silico.ch}
   s.executables = ["opentox-install-debian.sh", "yaml2owl.rb"]