Initial import of opentox-compounds-cactus

3 files changed, 118 insertions, 0 deletions

diff --git a/README b/README
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+OpenTox Compounds
+=================
+
+* A thin wrapper around the CACTUS REST webservice (http://cactus.nci.nih.gov/chemical/structure).
+
+* Implements a subset of the OpenTox compounds API (http://opentox.org/wiki/opentox/Structure).
+
+* Requirements:
+
+	- Sinatra (http://www.sinatrarb.com/),
+	- sinatra-url-for (http://github.com/emk/sinatra-url-for/)
+	- RestClient (http://rest-client.heroku.com/)
+	- Rack::Test (http://github.com/brynary/rack-test/) for the tests
diff --git a/compounds.rb b/compounds.rb
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+require 'rubygems'
+require 'sinatra'
+require 'rest_client'
+require 'sinatra/url_for'
+
+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/"
+
+get '/' do 
+	status 404
+	"No index available for this component."
+end
+
+get '/*.*' do
+	begin
+		identifier = params[:splat][0]
+		format = params[:splat][1]
+		case format 
+		when 'smiles'
+			RestClient.get "#{CACTUS_URI}#{identifier}/smiles"
+		when 'inchikey'
+			RestClient.get "#{CACTUS_URI}#{identifier}/stdinchikey"
+		when 'inchi'
+			RestClient.get "#{CACTUS_URI}#{identifier}/stdinchi"
+		when 'sdf'
+			RestClient.get "#{CACTUS_URI}#{identifier}/sdf"
+		when 'names'
+			RestClient.get "#{CACTUS_URI}#{identifier}/names"
+		when 'image'
+			RestClient.get "#{CACTUS_URI}#{identifier}/image"
+		else
+			status 400
+			"Cannot provide #{format}."
+		end
+	rescue
+		status 404
+		"Cannot find #{identifier}."
+	end
+end
+
+# TODO: select format by media type
+
+# default format is smiles
+get '/:identifier' do
+	begin
+		RestClient.get "#{CACTUS_URI}#{params[:identifier]}/smiles"
+	rescue
+		status 404
+		"Cannot find #{params[:identifier]}."
+	end
+end
+
+# return canonical uri
+post '/' do
+	begin
+		inchikey = RestClient.get "#{CACTUS_URI}#{params[:name]}/stdinchikey"
+		inchikey.chomp!
+		if inchikey.match(/\n/)
+			status 400
+			"More than one structure found for #{params[:identifier]}."
+		else
+			url_for("/", :full) + inchikey
+		end
+	rescue
+		"Cannot find an InChI Key for #{params[:name]}."
+	end
+end
+
+delete '/*' do
+	status 404
+	"Cannot delete - compounds are not stored permanently"
+end
diff --git a/test.rb b/test.rb
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+++ b/test.rb
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+require 'compounds'
+require 'test/unit'
+require 'rack/test'
+
+
+class CompoundsTest < Test::Unit::TestCase
+  include Rack::Test::Methods
+
+  def app
+    Sinatra::Application
+  end
+
+  def test_uri_generation
+    post '/', :name => 'c1ccccc1'
+		assert last_response.body.include?('InChIKey=UHOVQNZJYSORNB-UHFFFAOYSA-N')
+  end
+
+  def test_smiles
+    get '/InChIKey=UHOVQNZJYSORNB-UHFFFAOYSA-N'
+    assert last_response.body.include?('c1ccccc1')
+  end
+
+  def test_inchi
+    get '/Benzene.inchi'
+    assert last_response.body.include?('InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H')
+  end
+
+end