similarity calculations added

4 files changed, 219 insertions, 65 deletions

diff --git a/Rakefile b/Rakefile
index 16f597f..868e04a 100644
--- a/Rakefile
+++ b/Rakefile
@@ -5,3 +5,7 @@ require 'tasks/opentox'
 
 @gems = "sinatra emk-sinatra-url-for builder opentox-ruby-api-wrapper"
 
+desc "Run local tests"
+task :test do
+	load 'test/test.rb'
+end
diff --git a/application.rb b/application.rb
index 26bb3c3..f26d664 100644
--- a/application.rb
+++ b/application.rb
@@ -15,33 +15,105 @@ end
 
 set :default_content, :yaml
 
-helpers do
+class Dataset
 
-	def create_dataset(uri)
-		@@redis.set_add "datasets", uri
+	include OpenTox::Utils
+	attr_reader :uri, :name
+
+	def initialize(uri)
+		@name = File.basename(uri)
+		@uri = uri
 	end
 
-	def	add_feature(dataset_uri, compound_uri, feature_uri)
-		@@redis.set_add dataset_uri + '::compounds', compound_uri
-		@@redis.set_add dataset_uri + '::features', feature_uri
-		@@redis.set_add dataset_uri + '::' + compound_uri + '::features', feature_uri
-		@@redis.set_add dataset_uri + '::' + feature_uri + '::compounds', compound_uri
+	def self.create(uri)
+		dataset = Dataset.new(uri)
+		dataset.save
+		dataset
 	end
 
-	def delete_dataset(uri)
-		@@redis.set_members(uri + '::compounds').each do |compound_uri|
-			@@redis.delete uri + '::' + compound_uri
+	def self.find(uri)
+		if @@redis.set_member? "datasets", uri
+			Dataset.new(uri)
+		else
+			nil
 		end
-		@@redis.delete uri + '::compounds'
-		@@redis.set_members(uri + '::features').each do |feature_uri|
-			@@redis.delete uri + '::' + feature_uri
+	end
+
+	def self.exists?(uri)
+		@@redis.set_member? "datasets", uri
+	end
+
+	def self.find_all_uris
+		@@redis.set_members("datasets")
+	end
+
+	def save
+		@@redis.set_add "datasets", uri
+	end
+
+	def destroy
+		@@redis.set_members(@uri + '::compounds').each do |compound_uri|
+			@@redis.delete @uri + '::' + compound_uri
+		end
+		@@redis.delete @uri + '::compounds'
+		@@redis.set_members(@uri + '::features').each do |feature_uri|
+			@@redis.delete @uri + '::' + feature_uri
 		end
-		@@redis.delete uri + '::features'
-		@@redis.set_delete "datasets", uri
+		@@redis.delete @uri + '::features'
+		@@redis.set_delete "datasets", @uri
+	end
+
+	def add(compound_uri,feature_uri)
+		@@redis.set_add @uri + '::compounds', compound_uri
+		@@redis.set_add @uri + '::features', feature_uri
+		@@redis.set_add @uri + '::' + compound_uri + '::features', feature_uri
+		@@redis.set_add @uri + '::' + feature_uri + '::compounds', compound_uri
+	end
+
+	def compound_uris
+		@@redis.set_members(@uri + "::compounds")
 	end
 
+	def feature_uris
+		@@redis.set_members(@uri + "::features")
+	end
+
+	def feature_uris_for_compound(compound_uri)
+		@@redis.set_members(@uri + '::' + compound_uri + '::features')
+	end
+	 
+	def compound_uris_for_feature(feature_uri)
+		@@redis.set_members(@uri + '::' + feature_uri + '::compounds')
+	end
+
+	def tanimoto(compound_uris)
+		raise "Exactly 2 compounds are needed for similarity calculations" unless compound_uris.size == 2
+		compound_keys = compound_uris.collect{ |c| @uri + '::' + c + "::features" }
+		union_size = @@redis.set_union(compound_keys[0], compound_keys[1]).size
+		intersect_size = @@redis.set_intersect(compound_keys[0], compound_keys[1]).size
+		intersect_size.to_f/union_size.to_f
+	end
+
+	def weighted_tanimoto(compound_uris)
+		raise "Exactly 2 compounds are needed for similarity calculations" unless compound_uris.size == 2
+		compound_keys = compound_uris.collect{ |c| @uri + '::' + c + "::features" }
+		union = @@redis.set_union(compound_keys[0], compound_keys[1])
+		intersect = @@redis.set_intersect(compound_keys[0], compound_keys[1])
+
+		p_sum_union = 0.0
+		p_sum_intersect = 0.0
+
+		union.each{ |f| p_sum_union += gauss(OpenTox::Feature.new(:uri => f).value('p_value').to_f) }
+		intersect.each{ |f| p_sum_intersect += gauss(OpenTox::Feature.new(:uri => f).value('p_value').to_f) }
+		"#{p_sum_intersect/p_sum_union}"
+	end
+
+end
+
+helpers do
+
 	def not_found?
-		halt 404, "Dataset \"#{params[:name]}\" not found." unless @@redis.set_member? "datasets", uri(params[:name])
+		halt 404, "Dataset \"#{params[:name]}\" not found." unless Dataset.exists? uri(params[:name])
 	end
 
 	def uri(name)
@@ -53,12 +125,12 @@ end
 ## REST API
 
 get '/?' do
-	@@redis.set_members("datasets").collect{|d| uri(d)}.join("\n")
+	Dataset.find_all_uris.join("\n")
 end
 
 get '/:name' do
   not_found?
-  @dataset = {:uri => uri(params[:name]), :name => params[:name]}
+	@dataset = Dataset.find(uri params[:name])
   respond_to do |format|
     format.yaml { @dataset.to_yaml }
     format.xml {  builder :dataset }
@@ -72,71 +144,66 @@ end
 
 get '/:name/compounds' do
   not_found?
-  @@redis.set_members(uri(params[:name]) + "::compounds").join("\n")
+  Dataset.find(uri params[:name]).compound_uris.join("\n")
 end
 
 get '/:name/features' do
   not_found?
-  @@redis.set_members(uri(params[:name]) + "::features").join("\n")
+  Dataset.find(uri params[:name]).feature_uris.join("\n")
 end
 
-=begin
-get '/:name/:type/*/*/intersection' do
-  # CHECK/TEST
-  @@redis.set_intersect(params[:splat][0], params[:splat][1], URI.encode(params[:name]) + '/' + params[:type]).join("\n")
+get '/:name/compound/*/features' do 
+	not_found?
+	compound_uri = params[:splat].first.gsub(/ /,'+')
+	Dataset.find(uri params[:name]).feature_uris_for_compound(compound_uri).join("\n")
 end
 
-get '/:name/:type/*/*/union' do
-  # CHECK/TEST
-  @@redis.set_union(params[:splat][0], params[:splat][1], URI.encode(params[:name]) + '/' + params[:type]).join("\n")
+get '/:name/feature/*/compounds' do 
+	not_found?
+	Dataset.find(uri params[:name]).compound_uris_for_feature(params[:splat].first).join("\n")
 end
-=end
 
-get '/:name/*/features' do 
+get '/:name/tanimoto/compound/*/compound/*/?' do 
 	not_found?
-	# re-escape smiles (Sinatra unescapes params and splats)
-	compound_uri = params[:splat].first.sub(%r{(http://[\w\.:]+/)(.*)$}) {|s| $1 + URI.escape($2, /[^#{URI::PATTERN::UNRESERVED}]/)}
-	
-	#puts compound_uri
-  @@redis.set_members(uri(params[:name]) + '::' + compound_uri + '::features').join("\n")
+	compound_uris = params[:splat].collect{ |c| c.gsub(/ /,'+') }
+	"#{Dataset.find(uri params[:name]).tanimoto(compound_uris)}"
 end
 
-get '/:name/*/compounds' do 
+get '/:name/weighted_tanimoto/compound/*/compound/*/?' do 
 	not_found?
-  @@redis.set_members(uri(params[:name]) + '::' + params[:splat].first + '::compounds').join("\n")
+	compound_uris = params[:splat].collect{ |c| c.gsub(/ /,'+') }
+	Dataset.find(uri params[:name]).weighted_tanimoto(compound_uris)
 end
 
 post '/?' do
   #protected!
-	uri = uri(params[:name])
-  halt 403, "Dataset \"#{name}\" exists - please choose another name." if @@redis.set_member?("datasets", uri)
+  halt 403, "Dataset \"#{name}\" exists - please choose another name." if Dataset.exists?(uri params[:name])
 
-  @@redis.set_add "datasets", uri
+	dataset = Dataset.create(uri params[:name])
 
   if params[:file]
 		File.open(params[:file][:tempfile].path).each_line do |line|
 			record = line.chomp.split(/,\s*/)
 			compound_uri = OpenTox::Compound.new(:smiles => record[0]).uri
 			feature_uri = OpenTox::Feature.new(:name => params[:name], :values => {:classification => record[1]}).uri
-			add_feature(uri, compound_uri, feature_uri)
+			dataset.add(compound_uri, feature_uri)
 		end
   end
-	uri
+	dataset.uri
 end
 
 put '/:name/?' do
   #protected!
   not_found?
-	uri = uri(params[:name])
-	add_feature(uri, params[:compound_uri],params[:feature_uri])
-  uri + " sucessfully updated."
+	dataset = Dataset.find(uri params[:name])
+	dataset.add(params[:compound_uri],params[:feature_uri])
+  dataset.uri + " sucessfully updated."
 end
 
 delete '/:name/?' do
   # dangerous, because other datasets might refer to it
   #protected!
   not_found?
-	uri = uri(params[:name])
-	delete_dataset(uri)
-  "Successfully deleted dataset \"#{uri}\"."
+	Dataset.find(uri params[:name]).destroy
+  "Successfully deleted dataset \"#{params[:name]}\"."
 end
diff --git a/config.ru b/config.ru
index 961b2d8..63dd2ce 100644
--- a/config.ru
+++ b/config.ru
@@ -14,7 +14,7 @@ if ENV['RACK_ENV'] == 'production'
 		mail.to 'helma@in-silico.ch'
 		mail.subject '[ERROR] %s'
 	end 
-else
+elsif ENV['RACK_ENV'] == 'development'
   use Rack::Reloader 
   use Rack::ShowExceptions
 end
diff --git a/test/test.rb b/test/test.rb
index 5c4b2e7..b1bae83 100644
--- a/test/test.rb
+++ b/test/test.rb
@@ -32,28 +32,39 @@ class DatasetsTest < Test::Unit::TestCase
 
 	def test_create_dataset_and_insert_data
 		name = "Test dataset"
-		smiles = '[O-][N+](=O)C/C=C\C(=O)Cc1cc(C#N)ccc1'
-		compound_uri = OpenTox::Compound.new(:smiles => smiles).uri
-		feature_uri = OpenTox::Feature.new(:name => name, :values => {:classification => "true"}).uri
+		compounds = {
+			'[O-][N+](=O)C/C=C\C(=O)Cc1cc(C#N)ccc1' => 'true',
+			'F[B-](F)(F)F.[Na+]' => 'false',
+			'N#[N+]C1=CC=CC=C1.F[B-](F)(F)F' => 'false'
+		}
 		post '/', :name => name
 		assert last_response.ok?
 		uri = last_response.body.chomp
 		get uri
 		assert last_response.ok?
     assert last_response.body.include?("Test_dataset")
-		put uri, :compound_uri => compound_uri, :feature_uri => feature_uri
-		assert last_response.ok?
+
+		compounds.each do |smiles,activity|
+
+			compound_uri = OpenTox::Compound.new(:smiles => smiles).uri
+			feature_uri = OpenTox::Feature.new(:name => name, :values => {:classification => activity}).uri
+			put uri, :compound_uri => compound_uri, :feature_uri => feature_uri
+
+			assert last_response.ok?
+			get uri + '/compounds'
+			assert last_response.ok?
+			assert last_response.body.include?(compound_uri)
+			get uri + '/features'
+			assert last_response.ok?
+			assert last_response.body.include?(activity)
+			assert last_response.body.include?(feature_uri)
+			get uri + '/compound/' + compound_uri + '/features'
+			assert last_response.ok?
+			assert last_response.body.include?(activity)
+			assert_equal feature_uri, last_response.body
+		end
 		get uri + '/compounds'
-		assert last_response.ok?
-		assert_equal compound_uri, last_response.body
-		get uri + '/features'
-		assert last_response.ok?
-    assert last_response.body.include?("true")
-		assert_equal feature_uri, last_response.body
-		get uri + '/' + compound_uri + '/features'
-		assert last_response.ok?
-    assert last_response.body.include?("true")
-		assert_equal feature_uri, last_response.body
+		#puts last_response.body
 		delete uri
 		assert last_response.ok?
 		get "/Test_dataset"
@@ -70,7 +81,11 @@ class DatasetsTest < Test::Unit::TestCase
 		get uri + '/compounds'
 		assert last_response.ok?
 		assert last_response.body.include?(compound_uri)
-		get uri + '/' + compound_uri + '/features'
+		get uri + '/features'
+		assert last_response.ok?
+		assert last_response.body.include?("Hamster%20Carcinogenicity/classification/true")
+		assert last_response.body.include?("Hamster%20Carcinogenicity/classification/false")
+		get uri + '/compound/' + compound_uri + '/features'
 		assert last_response.ok?
     assert last_response.body.include?("Hamster%20Carcinogenicity/classification/true")
 		delete uri
@@ -86,7 +101,75 @@ class DatasetsTest < Test::Unit::TestCase
 		get uri
 		assert last_response.ok?
 	end
+=end
 
+	def test_tanimoto_similarity
+		#@feature_set = OpenTox::Algorithms::Fminer.new :dataset_uri => @dataset
+		name = "Similarity test dataset"
+		data = {
+			'[O-][N+](=O)C/C=C\C(=O)Cc1cc(C#N)ccc1' =>
+			{
+				'A' => 1.0,
+				'B' => 0.9,
+				'C' => 0.8,
+				'D' => 0.7,
+				'E' => 0.5
+			},
+			'F[B-](F)(F)F.[Na+]' => 
+			{
+				'F' => 0.9,
+				'B' => 0.9,
+				'C' => 0.8,
+				'D' => 0.7,
+				'E' => 0.5
+			},
+			'N#[N+]C1=CC=CC=C1.F[B-](F)(F)F' => 
+			{
+				'A' => 1.0,
+				'B' => 0.9,
+				'F' => 0.9,
+			}
+		}
+		post '/', :name => name
+		assert last_response.ok?
+		uri = last_response.body
+		get uri
+		assert last_response.ok?
+
+		data.each do |smiles,features|
+			compound_uri = OpenTox::Compound.new(:smiles => smiles).uri
+			features.each do |k,v|
+				feature_uri = OpenTox::Feature.new(:name => k, :values => {:p_value => v}).uri
+				put uri, :compound_uri => compound_uri, :feature_uri => feature_uri
+				assert last_response.ok?
+			end
+		end
+
+		data.each do |smiles,features|
+			compound_uri = OpenTox::Compound.new(:smiles => smiles).uri
+			data.each do |s,f|
+				unless s == smiles
+					neighbor_uri = OpenTox::Compound.new(:smiles => s).uri
+					get uri + "/tanimoto/compound/#{compound_uri}/compound/#{neighbor_uri}"
+					assert last_response.ok?
+					sim = last_response.body
+					features_a = data[smiles].keys
+					features_b = data[s].keys
+					union = features_a | features_b
+					intersect  = features_a & features_b
+					mysim = intersect.size.to_f/union.size.to_f
+					assert_equal sim, mysim.to_s
+					puts "tanimoto::#{smiles}::#{s}::#{last_response.body}"
+					get uri + "/weighted_tanimoto/compound/#{compound_uri}/compound/#{neighbor_uri}"
+					assert last_response.ok?
+					puts "weighted_tanimoto::#{smiles}::#{s}::#{last_response.body}"
+				end
+			end
+		end
+
+	end
+
+=begin
 	def test_unauthorized_create
 		post '/', :name => "Test dataset"
 		assert !last_response.ok?