compound and feature services integrated

3 files changed, 213 insertions, 81 deletions

diff --git a/application.rb b/application.rb
index a23b52a..b9f518d 100644
--- a/application.rb
+++ b/application.rb
@@ -1,5 +1,5 @@
 # SETUP
-[ 'rubygems', 'redis', 'opentox-ruby-api-wrapper' ].each do |lib|
+[ 'rubygems', 'redis', 'opentox-ruby-api-wrapper', 'openbabel' ].each do |lib|
   require lib
 end
 
@@ -15,15 +15,18 @@ end
 
 set :default_content, :yaml
 load File.join(File.dirname(__FILE__), 'dataset.rb')
+load File.join(File.dirname(__FILE__), 'compound.rb')
+load File.join(File.dirname(__FILE__), 'feature.rb')
 
 helpers do
 
-	def not_found?
-		halt 404, "Dataset \"#{params[:name]}\" not found." unless @dataset = Dataset.find(uri(params[:name]))
+	def find
+		uri = uri(params[:splat].first)
+		halt 404, "Dataset \"#{uri}\" not found." unless @set = Dataset.find(uri)
 	end
 
 	def uri(name)
-		uri = url_for("/", :full) + name.gsub(/\s|\n/,'_')
+		uri = url_for("/", :full) + URI.encode(name) #.gsub(/\s|\n/,'_')
 	end
 
 end
@@ -43,6 +46,89 @@ get '/?' do
 	Dataset.find_all.join("\n")
 end
 
+get '/*/tanimoto/*/?' do
+	find
+	@set.tanimoto(uri(params[:splat][1]))
+end
+
+get '/*/weighted_tanimoto/*/?' do
+	find
+	@set.weighted_tanimoto(uri(params[:splat][1]))
+end
+
+# catch the rest
+get '/*/?' do
+	find
+	@set.to_yaml
+end
+
+post '/?' do
+
+	dataset_uri = uri(params[:name])
+	halt 403, "Dataset \"#{dataset_uri}\" exists." if Dataset.find(dataset_uri)
+
+	@set = Dataset.create(dataset_uri)
+	@compounds_set = Dataset.create File.join(dataset_uri, "compounds")
+	#@activities_set = Dataset.create File.join(dataset_uri, "activities")
+	#@features_set = Dataset.create File.join(dataset_uri, "features")
+	@set.add(@compounds_set.uri)
+	#@set.add(@activities_set.uri)
+	#@set.add(@features_set.uri)
+	@set.uri
+
+end
+
+post '/*/activities/?' do
+
+	find
+	@compounds_set = Dataset.find File.join(@set.uri, "compounds")
+	#@activities_set = Dataset.find File.join(@set.uri, "activities")
+	File.open(params[:file][:tempfile].path).each_line do |line|
+		record = line.chomp.split(/,\s*/)
+		inchi = Compound.new(:smiles => record[0]).inchi
+		feature = Feature.new(:name => @set.name, :values => {:classification => record[1]})
+		@compound_activities = Dataset.find_or_create File.join(@set.uri, inchi)
+		#@activity_compounds = Dataset.find_or_create File.join(@set.uri, feature.path)
+		@compounds_set.add(inchi)
+		#@activities_set.add(feature.path)
+		@compound_activities.add(feature.path)
+		#@activity_compounds.add(inchi)
+	end
+	@set.uri
+
+end
+
+post '/*/features/?' do
+
+	find
+	@compounds_set = Dataset.find File.join(@set.uri, "compounds")
+	#@features_set = Dataset.find File.join(@set.uri, "features")
+	YAML.load(params[:features]).each do |inchi,features|
+		@compound_features = Dataset.find_or_create File.join(@set.uri, inchi)
+		features.each do |feature|
+			#@feature_compounds = Dataset.find_or_create File.join(@set.uri, feature)
+			@compounds_set.add(inchi)
+			#@features_set.add(feature)
+			@compound_features.add(feature)
+			#@feature_compounds.add(inchi)
+		end
+  end
+	@set.uri
+
+end
+
+delete '/*/?' do
+	find
+	@set.members.each{|m| Dataset.find(m).delete}
+	@set.delete
+end
+
+put '/*/?' do
+	find
+	@set.add(params[:uri])
+end
+
+=begin
 get '/:name' do
   not_found?
   respond_to do |format|
@@ -142,3 +228,4 @@ delete '/collection/:name/?' do
 	DatasetCollection.find(uri params[:name]).destroy
   "Successfully deleted dataset collection \"#{params[:name]}\"."
 end
+=end
diff --git a/dataset.rb b/dataset.rb
index 00872b9..25adf86 100644
--- a/dataset.rb
+++ b/dataset.rb
@@ -1,11 +1,92 @@
 class Dataset
 
-	#include OpenTox::Utils
+	include OpenTox::Utils
+	attr_reader :uri, :name, :members
+
+	def initialize(uri)
+		@uri = uri
+		begin
+			@name = URI.split(uri)[5]
+		rescue
+			puts "Bad URI #{uri}"
+		end
+		@members = @@redis.set_members(uri)
+	end
+
+	def self.create(uri)
+		@@redis.set_add "datasets", uri
+		Dataset.new(uri)
+	end
+
+	def self.find(uri)
+		if @@redis.set_member? "datasets", uri
+			Dataset.new(uri)
+		else
+			nil
+		end
+	end
+
+	def self.find_or_create(uri)
+		dataset = Dataset.create(uri) unless dataset = Dataset.find(uri)
+		dataset
+	end
+
+	def self.find_all_keys
+		@@redis.keys "*"
+	end
+
+	def self.find_all
+		@@redis.set_members "datasets"
+	end
+
+	def add(member_uri)
+		@@redis.set_add @uri , member_uri
+		@members << member_uri
+	end
+
+	def union(set_uri)
+		@@redis.set_union(@uri,set_uri)
+	end
+
+	def intersection(set_uri)
+		@@redis.set_intersect(@uri,set_uri)
+	end
+
+	def tanimoto(set_uri)
+		union_size = @@redis.set_union(@uri,set_uri).size
+		intersect_size = @@redis.set_intersect(@uri,set_uri).size
+		"#{intersect_size.to_f/union_size.to_f}"
+	end
+
+	def weighted_tanimoto(set_uri)
+		union = @@redis.set_union(@uri,set_uri)
+		intersect = @@redis.set_intersect(@uri,set_uri)
+
+		p_sum_union = 0.0
+		p_sum_intersect = 0.0
+
+		union.each{ |f| p_sum_union += OpenTox::Utils::gauss(Feature.value(f,'p_value').to_f) }
+		intersect.each{ |f| p_sum_intersect += OpenTox::Utils::gauss(Feature.value(f,'p_value').to_f) }
+		"#{p_sum_intersect/p_sum_union}"
+	end
+
+	def delete
+		@@redis.delete @uri 
+		@@redis.set_delete "datasets", @uri
+	end
+
+end
+
+=begin
+class Dataset
+
+	include OpenTox::Utils
 	attr_reader :uri, :name
 
 	def initialize(uri)
 		@name = File.basename(uri)
 		@uri = uri
+		@members = []
 	end
 
 	def self.create(uri)
@@ -93,7 +174,7 @@ class Dataset
 
 end
 
-class Set
+class Dataset
 
 	attr_accessor :uri, :set_uris
 
@@ -146,3 +227,4 @@ class Set
 	end
 
 end
+=end
diff --git a/test/test.rb b/test/test.rb
index 65959bf..611113b 100644
--- a/test/test.rb
+++ b/test/test.rb
@@ -1,12 +1,14 @@
 require 'application'
 require 'test/unit'
 require 'rack/test'
+require 'ruby-prof'
 
 set :environment, :test
 @@redis.flush_db
 
 class DatasetsTest < Test::Unit::TestCase
   include Rack::Test::Methods
+	#include RubyProf::Test
 
   def app
     Sinatra::Application
@@ -20,72 +22,32 @@ class DatasetsTest < Test::Unit::TestCase
 	def test_create_dataset
 		post '/', :name => "Test dataset"
 		assert last_response.ok?
-		uri = last_response.body.chomp
-		assert_equal "http://example.org/Test_dataset", uri
-		get uri
-		assert last_response.ok?
-		delete "/Test_dataset"
-		assert last_response.ok?
-		get "/Test_dataset"
-		assert !last_response.ok?
-	end
-
-	def test_create_dataset_and_insert_data
-		name = "Test dataset"
-		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
+		uri = last_response.body
+		assert_equal "http://example.org/Test%20dataset", uri
 		get uri
 		assert last_response.ok?
-    assert last_response.body.include?("Test_dataset")
-
-		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'
-		#puts last_response.body
 		delete uri
 		assert last_response.ok?
-		get "/Test_dataset"
+		get uri
 		assert !last_response.ok?
 	end
 
 	def test_create_dataset_from_csv
 		smiles = 'CC(=O)Nc1scc(n1)c1ccc(o1)[N+](=O)[O-]'
-		compound_uri = OpenTox::Compound.new(:smiles => smiles).uri
-		post '/', :name => "Hamster Carcinogenicity", :file => Rack::Test::UploadedFile.new(File.join(File.dirname(__FILE__), "hamster_carcinogenicity.csv"))
+		compound = Compound.new(:smiles => smiles)
+		post '/', :name => "Hamster Carcinogenicity"
 		uri = last_response.body
+		post uri + '/activities', :file => Rack::Test::UploadedFile.new(File.join(File.dirname(__FILE__), "hamster_carcinogenicity.csv"))
 		get 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?("Hamster%20Carcinogenicity/classification/true")
-		assert last_response.body.include?("Hamster%20Carcinogenicity/classification/false")
-		get uri + '/compound/' + compound_uri + '/features'
+		assert last_response.body.include?(compound.inchi)
+		#get uri + '/activities'
+		#assert last_response.ok?
+		#assert last_response.body.include?("Hamster%20Carcinogenicity/classification/true")
+		#assert last_response.body.include?("Hamster%20Carcinogenicity/classification/false")
+		get File.join(uri ,compound.inchi)
 		assert last_response.ok?
     assert last_response.body.include?("Hamster%20Carcinogenicity/classification/true")
 		delete uri
@@ -94,20 +56,21 @@ class DatasetsTest < Test::Unit::TestCase
 		assert !last_response.ok?
 	end
 
-=begin
 	def test_create_large_dataset_from_csv
-		post '/', :name => "Salmonella Mutagenicity", :file => Rack::Test::UploadedFile.new(File.join(File.dirname(__FILE__), "kazius.csv"))
+		post '/', :name => "Salmonella Mutagenicity"
+		uri = last_response.body
+		post uri + '/activities', :file => Rack::Test::UploadedFile.new(File.join(File.dirname(__FILE__), "kazius.csv"))
 		uri = last_response.body
 		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' =>
+			'c1ccccc1' =>
+			#'[O-][N+](=O)C/C=C\C(=O)Cc1cc(C#N)ccc1' =>
 			{
 				'A' => 1.0,
 				'B' => 0.9,
@@ -115,7 +78,8 @@ class DatasetsTest < Test::Unit::TestCase
 				'D' => 0.7,
 				'E' => 0.5
 			},
-			'F[B-](F)(F)F.[Na+]' => 
+				'CCCNN' =>
+			#'F[B-](F)(F)F.[Na+]' => 
 			{
 				'F' => 0.9,
 				'B' => 0.9,
@@ -123,7 +87,8 @@ class DatasetsTest < Test::Unit::TestCase
 				'D' => 0.7,
 				'E' => 0.5
 			},
-			'N#[N+]C1=CC=CC=C1.F[B-](F)(F)F' => 
+				'C1CO1' =>
+			#'N#[N+]C1=CC=CC=C1.F[B-](F)(F)F' => 
 			{
 				'A' => 1.0,
 				'B' => 0.9,
@@ -135,24 +100,29 @@ class DatasetsTest < Test::Unit::TestCase
 		uri = last_response.body
 		get uri
 		assert last_response.ok?
-		get uri + '/name'
-		name = last_response.body
+		name = URI.encode(name)
+		feature_data = {}
 
 		data.each do |smiles,features|
-			compound_uri = OpenTox::Compound.new(:smiles => smiles).uri
+			compound = Compound.new(:smiles => smiles).inchi
+			feature_data[compound] = []
 			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?
+				feature= Feature.new(:name => k, :values => {:p_value => v}).path
+				feature_data[compound] << feature
 			end
 		end
 
+		post uri + '/features', :features => feature_data.to_yaml
+		assert last_response.ok?
+
 		data.each do |smiles,features|
-			compound_uri = OpenTox::Compound.new(:smiles => smiles).uri
+			compound= Compound.new(:smiles => smiles).inchi
 			data.each do |s,f|
 				unless s == smiles
-					neighbor_uri = OpenTox::Compound.new(:smiles => s).uri
-					get "/tanimoto/#{name}/compound/#{compound_uri}/#{name}/compound/#{neighbor_uri}"
+					neighbor= Compound.new(:smiles => s).inchi
+					get "/#{name}/#{compound}/"
+					assert last_response.ok?
+					get "/#{name}/#{compound}/tanimoto/#{name}/#{neighbor}"
 					assert last_response.ok?
 					sim = last_response.body
 					features_a = data[smiles].keys
@@ -162,7 +132,7 @@ class DatasetsTest < Test::Unit::TestCase
 					mysim = intersect.size.to_f/union.size.to_f
 					assert_equal sim, mysim.to_s
 					puts "tanimoto::#{smiles}::#{s}::#{last_response.body}"
-					get "/weighted_tanimoto/#{name}/compound/#{compound_uri}/#{name}/compound/#{neighbor_uri}"
+					get "/#{name}/#{compound}/weighted_tanimoto/#{name}/#{neighbor}"
 					assert last_response.ok?
 					puts "weighted_tanimoto::#{smiles}::#{s}::#{last_response.body}"
 				end
@@ -171,11 +141,4 @@ class DatasetsTest < Test::Unit::TestCase
 
 	end
 
-=begin
-	def test_unauthorized_create
-		post '/', :name => "Test dataset"
-		assert !last_response.ok?
-	end
-=end
-
 end