Passes tests in opentox-test

8 files changed, 142 insertions, 326 deletions

diff --git a/.gitignore b/.gitignore
index 8839a06..e4a5a44 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,3 +1,4 @@
 tmp/*
 *.sqlite3
 log/*
+db/*
diff --git a/application.rb b/application.rb
index b5d8d4e..c86fe66 100644
--- a/application.rb
+++ b/application.rb
@@ -1,103 +1,5 @@
-['rubygems', 'sinatra', 'redis', 'builder', 'opentox-ruby-api-wrapper'].each do |lib|
-	require lib
-end
-
-load File.join(File.dirname(__FILE__), 'model.rb')
-
-case ENV['RACK_ENV']
-when 'production'
-  @@redis = Redis.new :db => 0
-when 'development'
-  @@redis = Redis.new :db => 1
-when 'test'
-  @@redis = Redis.new :db => 2
-  @@redis.flush_db
-end
+require 'rubygems'
+require 'opentox-ruby-api-wrapper'
+require 'lazar.rb'
 
 set :default_content, :yaml
-
-helpers do
-
-	def find
-		uri = uri(params[:splat].first)
-		halt 404, "Dataset \"#{uri}\" not found." unless @model = Model.find(uri)
-	end
-
-	def uri(name)
-		uri = url_for("/model/", :full) + URI.encode(name)
-	end
-end
-
-get '/algorithms' do
-	url_for("/algorithm/classification", :full)
-end
-
-post '/algorithm/classification/?' do # create a model
-	#halt 403, 
-	activity_dataset_uri = OpenTox::Dataset.find(:uri => params[:dataset_uri]).uri
-	feature_dataset_uri = OpenTox::Algorithm::Fminer.create(activity_dataset_uri)
-	Model.create(:activity_dataset_uri => activity_dataset_uri, :feature_dataset_uri => feature_dataset_uri).uri
-end
-
-get '/models/?' do # get index of models
-	Model.find_all.join("\n")
-end
-
-get '/model/*/?' do
-	#halt 404, "Model #{name} not found." unless @model = Model.find(request.url)
-	find
-	@model.to_yaml
-end
-
-delete '/model/*' do
-	name = params[:splat].first
-	halt 404, "Model #{name} not found." unless @model = Model.find(request.url)
-	@model.destroy
-	"Model #{params[:id]} succesfully deleted."
-end
-
-post '/model/*' do # create prediction
-	name = params[:splat].first
-	halt 404, "Model #{name} not found." unless @model = Model.find(request.url)
-	compound = OpenTox::Compound.new :uri => params[:compound_uri]
-	@model.predict(compound)
-end
-
-# PREDICTIONS
-get '/model/*/predictions?' do # get dataset URI
-	name = params[:splat].first
-	halt 404, "Model #{name} not found." unless @model = Model.find(request.url)
-	# Dataset.find
-end
-
-get '/model/*/prediction/*' do	# display prediction for a compound
-	name = params[:splat].first
-	compound_uri = params[:splat][1]
-	halt 404, "Model #{name} not found." unless @model = Model.find(request.url)
-	# prediction not found
-	#prediction.to_yaml
-	#xml prediction
-end
-
-get '/model/*/prediction/*/neighbors' do	
-	name = params[:splat].first
-	compound_uri = params[:splat][1]
-	halt 404, "Model #{name} not found." unless @model = Model.find(request.url)
-	# prediction not found
-	# prediction.neighbors
-end
-
-get '/model/*/prediction/*/features' do	
-	name = params[:splat].first
-	compound_uri = params[:splat][1]
-	halt 404, "Model #{name} not found." unless @model = Model.find(request.url)
-	# prediction not found
-	# prediction not found
-	# prediction.features
-end
-
-delete '/model/*/prediction/*' do	# display prediction for a compound
-	name = params[:splat].first
-	halt 404, "Model #{name} not found." unless @model = Model.find(request.url)
-	# Prediction.destroy
-end
diff --git a/config.ru b/config.ru
index 02ca8b3..c386f81 100644
--- a/config.ru
+++ b/config.ru
@@ -1,6 +1,8 @@
 require 'rubygems'
 require 'sinatra'
 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")
diff --git a/environment.rb b/environment.rb
index c6ebefb..067fc18 100644
--- a/environment.rb
+++ b/environment.rb
@@ -1,16 +1,5 @@
-['rubygems', 'sinatra', 'redis', 'builder', 'opentox-ruby-api-wrapper'].each do |lib|
-	require lib
-end
-
-case ENV['RACK_ENV']
-when 'production'
-	  @@redis = Redis.new :db => 0
-when 'development'
-	  @@redis = Redis.new :db => 1
-when 'test'
-	  @@redis = Redis.new :db => 2
-	  @@redis.flush_db
-end
+require 'rubygems'
+require 'opentox-ruby-api-wrapper'
 
 set :default_content, :yaml
 load 'models.rb'
diff --git a/lazar.rb b/lazar.rb
new file mode 100644
index 0000000..2b23495
--- /dev/null
+++ b/lazar.rb
@@ -0,0 +1,134 @@
+require 'datamapper'
+
+DataMapper::setup(:default, "sqlite3://#{Dir.pwd}/db/#{ENV['RACK_ENV']}.db")
+
+class LazarModel
+	include DataMapper::Resource
+	property :id, Serial
+	property :activity_dataset_uri, String, :length => 256 # default is too short for URIs
+	property :feature_dataset_uri, String, :length => 256 # default is too short for URIs
+	property :created_at, DateTime
+
+	def uri
+		File.join(OpenTox::Model::LazarClassification.base_uri,"lazar_classification", self.id.to_s)
+	end
+
+	def predict(compound)
+
+		training_activities = OpenTox::Dataset.find :uri => @activity_dataset_uri
+		# TODO: find database activities
+		# TODO: find prediction
+		training_features = OpenTox::Dataset.find :uri => @feature_dataset_uri
+
+		prediction_dataset = OpenTox::Dataset.find_or_create(:name => training_activities.name + '_predictions')
+		prediction_neighbors = OpenTox::Dataset.find_or_create(:name => training_activities.name + '_neighbors')
+		prediction_features = OpenTox::Dataset.find_or_create(:name => training_activities.name + '_prediction_features')
+
+		feature_uris = compound.match(training_features)
+		prediction_features.add({compound.uri => feature_uris}.to_yaml)
+
+		conf = 0.0
+		neighbors = []
+
+		training_features.compounds.each do |neighbor|
+			sim = OpenTox::Algorithm::Similarity.weighted_tanimoto(training_features,neighbor,prediction_features,compound).to_f
+			if sim > 0.3
+				neighbors << neighbor.uri
+				training_activities.features(neighbor).each do |a|
+					case OpenTox::Feature.new(:uri => a.uri).value('classification').to_s
+					when 'true'
+						conf += OpenTox::Utils.gauss(sim) 
+					when 'false'
+						conf -= OpenTox::Utils.gauss(sim)
+					end
+				end
+			end
+		end
+		conf = conf/neighbors.size
+		if conf > 0.0
+			classification = true
+		elsif conf < 0.0
+			classification = false
+		end
+
+		prediction = OpenTox::Feature.new(:name => training_activities.name + " prediction", :classification => classification, :confidence => conf)
+		prediction_neighbors.add({compound.uri => neighbors}.to_yaml)
+		prediction_dataset.add({compound.uri => [prediction.uri]}.to_yaml)
+
+		prediction.uri
+
+	end
+end
+
+# automatically create the post table
+LazarModel.auto_migrate! #unless LazarModel.table_exists?
+LazarModel.auto_migrate! if ENV['RACK_ENV'] == 'test'
+
+get '/lazar_classification/?' do # get index of models
+	LazarModel.all.collect{|m| m.uri}.join("\n")
+end
+
+get '/lazar_classification/:id/?' do
+	halt 404, "Model #{params[:id]} not found." unless @model = LazarModel.get(params[:id])
+	@model.to_yaml
+end
+
+delete '/lazar_classification/:id/?' do
+	halt 404, "Model #{params[:id]} not found." unless @model = LazarModel.get(params[:id])
+	@model.destroy
+	"Model #{params[:id]} succesfully deleted."
+end
+
+post '/lazar_classification/?' do # create model
+	halt 404, "Dataset #{params[:activity_dataset_uri]} not found" unless  OpenTox::Dataset.find(:uri => params[:activity_dataset_uri])
+	halt 404, "Dataset #{params[:feature_dataset_uri]} not found" unless OpenTox::Dataset.find(:uri => params[:feature_dataset_uri])
+	model = LazarModel.new(params)
+	model.save
+	model.uri
+end
+
+# PREDICTIONS
+post '/lazar_classification/:id/?' do # create prediction
+	halt 404, "Model #{params[:id]} not found." unless @model = LazarModel.get(params[:id])
+	compound = OpenTox::Compound.new :uri => params[:compound_uri]
+	@model.predict(compound)
+end
+
+get '/lazar_classification/*/predictions?' do # get dataset URI
+	name = params[:splat].first
+	halt 404, "Model #{name} not found." unless @model = LazarModel.get(request.url)
+	# Dataset.find
+end
+
+get '/lazar_classification/*/prediction/*' do	# display prediction for a compound
+	name = params[:splat].first
+	compound_uri = params[:splat][1]
+	halt 404, "Model #{name} not found." unless @model = LazarModel.get(request.url)
+	# prediction not found
+	#prediction.to_yaml
+	#xml prediction
+end
+
+get '/lazar_classification/*/prediction/*/neighbors' do	
+	name = params[:splat].first
+	compound_uri = params[:splat][1]
+	halt 404, "Model #{name} not found." unless @model = LazarModel.get(request.url)
+	# prediction not found
+	# prediction.neighbors
+end
+
+get '/lazar_classification/*/prediction/*/features' do	
+	name = params[:splat].first
+	compound_uri = params[:splat][1]
+	halt 404, "Model #{name} not found." unless @model = LazarModel.get(request.url)
+	# prediction not found
+	# prediction not found
+	# prediction.features
+end
+
+delete '/lazar_classification/*/prediction/*' do	# display prediction for a compound
+	name = params[:splat].first
+	halt 404, "Model #{name} not found." unless @model = LazarModel.get(request.url)
+	# Prediction.destroy
+end
+
diff --git a/model.rb b/model.rb
deleted file mode 100644
index 3a84217..0000000
--- a/model.rb
+++ /dev/null
@@ -1,83 +0,0 @@
-class Model 
-
-	include OpenTox::Utils
-	attr_accessor :uri, :activity_dataset_uri, :feature_dataset_uri, :name
-
-	def initialize(params)
-		@uri = params[:uri]
-		@activity_dataset_uri = params[:activity_dataset_uri]
-		@feature_dataset_uri = params[:feature_dataset_uri]
-		begin
-			@name = URI.split(@uri)[5]
-		rescue
-			puts "Bad URI #{@uri}"
-		end
-	end
-
-	def self.create(params)
-		params[:uri] = params[:activity_dataset_uri].sub(/dataset/,'model')
-		@@redis.set_add "models", params[:uri]
-		@@redis.set(File.join(params[:uri],"activity_dataset"), params[:activity_dataset_uri])
-		@@redis.set(File.join(params[:uri],"feature_dataset"), params[:feature_dataset_uri])
-		Model.new(params)
-	end
-
-	def self.find(uri)
-		if @@redis.set_member? "models", uri
-			activity_dataset_uri = @@redis.get File.join(uri,"activity_dataset")
-			feature_dataset_uri = @@redis.get File.join(uri,"feature_dataset")
-			Model.new(:uri => uri, :activity_dataset_uri => activity_dataset_uri, :feature_dataset_uri => feature_dataset_uri)
-		else
-			nil
-		end
-	end
-
-	def self.find_all
-		@@redis.set_members("models")
-	end
-
-	def predict(compound)
-
-		training_activities = OpenTox::Dataset.find :uri => @uri.sub(/model/,'dataset')
-		# find database activities
-		# find prediction
-		training_features = OpenTox::Dataset.find(:uri => @feature_dataset_uri)
-
-		prediction_dataset = OpenTox::Dataset.find_or_create(:name => training_activities.name + '_predictions')
-		prediction_neighbors = OpenTox::Dataset.find_or_create(:name => training_activities.name + '_neighbors')
-		prediction_features = OpenTox::Dataset.find_or_create(:name => training_activities.name + '_prediction_features')
-
-		feature_uris = compound.match(training_features)
-		prediction_features.add({compound.uri => feature_uris})
-
-		conf = 0.0
-		neighbors = []
-
-		training_features.compounds.each do |neighbor|
-			sim = OpenTox::Algorithm::Similarity.weighted_tanimoto(training_features,neighbor,prediction_features,compound).to_f
-			if sim > 0.3
-				neighbors << neighbor.uri
-				training_activities.features(neighbor).each do |a|
-					case OpenTox::Feature.new(:uri => a.uri).value('classification').to_s
-					when 'true'
-						conf += OpenTox::Utils.gauss(sim) 
-					when 'false'
-						conf -= OpenTox::Utils.gauss(sim)
-					end
-				end
-			end
-		end
-		conf = conf/neighbors.size
-		if conf > 0.0
-			classification = true
-		elsif conf < 0.0
-			classification = false
-		end
-
-		prediction_neighbors.add({compound.uri => neighbors})
-		prediction_uri = OpenTox::Feature.new(:name => @name, :values => {:classification => classification, :confidence => conf}).uri
-		prediction_uri
-
-	end
-
-end
diff --git a/test/hamster_carcinogenicity.csv b/test/hamster_carcinogenicity.csv
deleted file mode 100644
index 009808f..0000000
--- a/test/hamster_carcinogenicity.csv
+++ /dev/null
@@ -1,85 +0,0 @@
-CC=O,true

-C12C3=C(C=CC=C3)CC1=CC(=CC=2)NC(C)=O,true

-O=C(N)\C(C2=CC=CO2)=C/C1=CC=C([N+]([O-])=O)O1,true

-C1(N=CNN=1)N,false

-Br(=O)(=O)[O-].[K+],true

-[Cl-].[Cd+2].[Cl-],false

-O=S(=O)([O-])[O-].[Cd+2],false

-ClC1=CC(=NC(=N1)SCC(=O)O)NC2=CC=CC(=C2C)C,false

-ClCOC,true

-C=C(Cl)C=C,false

-Clc1ccc(cc1)c2ccc(COC(C)(C)C(O)=O)cc2,false

-O=C1OC2=C(C=CC=C2)C=C1,false

-ClC(=C(C1=CC=C(C=C1)Cl)C2=CC=C(C=C2)Cl)Cl,true

-ClC(C(C1=CC=C(C=C1)Cl)C2=CC=C(C=C2)Cl)(Cl)Cl,false

-C=CCN(CC=C)N=O,true

-Cl\C2=C(/Cl)C3(Cl)C1C4CC(C1C2(Cl)C3(Cl)Cl)C5OC45,false

-O=C(N(C)C)Cl,true

-CN(C)N,true

-N(NC)C.[H]Cl.[H]Cl,true

-CCO,false

-O=C(N(CC)N=O)NCCO,true

-O=C(N(CC)N=O)NCC(=O)C,true

-C=O,false

-[O-][N+](=O)C1=CC=C(O1)C2=CSC(=N2)NNC=O,true

-O=CC1=CC=CO1,false

-OCC1CO1,true

-O=C2C1=C(OC)C=C(OC)C(Cl)=C1O[C@]32C(OC)=CC(C[C@@](C)3[H])=O,false

-ClC1=C(C(=C(C(=C1Cl)Cl)Cl)Cl)Cl,true

-NN,true

-OS(=O)(=O)O.NN,true

-CC(=O)N(O)C1=CC2=C(C=C1)C3=CC=CC=C3C2,true

-OCCNN,false

-O=C(C1=CC=NC=C1)NN,false

-OC(=O)C1=CC=NC=C1,false

-O=C(NC1=CC=CC(=C1)Cl)OC(C)C,false

-O=C(NC1=CC=CC=C1)OC(C)C,false

-[O-]C(C)=O.[O-]C(C)=O.[Pb+2].[OH-].[OH-].[Pb+2].[OH-].[OH-].[Pb+2],false

-CN(C)CCN(CC2=CC=CS2)C1=NC=CC=C1.Cl,false

-NC1=C2C(=NC(=N1)N)N=CC(=N2)CN(C3=CC=C(C=C3)C(=O)N[C@@H](CCC(=O)O)C(=O)O)C,false

-CN(N)C=O,true

-O=C(C(=C)C)OC,false

-CNN,true

-O=C(C1=CC=CN=C1)CCCN(N=O)C,false

-CC1=CC(=O)NC(=S)N1,true

-CC(C(O)=O)(OC1=CC=C(C=C1)C2CCCC3=C2C=CC=C3)C,false

-O=N[O-].[Na+],false

-[O-][N+](C1=CC=C(C2=CSC(NC(C)=O)=N2)O1)=O,true

-[O-][N+](=O)C1=CC=C(O1)C2=CSC(=N2)NC=O,true

-O=[N+](C1=CC=C2C3=C1C=CC=C3CC2)[O-],false

-N(CC(CO)O)(CC(O)C)N=O,true

-N(CC(CO)O)(CC(C)=O)N=O,true

-N(CC(CO)O)(CCO)N=O,false

-O=C(C)CN(N=O)CCO,true

-C1C(N(C(CN1N=O)C)C)C,true

-N(CC(C)=O)(CC=C)N=O,true

-N(CC(CO)O)(C)N=O,true

-O=NN1CCOCC1,true

-N1C=CC=C(C=1)C2N(N=O)CCC2,true

-C1=CC=C(C=[N+]1[O-])C2CCCN2N=O,false

-O=NN1CCCCC1,true

-O=NN1CCCC1,true

-O=C(N(CC(C)=O)N=O)NCCCl,true

-N(C(=O)N)(N=O)CC(C)=O,true

-C1(CCN=C=S)=CC=CC=C1,false

-O=C1C(C2=CC=CC=C2)(C(=O)NC(=O)N1)CC,false

-C1=C2C(=CC=C1NC3=CC=CC=C3)C=CC=C2,false

-O=C1N2C(C3=C(C=CC=C3)CC2)CN(C1)C(=O)C4CCCCC4,false

-C1(=CC(=C(O)C=C1)O)C(O)=O,false

-O=C1C2=C(C=C(C=C2O)O)O/C(=C\1O)C3=CC(=C(C=C3)O)O.O.O,false

-C1=C(C=CC(=C1)C(C2=CC=C(N)C(=C2)C)=C3C=CC(=N)C=C3)N.[H]Cl,false

-C(C1=CC=C(C=C1)N)(C2=CC=C(C=C2)N)=C3C=CC(C=C3)=N.[H]Cl,false

-OC2=CC1=C(C(O)=C2)C(C(O[C@@H]4O[C@@H]([C@H]([C@H](O)[C@H]4O)O)CO[C@H]3[C@H](O)[C@H](O)[C@H]([C@H](C)O3)O)=C(C5=CC(O)=C(C=C5)O)O1)=O,false

-ClC(=CCl)Cl,false

-NC(=O)OCC,true

-C=CCl,true

-N#[N+]C1=CC=CC=C1.F[B-](F)(F)F,false

-C1(CN(CC(N1N=O)C)N=O)C,true

-N(CCN(C)C)(C)N=O,true

-C1(CN(N=O)CC(O1)C)C,true

-O1C(N(CC1C)N=O)=O,true

-CCOC(=O)N(C)N=O,true

-C1N(COC1)N=O,true

-O=C(N(CCC1=CC=CC=C1)N=O)N,true

-O=NN1CCC1,true

-F[B-](F)(F)F.[Na+],false

diff --git a/test/test.rb b/test/test.rb
deleted file mode 100644
index f374bb4..0000000
--- a/test/test.rb
+++ /dev/null
@@ -1,44 +0,0 @@
-require 'application'
-require 'test/unit'
-require 'rack/test'
-
-set :environment, :test
-
-class LazarTest < Test::Unit::TestCase
-  include Rack::Test::Methods
-
-  def app
-    Sinatra::Application
-  end
-
-	def setup
-		@dataset = OpenTox::Dataset.create :name => "Hamster Carcinogenicity"
-	 	@dataset.import :csv => File.join(File.dirname(__FILE__), "hamster_carcinogenicity.csv"), :compound_format => "smiles", :feature_type => "activity"
-	end
-
-	def teardown
-		@dataset.delete
-	end
-
-	def test_algorithms
-		get '/algorithms'
-		assert last_response.body.include?("classification")
-	end
-
-	def test_create_model_and_predict
-		post '/algorithm/classification', :dataset_uri => @dataset.uri
-		assert last_response.ok?
-		model_uri = last_response.body
-		get model_uri
-		assert last_response.ok?
-		get '/models'
-		assert last_response.body.include? model_uri
-		query_structure = OpenTox::Compound.new :smiles => 'c1ccccc1NN'
-		#query_structure = OpenTox::Compound.new :smiles => '[O-]C(C)=O.[O-]C(C)=O.[Pb+2].[OH-].[OH-].[Pb+2].[OH-].[OH-].[Pb+2]'
-		post model_uri, :compound_uri => query_structure.uri
-		assert last_response.ok?
-		assert last_response.body.include? 'classification/true'
-		puts last_response.body
-	end
-
-end