Passes tests in opentox-test

11 files changed, 84 insertions, 43 deletions

diff --git a/lib/algorithm.rb b/lib/algorithm.rb
index 7007e3a..43f7ede 100644
--- a/lib/algorithm.rb
+++ b/lib/algorithm.rb
@@ -3,20 +3,24 @@ module OpenTox
 
 		class Fminer < OpenTox
 			# Create a new dataset with BBRC features
-			def self.create(training_dataset_uri)
-				RestClient.post @@config[:services]["opentox-fminer"], :dataset_uri => training_dataset_uri
+			def self.create(params)
+				puts  params[:dataset_uri]
+				uri = RestClient.post File.join(@@config[:services]["opentox-algorithm"],'fminer'), :dataset_uri => params[:dataset_uri]
+				print "fminer finsihed "
+				puts uri
+				uri
 			end
 		end
 
 		class Similarity < OpenTox
 
 			def self.tanimoto(dataset1,compound1,dataset2,compound2)
-				RestClient.get File.join(@@config[:services]["opentox-dataset"], 'algorithm/tanimoto/dataset',dataset1.name,compound1.inchi,'dataset',dataset2.name,compound2.inchi)
+				RestClient.get File.join(@@config[:services]["opentox-algorithm"], 'tanimoto/dataset',dataset1.name,compound1.inchi,'dataset',dataset2.name,compound2.inchi)
 			end
 
 			def self.weighted_tanimoto(dataset1,compound1,dataset2,compound2)
 				# URI.escape does not work here
-				uri = File.join(@@config[:services]["opentox-dataset"], 'algorithm/weighted_tanimoto/dataset',CGI.escape(dataset1.name),'compound',CGI.escape(compound1.inchi),'dataset',CGI.escape(dataset2.name),'compound',CGI.escape(compound2.inchi))
+				uri = File.join(@@config[:services]["opentox-algorithm"], 'weighted_tanimoto/dataset',CGI.escape(dataset1.name),'compound',CGI.escape(compound1.inchi),'dataset',CGI.escape(dataset2.name),'compound',CGI.escape(compound2.inchi))
 				RestClient.get uri
 			end
 
@@ -24,8 +28,8 @@ module OpenTox
 
 		class Lazar < OpenTox
 			# Create a new prediction model from a dataset
-			def initialize(params)
-				@uri = RestClient.post @@config[:services]["opentox-lazar"] + 'models' , :dataset_uri => params[:dataset_uri]
+			def self.create(params)
+				RestClient.post File.join(@@config[:services]["opentox-algorithm"],"lazar_classification"), params
 			end
 		end
 
diff --git a/lib/compound.rb b/lib/compound.rb
index 67c8004..c4ba8d9 100644
--- a/lib/compound.rb
+++ b/lib/compound.rb
@@ -10,13 +10,13 @@ module OpenTox
 			@@cactus_uri="http://cactus.nci.nih.gov/chemical/structure/"
 			if params[:smiles]
 				@inchi = smiles2inchi(params[:smiles])
-				@uri = File.join(@@config[:services]["opentox-dataset"],"compound",@inchi)
+				@uri = File.join(@@config[:services]["opentox-compound"],URI.escape(@inchi))
 			elsif params[:inchi]
-				@inchi = inchi
-				@uri = File.join(@@config[:services]["opentox-dataset"],"compound",@inchi)
+				@inchi = params[:inchi]
+				@uri = File.join(@@config[:services]["opentox-compound"],URI.escape(@inchi))
 			elsif params[:name]
 				@inchi = RestClient.get "#{@@cactus_uri}#{params[:name]}/stdinchi"
-				@uri = File.join(@@config[:services]["opentox-dataset"],"compound",@inchi)
+				@uri = File.join(@@config[:services]["opentox-compound"],URI.escape(@inchi))
 			elsif params[:uri]
 				@inchi = params[:uri].sub(/^.*InChI/, 'InChI')
 				@uri = params[:uri]
diff --git a/lib/dataset.rb b/lib/dataset.rb
index b635985..754e7f4 100644
--- a/lib/dataset.rb
+++ b/lib/dataset.rb
@@ -14,7 +14,7 @@ module OpenTox
 		end
 
 		def self.create(params)
-			uri = RestClient.post File.join(@@config[:services]["opentox-dataset"],"datasets"), :name => params[:name]
+			uri = RestClient.post @@config[:services]["opentox-dataset"], :name => params[:name]
 			Dataset.new(uri.to_s)
 		end
 
@@ -36,6 +36,10 @@ module OpenTox
 			self.create(params) unless self.find(params)
 		end
 
+		def self.base_uri
+			@@config[:services]["opentox-dataset"]
+		end
+
 		def import(params)
 			if params[:csv]
 				# RestClient seems not to work for file uploads
@@ -45,7 +49,7 @@ module OpenTox
 		end
 
 		def add(features)
-			RestClient.post @uri, :features => features.to_yaml
+			RestClient.put @uri, :features => features
 		end
 
 		# Get all compounds from a dataset
diff --git a/lib/environment.rb b/lib/environment.rb
index c65e968..3a9319d 100644
--- a/lib/environment.rb
+++ b/lib/environment.rb
@@ -1,7 +1,7 @@
-# load configuration
-
+# set default environment
 ENV['RACK_ENV'] = 'test' unless ENV['RACK_ENV']
 
+# load configuration
 basedir = File.join(ENV['HOME'], ".opentox")
 config_dir = File.join(basedir, "config")
 @@tmp_dir = File.join(basedir, "tmp")
@@ -16,3 +16,18 @@ else
 	puts "Please edit #{config_file} and restart your application."
 	exit
 end
+
+# configure redis database
+begin
+	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
+rescue
+	puts "Redis database not running, please start it with 'rake redis:start'."
+end
diff --git a/lib/feature.rb b/lib/feature.rb
index 8b0839f..a3ba333 100644
--- a/lib/feature.rb
+++ b/lib/feature.rb
@@ -9,31 +9,33 @@ module OpenTox
 			if params[:uri]
 				@uri = params[:uri]
 				items = URI.split(@uri)[5].split(/\//)
-				@name = items[2]
+				@name = items[1]
 				@values = {}
-				i = 4
+				i = 2
 				while i < items.size
 					@values[items[i]] = items[i+1]
 					i += 2
 				end
 			else 
 				@name = params[:name]
-				#@name = URI.encode(URI.decode(params[:name]))
-				@values = params[:values]
-				@uri = File.join(@@config[:services]["opentox-dataset"],"feature",path)
+				@values = {}
+				params.each do |k,v|
+					@values[k] = v unless k.to_s == 'name'
+				end
+				@uri = File.join(@@config[:services]["opentox-feature"],path)
 			end
 		end
 
 		def values_path
 			path = '' 
 			@values.each do |k,v|
-				path += '/' + URI.encode(k.to_s) + '/' + URI.encode(v.to_s)
+				path = File.join path, URI.encode(k.to_s), URI.encode(v.to_s)
 			end
 			path
 		end
 
 		def path
-			File.join(@name,values_path)
+			File.join(URI.encode(@name),values_path)
 		end
 
 		def value(property)
diff --git a/lib/model.rb b/lib/model.rb
index 0fa3be6..ec4d069 100644
--- a/lib/model.rb
+++ b/lib/model.rb
@@ -1,22 +1,27 @@
 module OpenTox
 
-	# key: /models
-	# set: dataset uris
 	module Model 
 
-		class Lazar < OpenTox
+		class LazarClassification < OpenTox
 
 			# Create a new prediction model from a dataset
-			def initialize(params)
-				super(params[:uri])
+			def initialize(uri)
+				super(uri)
+			end
+
+			def self.create(params)
+				uri = RestClient.post File.join(@@config[:services]["opentox-model"], 'lazar_classification'), params
+				puts "URI: " + uri
+				LazarClassification.new(uri.to_s)
 			end
 
 			def self.find(name)
-				RestClient.get File.join(@@config[:services]["opentox-lazar"], 'model', URI.encode(params[:name]))
+				uri = RestClient.get File.join(@@config[:services]["opentox-model"], 'lazar_classification', URI.encode(params[:name]))
+				LazarClassification.new(uri)
 			end
 
 			def self.find_all
-				RestClient.get File.join(@@config[:services]["opentox-lazar"], 'models')#.split("\n")
+				RestClient.get File.join(@@config[:services]["opentox-model"], 'lazar_classification')#.split("\n")
 			end
 
 			# Predict a compound
@@ -24,6 +29,10 @@ module OpenTox
 				LazarPrediction.new(:uri => RestClient.post(@uri, :compound_uri => compound.uri))
 			end
 
+			def self.base_uri
+				@@config[:services]["opentox-model"]
+			end
+
 		end
 
 	end
diff --git a/lib/opentox-ruby-api-wrapper.rb b/lib/opentox-ruby-api-wrapper.rb
index fd68e72..3e66528 100644
--- a/lib/opentox-ruby-api-wrapper.rb
+++ b/lib/opentox-ruby-api-wrapper.rb
@@ -1,7 +1,7 @@
-['rubygems', 'sinatra', 'sinatra/url_for', 'builder', 'rest_client', 'yaml', 'cgi', 'openbabel'].each do |lib|
+['rubygems', 'sinatra', 'sinatra/url_for',  'redis','builder', 'rest_client', 'yaml', 'cgi', 'openbabel', 'spork', 'environment'].each do |lib|
 	require lib
 end
 
-['environment', 'opentox', 'compound','feature','dataset','algorithm','model','utils'].each do |lib|
+['opentox', 'compound','feature','dataset','algorithm','model','task','utils'].each do |lib|
 	require lib
 end
diff --git a/lib/opentox.rb b/lib/opentox.rb
index 1a12123..9b1226b 100644
--- a/lib/opentox.rb
+++ b/lib/opentox.rb
@@ -25,4 +25,3 @@ module OpenTox
 	end
 
 end
-
diff --git a/lib/tasks/opentox.rb b/lib/tasks/opentox.rb
index 0dace9a..4cac9a5 100644
--- a/lib/tasks/opentox.rb
+++ b/lib/tasks/opentox.rb
@@ -1,4 +1,16 @@
-load File.join(File.dirname(__FILE__), '..', 'environment.rb')
+require File.join(File.dirname(__FILE__), '..', 'opentox-ruby-api-wrapper.rb')
+require File.join(File.dirname(__FILE__), 'redis.rb')
+
+namespace :redis do
+
+	desc "Flush Redis testing database"
+	task :flush do
+		require 'redis'
+		r = Redis.new :db => 2
+		r.flushdb
+	end
+
+end
 
 namespace :opentox do
 
@@ -19,8 +31,6 @@ namespace :opentox do
 			@@config[:services].each do |service,uri|
 				dir = File.join(@@config[:base_dir], service)
 				server = @@config[:webserver]
-				#puts "Starting Redis database"
-				#puts `redis-server /etc/redis.conf &`
 				case server
 				when /thin|mongrel|webrick/
 					port = uri.sub(/^.*:/,'').sub(/\/$/,'')
diff --git a/lib/templates/config.yaml b/lib/templates/config.yaml
index 14326fe..7b46d43 100644
--- a/lib/templates/config.yaml
+++ b/lib/templates/config.yaml
@@ -1,10 +1,10 @@
 :base_dir: /home/ch/webservices
 :webserver: thin
 :services:
-# make sure to provide a full uri (including training slash)
-  opentox-feature:      "http://localhost:5000/"
-  opentox-compound:     "http://localhost:5001/"
-  opentox-dataset:      "http://localhost:5002/"
-  opentox-fminer:       "http://localhost:5003/"
-  opentox-similarity:   "http://localhost:5004/"
-  opentox-lazar:        "http://localhost:5005/"
+# make sure to enter a full uri (including training slash)
+  opentox-compound:      "http://localhost:4000/"
+  opentox-feature:       "http://localhost:4001/"
+  opentox-dataset:       "http://localhost:4002/"
+  opentox-algorithm:     "http://localhost:4003/"
+  opentox-model:         "http://localhost:4004/"
+  #opentox-task:          "http://localhost:4005/"
diff --git a/lib/utils.rb b/lib/utils.rb
index 2716f45..cccb5ea 100644
--- a/lib/utils.rb
+++ b/lib/utils.rb
@@ -1,11 +1,9 @@
 module OpenTox
 	module Utils
-
 		# gauss kernel
 		def self.gauss(sim, sigma = 0.3) 
 			x = 1.0 - sim
 			Math.exp(-(x*x)/(2*sigma*sigma))
 		end
-
 	end
 end