api separated into individual components, adapted for new webservice versions

11 files changed, 400 insertions, 192 deletions

diff --git a/lib/algorithm.rb b/lib/algorithm.rb
new file mode 100644
index 0000000..912e14d
--- /dev/null
+++ b/lib/algorithm.rb
@@ -0,0 +1,35 @@
+module OpenTox
+	module Algorithm 
+
+		class Fminer < OpenTox
+			# Create a new dataset with BBRC features
+			def initialize(training_dataset)
+				@uri = RestClient.post @@config[:services]["opentox-fminer"], :dataset_uri => training_dataset.uri
+			end
+		end
+
+		class Similarity < OpenTox
+
+			def initialize
+				@uri = @@config[:services]["opentox-similarity"]
+			end
+
+			def self.tanimoto(dataset,compounds)
+				RestClient.post @uri + 'tanimoto', :dataset_uri => dataset.uri, :compound_uris => compounds.collect{ |c| c.uri }
+			end
+
+			def self.weighted_tanimoto(dataset,compounds)
+				RestClient.post @uri + 'weighted_tanimoto', :dataset_uri => dataset.uri, :compound_uris => compounds.collect{ |c| c.uri }
+			end
+
+		end
+
+		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]
+			end
+		end
+
+	end
+end
diff --git a/lib/compound.rb b/lib/compound.rb
new file mode 100644
index 0000000..4652770
--- /dev/null
+++ b/lib/compound.rb
@@ -0,0 +1,67 @@
+module OpenTox
+
+	# uri: /compound/:inchi
+	class Compound < OpenTox
+
+		attr_reader :inchi
+
+		# Initialize with <tt>:uri => uri</tt>, <tt>:smiles => smiles</tt> or <tt>:name => name</tt> (name can be also an InChI/InChiKey, CAS number, etc)
+		def initialize(params)
+			@@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)
+			elsif params[:inchi]
+				@inchi = inchi
+				@uri = File.join(@@config[:services]["opentox-dataset"],"compound",@inchi)
+			elsif params[:name]
+				@inchi = RestClient.get "#{@@cactus_uri}#{params[:name]}/stdinchi"
+				@uri = File.join(@@config[:services]["opentox-dataset"],"compound",@inchi)
+			elsif params[:uri]
+				@inchi = params[:uri].sub(/^.*InChI/, 'InChI')
+				@uri = params[:uri]
+			end
+		end
+
+		# Get the (canonical) smiles
+		def smiles
+			obconversion(@inchi,'inchi','can')
+		end
+
+		def sdf
+			obconversion(@inchi,'inchi','sdf')
+		end
+
+		# Matchs a smarts string
+		def match?(smarts)
+			obconversion = OpenBabel::OBConversion.new
+			obmol = OpenBabel::OBMol.new
+			obconversion.set_in_format('inchi')
+			obconversion.read_string(obmol,@inchi) 
+			smarts_pattern = OpenBabel::OBSmartsPattern.new
+			smarts_pattern.init(smarts)
+			smarts_pattern.match(obmol)
+		end
+
+		# Match an array of smarts features, returns matching features
+		def match(smarts_features)
+			smarts_features.all_features.collect{ |smarts| smarts if self.match?(smarts.name) }.compact
+		end
+
+		def smiles2inchi(smiles)
+			obconversion(smiles,'smi','inchi')
+		end
+
+		def smiles2cansmi(smiles)
+			obconversion(smiles,'smi','can')
+		end
+
+		def obconversion(identifier,input_format,output_format)
+			obconversion = OpenBabel::OBConversion.new
+			obmol = OpenBabel::OBMol.new
+			obconversion.set_in_and_out_formats input_format, output_format
+			obconversion.read_string obmol, identifier
+			obconversion.write_string(obmol).gsub(/\s/,'').chomp
+		end
+	end
+end
diff --git a/lib/dataset.rb b/lib/dataset.rb
new file mode 100644
index 0000000..ca82f11
--- /dev/null
+++ b/lib/dataset.rb
@@ -0,0 +1,76 @@
+module OpenTox
+
+	# key: /datasets
+	# set: dataset uris
+	# key: /dataset/:dataset/compounds
+	# set: compound uris
+	# key: /dataset/:dataset/compound/:inchi/:feature_type
+	# set: feature uris
+	class Dataset < OpenTox
+
+		# Initialize with <tt>:uri => uri</tt> or <tt>:name => name</tt> (creates a new dataset)
+		def initialize(uri)
+			super(uri)
+		end
+
+		def self.create(params)
+			uri = RestClient.post File.join(@@config[:services]["opentox-dataset"],"datasets"), :name => params[:name]
+			Dataset.new(uri.to_s)
+		end
+
+		def self.find(params)
+			if params[:name]
+				uri = RestClient.get File.join(@@config[:services]["opentox-dataset"], params[:name])
+			elsif params[:uri]
+				uri = params[:uri]
+			end
+			if RestClient.get uri
+				Dataset.new(uri)
+			else
+				nil
+			end
+		end
+
+		def import(params)
+			if params[:csv]
+				# RestClient seems not to work for file uploads
+				`curl -X POST -F "file=@#{params[:csv]};type=text/csv" -F compound_format=#{params[:compound_format]} -F feature_type=#{params[:feature_type]} #{@uri + '/import'}`
+			end
+		end
+
+		def add_features(features,feature_type)
+			#puts @uri
+			#puts feature_type
+			#puts features.to_yaml
+			HTTPClient.post @uri, {:feature_type => feature_type, :features => features.to_yaml}
+			#`curl -X POST -F feature_type="#{feature_type}" -F features="#{features.to_yaml}" #{@uri}`
+		end
+
+		# Get all compounds from a dataset
+		def compound_uris
+			RestClient.get(File.join(@uri, 'compounds')).split("\n")
+		end
+
+		def compounds
+			compound_uris.collect{|uri| Compound.new(:uri => uri)}
+		end
+
+		# Get all features for a compound
+		def feature_uris(compound,feature_type)
+			#puts File.join(@uri, 'compound', compound.inchi, feature_type)
+			RestClient.get(File.join(@uri, 'compound', compound.inchi, feature_type)).split("\n")
+		end
+
+		# Get all features for a compound
+		def features(compound,feature_type)
+			feature_uris(compound,feature_type).collect{|uri| Feature.new(:uri => uri)}
+		end
+
+		# Delete a dataset
+		def delete
+			RestClient.delete @uri
+		end
+
+	end
+
+end
diff --git a/lib/environment.rb b/lib/environment.rb
index 793fef9..c65e968 100644
--- a/lib/environment.rb
+++ b/lib/environment.rb
@@ -1,14 +1,18 @@
 # load configuration
 
-ENV['RACK_ENV'] = 'development' unless ENV['RACK_ENV']
+ENV['RACK_ENV'] = 'test' unless ENV['RACK_ENV']
+
+basedir = File.join(ENV['HOME'], ".opentox")
+config_dir = File.join(basedir, "config")
+@@tmp_dir = File.join(basedir, "tmp")
+config_file = File.join(config_dir, "#{ENV['RACK_ENV']}.yaml")
 
-config_file = File.join(ENV['HOME'], ".opentox/config/#{ENV['RACK_ENV']}.yaml")
 if File.exist?(config_file)
 	@@config = YAML.load_file(config_file)
 else
-	FileUtils.mkdir_p File.dirname(config_file)
+	FileUtils.mkdir_p config_dir
+	FileUtils.mkdir_p @@tmp_dir
 	FileUtils.cp(File.join(File.dirname(__FILE__), 'templates/config.yaml'), config_file)
 	puts "Please edit #{config_file} and restart your application."
 	exit
 end
-
diff --git a/lib/feature.rb b/lib/feature.rb
new file mode 100644
index 0000000..0cad7c0
--- /dev/null
+++ b/lib/feature.rb
@@ -0,0 +1,45 @@
+module OpenTox
+
+	# uri: /feature/:name/:property_name/:property_value/...
+	class Feature < OpenTox
+
+		attr_accessor :name, :values
+
+		def initialize(params)
+			if params[:uri]
+				@uri = params[:uri]
+				items = URI.split(@uri)[5].split(/\//)
+				@name = items[1]
+				@values = {}
+				i = 3
+				while i < items.size
+					@values[items[i]] = items[i+1]
+					i += 2
+				end
+			else 
+				@name = URI.encode(URI.decode(params[:name]))
+				@values = params[:values]
+				@uri = File.join(@@config[:services]["opentox-dataset"],"feature",path)
+			end
+		end
+
+		def values_path
+			path = '' 
+			@values.each do |k,v|
+				path += '/' + URI.encode(k.to_s) + '/' + URI.encode(v.to_s)
+			end
+			path
+		end
+
+		def path
+			File.join(@name,values_path)
+		end
+
+		def value(property)
+			items = @uri.split(/\//)
+			i = items.index(property)
+			items[i+1]
+		end
+
+	end
+end
diff --git a/lib/model.rb b/lib/model.rb
new file mode 100644
index 0000000..7f43860
--- /dev/null
+++ b/lib/model.rb
@@ -0,0 +1,51 @@
+module OpenTox
+	module Model 
+
+		class Lazar < OpenTox
+
+			# Create a new prediction model from a dataset
+			def initialize(params)
+				super(params[:uri])
+			end
+
+			# Predict a compound
+			def predict(compound)
+				LazarPrediction.new(:uri => RestClient.post(@uri, :compound_uri => compound.uri))
+			end
+
+		end
+
+	end
+
+	module Prediction
+
+		module Classification
+
+			class Lazar < OpenTox
+
+				def initialize(params)
+					super(params[:uri])
+				end
+
+				def classification
+					YAML.load(RestClient.get @uri)[:classification]
+				end
+
+				def confidence
+					YAML.load(RestClient.get @uri)[:confidence]
+				end
+
+				def neighbors
+					RestClient.get @uri + '/neighbors' 
+				end
+
+				def features
+					RestClient.get @uri + '/features' 
+				end
+
+			end
+
+		end
+
+	end
+end
diff --git a/lib/opentox-ruby-api-wrapper.rb b/lib/opentox-ruby-api-wrapper.rb
index d74b412..e504e65 100644
--- a/lib/opentox-ruby-api-wrapper.rb
+++ b/lib/opentox-ruby-api-wrapper.rb
@@ -1,4 +1,5 @@
-['rubygems', 'sinatra', 'sinatra/respond_to', 'sinatra/url_for', 'builder', 'rest_client', 'yaml', 'spork', 'environment'].each do |lib|
+#['rubygems', 'sinatra', 'sinatra/respond_to', 'sinatra/url_for', 'builder', 'rest_client', 'yaml', 'spork', 'environment', 'openbabel', 'httpclient'].each do |lib|
+['rubygems', 'sinatra', 'sinatra/url_for', 'builder', 'rest_client', 'yaml', 'spork', 'environment', 'openbabel', 'httpclient'].each do |lib|
 	require lib
 end
 
@@ -7,10 +8,8 @@ module OpenTox
 	class OpenTox
 		attr_reader :uri
 
-		# Escape all nonword characters
-		def uri_escape(string)
-			#URI.escape(string, /[^\w]/)
-			URI.escape(string, /[^#{URI::PATTERN::UNRESERVED}]/)
+		def initialize(uri)
+			@uri = uri
 		end
 
 		# Get the object name
@@ -23,168 +22,15 @@ module OpenTox
 			RestClient.delete @uri
 		end
 
-	end
-
-	class Compound < OpenTox
-
-		# Initialize with <tt>:uri => uri</tt>, <tt>:smiles => smiles</tt> or <tt>:name => name</tt> (name can be also an InChI/InChiKey, CAS number, etc)
-		def initialize(params)
-			if params[:uri]
-				@uri = params[:uri].to_s
-			elsif params[:smiles]
-				@uri = RestClient.post @@config[:services]["opentox-compound"] ,:smiles => uri_escape(params[:smiles])
-			elsif params[:name]
-				@uri = RestClient.post @@config[:services]["opentox-compound"] ,:name => uri_escape(params[:name])
-			end
-		end
-
-		# Get the (canonical) smiles
-		def smiles
-			RestClient.get @uri
-		end
-
-		# Get the unique id (URI encoded canonical smiles)
-		def uid
-			RestClient.get @uri + '.uid'
-		end
-
-		# Matchs a smarts string
-		def match?(smarts)
-			if RestClient.get(@uri + '/match/' + uri_escape(smarts)) == 'true'
-				true
-			else
-				false
-			end
-		end
-
-		# Match an array of smarts features, returns matching features
-		def match(smarts_features)
-			smarts_features.collect{ |smarts| smarts if self.match?(smarts.name) }.compact
-		end
-
-	end
-
-	class Feature < OpenTox
-
-		# Initialize with <tt>:uri => uri</tt>, or <tt>:name => name, :values => hash_of_property_names_and_values</tt>
-		def initialize(params)
-			if params[:uri]
-				@uri = params[:uri].to_s
-			else
-				@uri = @@config[:services]["opentox-feature"] + uri_escape(params[:name]) 
-				params[:values].each do |k,v|
-					@uri += '/' + k.to_s + '/' + v.to_s
-				end
-			end
-		end
-
-		# Get the value of a property
-		def value(property)
-			RestClient.get @uri + '/' + property
+		# Object path without hostname
+		def path
+			URI.split(@uri)[5]
 		end
 
 	end
 
-	class Dataset < OpenTox
-
-		# Initialize with <tt>:uri => uri</tt> or <tt>:name => name</tt> (creates a new dataset)
-		def initialize(params)
-			if params[:uri]
-				@uri = params[:uri].to_s
-			elsif params[:name] and params[:filename]
-				@uri = `curl -X POST -F file=@#{params[:filename]} -F name="#{params[:name]}" #{@@config[:services]["opentox-dataset"]}`
-			elsif params[:name] 
-				@uri = RestClient.post @@config[:services]["opentox-dataset"], :name => params[:name]
-			end
-		end
-
-		# Get all compounds from a dataset
-		def compounds
-			RestClient.get(@uri + '/compounds').split("\n").collect{ |c| Compound.new(:uri => c) }
-		end
-
-		# Get all compounds and features from a dataset, returns a hash with compound_uris as keys and arrays of feature_uris as values
-		def all_compounds_and_features_uris
-			YAML.load(RestClient.get(@uri + '/compounds/features.yaml'))
-		end
-
-		# Get all features from a dataset
-		def all_features
-			RestClient.get(@uri + '/features').split("\n").collect{|f| Feature.new(:uri => f)}
-		end
-
-		# Get all features for a compound
-		def features(compound)
-			RestClient.get(@uri + '/compound/' + uri_escape(compound.uri) + '/features').split("\n").collect{|f| Feature.new(:uri => f) }
-		end
-
-		# Add a compound and a feature to a dataset
-		def add(compound,feature)
-			RestClient.put @uri, :compound_uri => compound.uri, :feature_uri => feature.uri
-		end
-
-		# Tell the dataset that it is complete
-		def close
-			RestClient.put @uri, :finished => 'true'
-		end
-
-	end
-
-	class Fminer < OpenTox
-
-		# Create a new dataset with BBRC features
-		def initialize(training_dataset)
-			@dataset_uri = RestClient.post @@config[:services]["opentox-fminer"], :dataset_uri => training_dataset.uri
-		end
-
-		def dataset
-			Dataset.new(:uri => @dataset_uri)
-		end
-
-	end
-
-	class Lazar < OpenTox
-
-		# Create a new prediction model from a dataset
-		def initialize(params)
-			if params[:uri]
-				@uri = params[:uri]
-			elsif params[:dataset_uri]
-				@uri = RestClient.post @@config[:services]["opentox-lazar"] + 'models' , :dataset_uri => params[:dataset_uri]
-			end
-		end
-
-		# Predict a compound
-		def predict(compound)
-			LazarPrediction.new(:uri => RestClient.post(@uri, :compound_uri => compound.uri))
-		end
-
-	end
-
-	class LazarPrediction < OpenTox
-
-		def initialize(params)
-			if params[:uri]
-				@uri = params[:uri]
-			end
-		end
-
-		def classification
-			YAML.load(RestClient.get @uri)[:classification]
-		end
-
-		def confidence
-			YAML.load(RestClient.get @uri)[:confidence]
-		end
-
-		def neighbors
-			RestClient.get @uri + '/neighbors' 
-		end
-
-		def features
-			RestClient.get @uri + '/features' 
-		end
-
-	end
+end
 
+['compound','feature','dataset','algorithm','model','utils'].each do |lib|
+	require lib
 end
diff --git a/lib/tasks/opentox.rb b/lib/tasks/opentox.rb
index 6f1284f..afb8cb6 100644
--- a/lib/tasks/opentox.rb
+++ b/lib/tasks/opentox.rb
@@ -1,4 +1,4 @@
-require "environment"
+load File.join(File.dirname(__FILE__), '..', 'environment.rb')
 
 namespace :opentox do
 
@@ -18,18 +18,22 @@ namespace :opentox do
 		task :start do
 			@@config[:services].each do |service,uri|
 				dir = File.join(@@config[:base_dir], service)
-				case @@config[:webserver]
-				when 'thin'
+				server = @@config[:webserver]
+				`redis-server &`
+				case server
+				when /thin|mongrel|webrick/
 					port = uri.sub(/^.*:/,'').sub(/\/$/,'')
 					Dir.chdir dir
+					pid_file = File.join(@@tmp_dir,"#{service}.pid") 
 					begin
-						`thin --trace --rackup config.ru start -p #{port} -e #{ENV['RACK_ENV']} &`
-						puts "#{service} started on port #{port}."
+						`#{server} --trace --rackup config.ru start -p #{port} -e #{ENV['RACK_ENV']} -P #{pid_file} -d &`
+						puts "#{service} started on localhost:#{port} in #{ENV['RACK_ENV']} environment with PID file #{pid_file}."
 					rescue
 						puts "Cannot start #{service} on port #{port}."
 					end
 				when 'passenger'
-					puts "not yet implemented"
+					`touch #{File.join(dir, 'tmp/restart.txt')}`
+					puts "#{service} restarted."
 				else
 					puts "not yet implemented"
 				end
@@ -38,9 +42,18 @@ namespace :opentox do
 
 		desc "Stop opentox services"
 		task :stop do
-			@@config[:services].each do |service,uri|
-				port = uri.sub(/^.*:/,'').sub(/\/$/,'')
-				`echo "SHUTDOWN" | nc localhost #{port}` if port
+			server = @@config[:webserver]
+			if server =~ /thin|mongrel|webrick/
+				@@config[:services].each do |service,uri|
+					port = uri.sub(/^.*:/,'').sub(/\/$/,'')
+					pid_file = File.join(@@tmp_dir,"#{service}.pid") 
+					begin
+						puts `#{server} stop -P #{pid_file}` 
+						puts "#{service} stopped on localhost:#{port}"
+					rescue
+						puts "Cannot stop #{service} on port #{port}."
+					end
+				end
 			end
 		end
 
@@ -49,20 +62,55 @@ namespace :opentox do
 
 	end
 
-	namespace :test do
+	desc "Run all OpenTox tests"
+	task :test do
+		@@config[:services].each do |service,uri|
+			dir = File.join(@@config[:base_dir], service)
+			Dir.chdir dir
+			puts "Running tests in #{dir}"
+			`rake test -t 1>&2`
+		end
+	end
 
-		ENV['RACK_ENV'] = 'test'
-		test = "#{Dir.pwd}/test/test.rb"
+end
 
-		desc "Run local tests"
-		task :local => "opentox:services:restart" do
-			load test
+desc "Start service in current directory"
+task :start do
+	service = File.basename(Dir.pwd).intern
+	server = @@config[:webserver]
+	case server 
+		when /thin|mongrel|webrick/
+			port = @@config[:services][service].sub(/^.*:/,'').sub(/\/$/,'')
+			pid_file = File.join(@@tmp_dir,"#{service}.pid") 
+			begin
+				`#{server} --trace --rackup config.ru start -p #{port} -e #{ENV['RACK_ENV']} -P #{pid_file} -d &`
+				puts "#{service} started on localhost:#{port} in #{ENV['RACK_ENV']} environment with PID file #{pid_file}."
+			rescue
+				puts "Cannot start #{service} on port #{port}."
+			end
+		when 'passenger'
+			`touch tmp/restart.txt`
+			puts "#{service} restarted."
+		else
+			puts "not yet implemented"
 		end
+end
 
-		task :remote do
-			#load 'test.rb'
+desc "Stop service in current directory"
+task :stop do
+	service = File.basename(Dir.pwd).intern
+	server = @@config[:webserver]
+	if server =~ /thin|mongrel|webrick/
+		port = @@config[:services][service].sub(/^.*:/,'').sub(/\/$/,'')
+		pid_file = File.join(@@tmp_dir,"#{service}.pid") 
+		begin
+			puts `thin stop -P #{pid_file}` 
+			puts "#{service} stopped on localhost:#{port}"
+		rescue
+			puts "Cannot stop #{service} on port #{port}."
 		end
-
 	end
-
 end
+
+desc "Restart service in current directory"
+task :restart  => [:stop, :start]
diff --git a/lib/templates/config.ru b/lib/templates/config.ru
new file mode 100644
index 0000000..63dd2ce
--- /dev/null
+++ b/lib/templates/config.ru
@@ -0,0 +1,23 @@
+require 'rubygems'
+require 'sinatra'
+require 'application.rb'
+require 'rack'
+require 'rack/contrib'
+
+FileUtils.mkdir_p 'log' unless File.exists?('log')
+log = File.new("log/#{ENV["RACK_ENV"]}.log", "a")
+$stdout.reopen(log)
+$stderr.reopen(log)
+ 
+if ENV['RACK_ENV'] == 'production'
+	use Rack::MailExceptions do |mail|
+		mail.to 'helma@in-silico.ch'
+		mail.subject '[ERROR] %s'
+	end 
+elsif ENV['RACK_ENV'] == 'development'
+  use Rack::Reloader 
+  use Rack::ShowExceptions
+end
+
+run Sinatra::Application
+
diff --git a/lib/templates/config.yaml b/lib/templates/config.yaml
index 768fa01..14326fe 100644
--- a/lib/templates/config.yaml
+++ b/lib/templates/config.yaml
@@ -1,8 +1,10 @@
 :base_dir: /home/ch/webservices
 :webserver: thin
 :services:
-  - opentox-feature
-  - opentox-compound
-  - opentox-dataset
-  - opentox-fminer
-  - opentox-lazar
+# 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/"
diff --git a/lib/utils.rb b/lib/utils.rb
new file mode 100644
index 0000000..2716f45
--- /dev/null
+++ b/lib/utils.rb
@@ -0,0 +1,11 @@
+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