opentox-ruby-api-wrapper 1.2.5 → 1.2.6

data/Rakefile

@@ -10,7 +10,7 @@ begin
     gem.email = "helma@in-silico.ch"
     gem.homepage = "http://github.com/helma/opentox-ruby-api-wrapper"
     gem.authors = ["Christoph Helma"]
-		["sinatra", "rest-client", "rack", "rack-contrib", "thin", "emk-sinatra-url-for", "cehoffman-sinatra-respond_to", "dm-more", "dm-core"].each do |dep|
+		["sinatra", "rest-client", "rack", "rack-contrib", "rack-flash", "thin", "emk-sinatra-url-for", "cehoffman-sinatra-respond_to", "dm-more", "dm-core", "sinatra-static-assets"].each do |dep|
 			gem.add_dependency dep
 		end
 		gem.add_development_dependency "cucumber"

data/VERSION

@@ -1 +1 @@
-1.2.5
+1.2.6

data/lib/compound.rb

@@ -20,13 +20,21 @@ module OpenTox
 				@inchi = RestClient.get("#{@@cactus_uri}#{params[:name]}/stdinchi").chomp
 				@uri = File.join(@@config[:services]["opentox-compound"],URI.escape(@inchi))
 			elsif params[:uri]
-				@inchi = params[:uri].sub(/^.*InChI/, 'InChI')
 				@uri = params[:uri]
+				if params[:uri].match(/InChI/) # shortcut for IST services
+					@inchi = params[:uri].sub(/^.*InChI/, 'InChI')
+				else
+					@inchi = RestClient.get @uri, :accept => 'chemical/x-inchi'
+					# AMBIT does not provide InChIs
+					#smiles = RestClient.get(@uri, :accept => 'chemical/x-daylight-smiles').split(/\s+/).first # fix ambit output
+					#@inchi = obconversion(smiles,'smi','inchi')
+				end
 			end
 		end
 
 		# Get the (canonical) smiles
 		def smiles
+			#RestClient.get(@uri, :accept => 'chemical/x-daylight-smiles').split(/\s+/).first # fix ambit output
 			obconversion(@inchi,'inchi','can')
 		end
 

data/lib/dataset.rb

@@ -85,14 +85,11 @@ module OpenTox
 		end
 
 		def self.find(uri)
-			begin
-        dataset = Dataset.new
-        data = RestClient.get uri, :accept => 'application/rdf+xml' # check if the resource is available
-        dataset.rdf = data
-				dataset
-			rescue
-				nil
-			end
+			dataset = Dataset.new
+			data = `curl "#{uri}"`
+			#data = RestClient.get uri, :accept => 'application/rdf+xml' # unclear why this does not work for complex uris, Dataset.find works from irb
+			dataset.rdf = data
+			dataset
 		end
 
 		def features
@@ -107,57 +104,44 @@ module OpenTox
 			data = {}
 			@model.subjects(RDF['type'], OT['DataEntry']).each do |data_entry|
 				compound_node  = @model.object(data_entry, OT['compound'])
-				@model.find(compound_node, OT['identifier'],nil) {|s,p,o| puts o.to_s}
 				compound_uri = @model.object(compound_node, DC['identifier']).to_s
-				data[compound_uri] = [] unless data[compound_uri]
 				@model.find(data_entry, OT['values'], nil) do |s,p,values|
-					entry = {}
 					feature_node = @model.object values, OT['feature']
-					feature_uri = @model.object(feature_node, DC['identifier']).to_s
-					# TODO simple features
+					feature_uri = @model.object(feature_node, DC['identifier']).to_s.sub(/\^\^.*$/,'') # remove XML datatype
 					type = @model.object(values, RDF['type'])
 					if type == OT['FeatureValue']
-						#entry[feature_uri] = [] unless entry[feature_uri]
-						entry[feature_uri] = @model.object(values, OT['value']).to_s
+						value = @model.object(values, OT['value']).to_s
+						case value.to_s
+						when TRUE_REGEXP # defined in environment.rb
+							value = true
+						when FALSE_REGEXP # defined in environment.rb
+							value = false
+						else
+							LOGGER.warn compound_uri + " has value '" + value.to_s + "' for feature " + feature_uri
+							value = nil
+						end
+						data[compound_uri] = {} unless data[compound_uri]
+						data[compound_uri][feature_uri] = [] unless data[compound_uri][feature_uri]
+						data[compound_uri][feature_uri] << value unless value.nil?
 					elsif type == OT['Tuple']
-						entry[feature_uri] = {} unless entry[feature_uri]
+						entry = {}
+						data[compound_uri] = {} unless data[compound_uri]
+						data[compound_uri][feature_uri] = [] unless data[compound_uri][feature_uri]
 						@model.find(values, OT['complexValue'],nil) do |s,p,complex_value|
 							name_node = @model.object complex_value, OT['feature']
 							name = @model.object(name_node, DC['title']).to_s
 							value = @model.object(complex_value, OT['value']).to_s
-							entry[feature_uri][name] = value
+							v = value.sub(/\^\^.*$/,'') # remove XML datatype
+							v = v.to_f if v.match(/^[\.|\d]+$/) # guess numeric datatype
+							entry[name] = v
 						end
+						data[compound_uri][feature_uri] << entry
 					end
-					data[compound_uri] << entry
 				end
 			end
 			data
 		end
 
-		def feature_values(feature_uri)
-			features = {}
-			feature = @model.subject(DC["identifier"],feature_uri)
-			@model.subjects(RDF['type'], OT["Compound"]).each do |compound_node|
-				compound = @model.object(compound_node,  DC["identifier"]).to_s.sub(/^\[(.*)\]$/,'\1')
-				features[compound] = [] unless features[compound]
-				data_entry = @model.subject(OT['compound'], compound_node)
-				@model.find( data_entry, OT['values'], nil ) do |s,p,values|
-					if feature == @model.object(values, OT['feature'])
-						value = @model.object(values, OT['value'])
-						case value.to_s
-						when "true"
-							features[compound] << true
-						when "false"
-							features[compound] << false
-						else
-							features[compound] << value.to_s
-						end
-					end
-				end
-			end
-			features
-		end
-
 		def compounds
 			compounds = []
 			@model.subjects(RDF['type'], OT["Compound"]).each do |compound_node|
@@ -183,7 +167,8 @@ module OpenTox
 				:source => self.source,
 				:identifier => self.identifier,
 				:compounds => self.compounds.collect{|c| c.to_s.to_s.sub(/^\[(.*)\]$/,'\1')},
-				:features => self.features.collect{|f| f.to_s }
+				:features => self.features.collect{|f| f.to_s },
+				:data => self.data
 			}.to_yaml
 		end
 

data/lib/environment.rb

@@ -1,21 +1,27 @@
+require 'logger'
 # 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")
 config_file = File.join(config_dir, "#{ENV['RACK_ENV']}.yaml")
 
+TMP_DIR = File.join(basedir, "tmp")
+LOG_DIR = File.join(basedir, "log")
+
 if File.exist?(config_file)
 	@@config = YAML.load_file(config_file)
 else
-	FileUtils.mkdir_p config_dir
-	FileUtils.mkdir_p @@tmp_dir
+	FileUtils.mkdir_p TMP_DIR
+	FileUtils.mkdir_p LOG_DIR
 	FileUtils.cp(File.join(File.dirname(__FILE__), 'templates/config.yaml'), config_file)
 	puts "Please edit #{config_file} and restart your application."
 	exit
 end
+logfile = "#{LOG_DIR}/#{ENV["RACK_ENV"]}.log"
+LOGGER = Logger.new(logfile,'daily') # daily rotation
+LOGGER.level = Logger::DEBUG
 
 # RDF namespaces
 RDF = Redland::Namespace.new 'http://www.w3.org/1999/02/22-rdf-syntax-ns#'
@@ -23,19 +29,6 @@ OWL = Redland::Namespace.new 'http://www.w3.org/2002/07/owl#'
 DC = Redland::Namespace.new 'http://purl.org/dc/elements/1.1/'
 OT = Redland::Namespace.new 'http://www.opentox.org/api/1.1#'
 
-# configure redis database
-=begin
-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
-=end
+# Regular expressions for parsing classification data
+TRUE_REGEXP = /^(true|active|1)/
+FALSE_REGEXP = /^(false|inactive|0)/

data/lib/model.rb

@@ -31,6 +31,11 @@ module OpenTox
 			def self.find_all
 				RestClient.get(@@config[:services]["opentox-model"]).split("\n")
 			end
+
+			def self.find(uri)
+				yaml = RestClient.get(uri, :accept => "application/x-yaml")
+				OpenTox::Model::Lazar.from_yaml(yaml)
+			end
 			
 			# Predict a compound
 			def predict(compound)
@@ -46,7 +51,7 @@ module OpenTox
 			end
 
 			def endpoint
-				YAML.load(RestClient.get uri)[:endpoint]
+				YAML.load(RestClient.get(uri))[:endpoint]
 			end
 
 			def algorithm=(algorithm)

data/lib/owl.rb

@@ -42,7 +42,8 @@ module OpenTox
 			# I have no idea, why 2 subjects are returned
 			# iterating over all subjects leads to memory allocation problems
 			# SPARQL queries also do not work 
-			me = @model.subjects(RDF['type'],OT[self.owl_class])[1]
+			#me = @model.subjects(RDF['type'],OT[self.owl_class])[1]
+			me = @model.subject(RDF['type'],OT[self.owl_class])
 			@model.object(me, DC['title']).to_s
 		end
 

data/lib/task.rb

@@ -22,6 +22,11 @@ module OpenTox
 			@@config[:services]["opentox-task"]
 		end
 
+		def self.all
+			task_uris = RestClient.get(@@config[:services]["opentox-task"]).split(/\n/)
+			task_uris.collect{|uri| Task.new(uri)}
+		end
+
 		def started
 			#LOGGER.info File.join(@uri,'started')
 			RestClient.put File.join(@uri,'started'), {}
@@ -35,6 +40,14 @@ module OpenTox
 			RestClient.put File.join(@uri,'completed'), :resource => uri
 		end
 		 
+		def created_at
+			RestClient.get File.join(@uri, 'created_at')
+		end
+		 
+		def finished_at
+			RestClient.get File.join(@uri, 'finished_at')
+		end
+		 
 		def status
 			RestClient.get File.join(@uri, 'status')
 		end
@@ -42,6 +55,10 @@ module OpenTox
 		def resource
 			RestClient.get File.join(@uri, 'resource')
 		end
+		 
+		def pid=(pid)
+			RestClient.put File.join(@uri, 'pid'), :pid => pid
+		end
 
 		def completed?
 			self.status.to_s == 'completed'
@@ -49,7 +66,7 @@ module OpenTox
 
 		def wait_for_completion
 			until self.completed?
-				sleep 0.1
+				sleep 1
 			end
 		end
 

data/lib/tasks/config.rb

@@ -0,0 +1,19 @@
+require 'rubygems'
+require 'rack'
+require 'rack/contrib'
+require 'application.rb'
+
+# log at centralized place
+logfile = "#{LOG_DIR}/#{ENV["RACK_ENV"]}.log"
+log = File.new(logfile, "a+")
+$stdout.reopen(log)
+$stderr.reopen(log)
+$stdout.sync = true
+$stderr.sync = true
+set :raise_errors, true 
+
+['public','tmp'].each do |dir|
+	FileUtils.mkdir_p dir unless File.exists?(dir)
+end
+ 
+use Rack::ShowExceptions

data/lib/tasks/opentox.rb

@@ -13,7 +13,7 @@ namespace :opentox do
 				when /thin|mongrel|webrick/
 					port = uri.sub(/^.*:/,'').sub(/\/$/,'')
 					Dir.chdir dir
-					pid_file = File.join(@@tmp_dir,"#{service}.pid") 
+					pid_file = File.join(TMP_DIR,"#{service}.pid") 
 					begin
 						`#{server} --trace --rackup config.ru start -p #{port} -e #{ENV['RACK_ENV']} -P #{pid_file} -d &`
 						puts "#{service} started on localhost:#{port} in #{ENV['RACK_ENV']} environment with PID file #{pid_file}."
@@ -36,7 +36,7 @@ namespace :opentox do
 			if server =~ /thin|mongrel|webrick/
 				@@config[:services].each do |service,uri|
 					port = uri.sub(/^.*:/,'').sub(/\/$/,'')
-					pid_file = File.join(@@tmp_dir,"#{service}.pid") 
+					pid_file = File.join(TMP_DIR,"#{service}.pid") 
 					begin
 						puts `#{server} stop -P #{pid_file}` 
 						puts "#{service} stopped on localhost:#{port}"
@@ -71,7 +71,7 @@ task :start do
 	case server 
 		when /thin|mongrel|webrick/
 			port = @@config[:services][service].sub(/^.*:/,'').sub(/\/$/,'')
-			pid_file = File.join(@@tmp_dir,"#{service}.pid") 
+			pid_file = File.join(TMP_DIR,"#{service}.pid") 
 			begin
 				`#{server} --trace --rackup config.ru start -p #{port} -e #{ENV['RACK_ENV']} -P #{pid_file} -d &`
 				puts "#{service} started on localhost:#{port} in #{ENV['RACK_ENV']} environment with PID file #{pid_file}."
@@ -93,7 +93,7 @@ task :stop do
 	server = @@config[:webserver]
 	if server =~ /thin|mongrel|webrick/
 		port = @@config[:services][service].sub(/^.*:/,'').sub(/\/$/,'')
-		pid_file = File.join(@@tmp_dir,"#{service}.pid") 
+		pid_file = File.join(TMP_DIR,"#{service}.pid") 
 		begin
 			puts `thin stop -P #{pid_file}` 
 			puts "#{service} stopped on localhost:#{port}"

data/lib/templates/config.yaml

@@ -1,10 +1,20 @@
-:base_dir: /home/ch/webservices
-:webserver: thin
-:services:
-# 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/"
+# Example configuration for OpenTox, please adjust to your settings
+# 
+# Example 1: Using external test services
+#
+# :services:
+#  opentox-compound:      "http://webservices.in-silico.ch/test/compound/"
+#  opentox-dataset:       "http://webservices.in-silico.ch/test/dataset/"
+#  opentox-algorithm:     "http://webservices.in-silico.ch/test/algorithm/"
+#  opentox-model:         "http://webservices.in-silico.ch/test/model/"
+#  opentox-task:         "http://webservices.in-silico.ch/test/task/"
+#
+# Example 2: Using local services
+# :base_dir: /home/ch/webservices
+# :webserver: thin
+# :services:
+#   opentox-compound:      "http://localhost:4000/"
+#   opentox-dataset:       "http://localhost:4001/"
+#   opentox-algorithm:     "http://localhost:4002/"
+#   opentox-model:         "http://localhost:4003/"
+#   opentox-task:          "http://localhost:4004/"

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification 
 name: opentox-ruby-api-wrapper
 version: !ruby/object:Gem::Version 
-  version: 1.2.5
+  version: 1.2.6
 platform: ruby
 authors: 
 - Christoph Helma
@@ -9,7 +9,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2010-01-11 00:00:00 +01:00
+date: 2010-01-31 00:00:00 +01:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -52,6 +52,16 @@ dependencies:
       - !ruby/object:Gem::Version 
         version: "0"
     version: 
+- !ruby/object:Gem::Dependency 
+  name: rack-flash
+  type: :runtime
+  version_requirement: 
+  version_requirements: !ruby/object:Gem::Requirement 
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: "0"
+    version: 
 - !ruby/object:Gem::Dependency 
   name: thin
   type: :runtime
@@ -102,6 +112,16 @@ dependencies:
       - !ruby/object:Gem::Version 
         version: "0"
     version: 
+- !ruby/object:Gem::Dependency 
+  name: sinatra-static-assets
+  type: :runtime
+  version_requirement: 
+  version_requirements: !ruby/object:Gem::Requirement 
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: "0"
+    version: 
 - !ruby/object:Gem::Dependency 
   name: cucumber
   type: :development
@@ -140,9 +160,8 @@ files:
 - lib/owl.rb
 - lib/spork.rb
 - lib/task.rb
+- lib/tasks/config.rb
 - lib/tasks/opentox.rb
-- lib/tasks/redis.rb
-- lib/templates/config.ru
 - lib/templates/config.yaml
 - lib/utils.rb
 has_rdoc: true

data/lib/tasks/redis.rb

@@ -1,125 +0,0 @@
-# Inspired by rabbitmq.rake the Redbox project at http://github.com/rick/redbox/tree/master
-require 'fileutils'
-require 'open-uri'
-
-class RedisRunner
-  
-  def self.redisdir
-    "/tmp/redis/"
-  end
-  
-  def self.redisconfdir
-    '/etc/redis.conf'
-  end
-
-  def self.dtach_socket
-    '/tmp/redis.dtach'
-  end
-
-  # Just check for existance of dtach socket
-  def self.running?
-    File.exists? dtach_socket
-  end
-  
-  def self.start
-    puts 'Detach with Ctrl+\  Re-attach with rake redis:attach'
-    sleep 3
-    exec "dtach -A #{dtach_socket} redis-server #{redisconfdir}"
-  end
-  
-  def self.attach
-    exec "dtach -a #{dtach_socket}"
-  end
-  
-  def self.stop
-    sh 'echo "SHUTDOWN" | nc localhost 6379'
-  end
-
-end
-
-namespace :redis do
-  
-  desc 'About redis'
-  task :about do
-    puts "\nSee http://code.google.com/p/redis/ for information about redis.\n\n"
-  end
-  
-  desc 'Start redis'
-  task :start do
-    RedisRunner.start
-  end
-  
-  desc 'Stop redis'
-  task :stop do
-    RedisRunner.stop
-  end
-  
-  desc 'Restart redis'
-  task :restart do
-    RedisRunner.stop
-    RedisRunner.start
-  end
-
-  desc 'Attach to redis dtach socket'
-  task :attach do
-    RedisRunner.attach
-  end
-  
-  desc 'Install the lastest verison of Redis from Github (requires git, duh)'
-  task :install => [:about, :download, :make] do
-    %w(redis-benchmark redis-cli redis-server).each do |bin|
-      sh "sudo cp /tmp/redis/#{bin} /usr/bin/"
-    end
-
-    puts "Installed redis-benchmark, redis-cli and redis-server to /usr/bin/"
-        
-    unless File.exists?('/etc/redis.conf')
-      sh 'sudo cp /tmp/redis/redis.conf /etc/'
-      puts "Installed redis.conf to /etc/ \n You should look at this file!"
-    end  
-  end
-  
-  task :make do
-    sh "cd #{RedisRunner.redisdir} && make clean"
-    sh "cd #{RedisRunner.redisdir} && make"
-  end
-  
-  desc "Download package"
-  task :download do
-    sh 'rm -rf /tmp/redis/' if File.exists?("#{RedisRunner.redisdir}/.svn")
-    sh 'git clone git://github.com/antirez/redis.git /tmp/redis' unless File.exists?(RedisRunner.redisdir)
-    sh "cd #{RedisRunner.redisdir} && git pull" if File.exists?("#{RedisRunner.redisdir}/.git")
-  end    
-
-end
-
-namespace :dtach do
-  
-  desc 'About dtach'
-  task :about do
-    puts "\nSee http://dtach.sourceforge.net/ for information about dtach.\n\n"
-  end
-  
-  desc 'Install dtach 0.8 from source'
-  task :install => [:about] do
-    
-    Dir.chdir('/tmp/')
-    unless File.exists?('/tmp/dtach-0.8.tar.gz')
-      require 'net/http'
-      
-      url = 'http://downloads.sourceforge.net/project/dtach/dtach/0.8/dtach-0.8.tar.gz'
-      open('/tmp/dtach-0.8.tar.gz', 'wb') do |file| file.write(open(url).read) end
-    end
-
-    unless File.directory?('/tmp/dtach-0.8')    
-      system('tar xzf dtach-0.8.tar.gz')
-    end
-    
-    Dir.chdir('/tmp/dtach-0.8/')
-    sh 'cd /tmp/dtach-0.8/ && ./configure && make'    
-    sh 'sudo cp /tmp/dtach-0.8/dtach /usr/bin/'
-    
-    puts 'Dtach successfully installed to /usr/bin.'
-  end
-end
-  

data/lib/templates/config.ru

@@ -1,23 +0,0 @@
-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
-