opentox-ruby-api-wrapper 1.1.0

data/lib/opentox-ruby-api-wrapper.rb

@@ -0,0 +1,13 @@
+['rubygems', 'sinatra', 'sinatra/url_for',  'redis','builder', 'rest_client', 'yaml', 'cgi', 'spork', 'environment'].each do |lib|
+	require lib
+end
+
+begin
+	require 'openbabel'
+rescue LoadError
+	puts "Please install Openbabel with 'rake openbabel:install' in the compound component"
+end
+
+['opentox', 'compound','feature','dataset','algorithm','model','task','utils'].each do |lib|
+	require lib
+end

data/lib/opentox.rb

@@ -0,0 +1,27 @@
+module OpenTox
+
+	class OpenTox
+		attr_accessor :uri
+
+		def initialize(uri)
+			@uri = uri
+		end
+
+		# Get the object name
+		def name
+			RestClient.get @uri + '/name'
+		end
+
+		# Deletes an object
+		def destroy
+			RestClient.delete @uri
+		end
+
+		# Object path without hostname
+		def path
+			URI.split(@uri)[5]
+		end
+
+	end
+
+end

data/lib/spork.rb

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+# A way to cleanly handle process forking in Sinatra when using Passenger, aka "sporking some code".
+# This will allow you to properly execute some code asynchronously, which otherwise does not work correctly.
+#
+# Written by Ron Evans
+# More info at http://deadprogrammersociety.com
+#
+# Mostly lifted from the Spawn plugin for Rails (http://github.com/tra/spawn)
+# but with all of the Rails stuff removed.... cause you are using Sinatra. If you are using Rails, Spawn is
+# what you need. If you are using something else besides Sinatra that is Rack-based under Passenger, and you are having trouble with
+# asynch processing, let me know if spork helped you.
+# 
+module Spork
+  # things to close in child process
+  @@resources = []
+  def self.resources
+    @@resources
+  end
+  
+  # set the resource to disconnect from in the child process (when forking)
+  def self.resource_to_close(resource)
+    @@resources << resource
+  end
+
+  # close all the resources added by calls to resource_to_close
+  def self.close_resources
+    @@resources.each do |resource|
+      resource.close if resource && resource.respond_to?(:close) && !resource.closed?
+    end
+    @@resources = []
+  end
+
+  # actually perform the fork... er, spork
+  # valid options are:
+  # :priority => to set the process priority of the child
+  # :logger => a logger object to use from the child
+  # :no_detach => true if you want to keep the child process under the parent control. usually you do NOT want this
+  def self.spork(options={})
+    logger = options[:logger]
+    logger.debug "spork> parent PID = #{Process.pid}" if logger
+    child = fork do
+      begin
+        start = Time.now
+        logger.debug "spork> child PID = #{Process.pid}" if logger
+
+        # set the nice priority if needed
+        Process.setpriority(Process::PRIO_PROCESS, 0, options[:priority]) if options[:priority]
+
+        # disconnect from the rack
+        Spork.close_resources
+
+        # run the block of code that takes so long
+        yield
+
+      rescue => ex
+        logger.error "spork> Exception in child[#{Process.pid}] - #{ex.class}: #{ex.message}" if logger
+      ensure
+        logger.info "spork> child[#{Process.pid}] took #{Time.now - start} sec" if logger
+        # this form of exit doesn't call at_exit handlers
+        exit!(0)
+      end
+    end
+
+    # detach from child process (parent may still wait for detached process if they wish)
+    Process.detach(child) unless options[:no_detach]
+
+    return child
+  end
+  
+end
+
+# Patch to work with passenger
+if defined? Passenger::Rack::RequestHandler
+  class Passenger::Rack::RequestHandler
+    alias_method :orig_process_request, :process_request
+    def process_request(env, input, output)
+      Spork.resource_to_close(input)
+      Spork.resource_to_close(output)
+      orig_process_request(env, input, output)
+    end
+  end
+end

data/lib/task.rb

@@ -0,0 +1,55 @@
+module OpenTox
+
+	class Task < OpenTox
+		#private :new
+
+		def initialize(uri)
+			super(uri)
+		end
+
+		def self.create(params)
+			uri = RestClient.post @@config[:services]["opentox-task"], :resource_uri => params[:resource_uri]
+			Task.new uri
+		end
+
+		def self.find(params)
+			Task.new(params[:uri])
+		end
+
+		def self.base_uri
+			@@config[:services]["opentox-task"]
+		end
+
+		def start
+			RestClient.put @uri, :status => 'started'
+		end
+
+		def stop
+			RestClient.put @uri, :status => 'stopped'
+		end
+
+		def completed
+			RestClient.put @uri, :status => 'completed'
+		end
+		 
+		def status
+			RestClient.get File.join(@uri, 'status')
+		end
+
+		def completed?
+			self.status == 'completed'
+		end
+
+		def resource
+			RestClient.get @uri
+		end
+
+		def wait_for_completion
+			until self.completed?
+				sleep 1
+			end
+		end
+
+	end
+
+end

data/lib/tasks/opentox.rb

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+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.flush_db
+	end
+
+	desc "Flush all Redis databases"
+	task :flushall do
+		require 'redis'
+		r = Redis.new
+		r.flush_all
+	end
+
+
+end
+
+namespace :opentox do
+
+	desc "Install required gems"
+	task :install do
+		puts `sudo gem install #{@gems}`
+	end
+
+	desc "Update gems"
+	task :update do
+		puts `sudo gem update #{@gems}`
+	end
+
+	namespace :services do
+
+		desc "Run opentox services"
+		task :start do
+			@@config[:services].each do |service,uri|
+				dir = File.join(@@config[:base_dir], service)
+				server = @@config[:webserver]
+				case server
+				when /thin|mongrel|webrick/
+					port = uri.sub(/^.*:/,'').sub(/\/$/,'')
+					Dir.chdir dir
+					pid_file = File.join(@@tmp_dir,"#{service}.pid") 
+					begin
+						`#{server} --trace --rackup config.ru start -p #{port} -e #{ENV['RACK_ENV']} -P #{pid_file} -d &`
+						puts "#{service} started on localhost:#{port} in #{ENV['RACK_ENV']} environment with PID file #{pid_file}."
+					rescue
+						puts "Cannot start #{service} on port #{port}."
+					end
+				when 'passenger'
+					`touch #{File.join(dir, 'tmp/restart.txt')}`
+					puts "#{service} restarted."
+				else
+					puts "not yet implemented"
+				end
+			end
+		end
+
+		desc "Stop opentox services"
+		task :stop do
+			server = @@config[:webserver]
+			if server =~ /thin|mongrel|webrick/
+				@@config[:services].each do |service,uri|
+					port = uri.sub(/^.*:/,'').sub(/\/$/,'')
+					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
+
+		desc "Restart opentox services"
+		task :restart => [:stop, :start]
+
+	end
+
+	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
+
+end
+
+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(/\/$/,'')
+			pid_file = File.join(@@tmp_dir,"#{service}.pid") 
+			begin
+				`#{server} --trace --rackup config.ru start -p #{port} -e #{ENV['RACK_ENV']} -P #{pid_file} -d &`
+				puts "#{service} started on localhost:#{port} in #{ENV['RACK_ENV']} environment with PID file #{pid_file}."
+			rescue
+				puts "Cannot start #{service} on port #{port}."
+			end
+		when 'passenger'
+			`touch tmp/restart.txt`
+			puts "#{service} restarted."
+		else
+			puts "not yet implemented"
+		end
+end
+
+desc "Stop service in current directory"
+task :stop do
+	service = File.basename(Dir.pwd).intern
+	server = @@config[:webserver]
+	if server =~ /thin|mongrel|webrick/
+		port = @@config[:services][service].sub(/^.*:/,'').sub(/\/$/,'')
+		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]

data/lib/tasks/redis.rb

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+# 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

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+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
+