Module: R

Defined in:
lib/rbbt/util/R.rb,
lib/rbbt/util/R/eval.rb,
lib/rbbt/util/R/plot.rb,
lib/rbbt/util/R/model.rb

Defined Under Namespace

Modules: GIF, PNG, SVG Classes: Model

Constant Summary collapse

LIB_DIR = 
Path.setup(File.join(File.expand_path(File.dirname(__FILE__)),'../../../share/Rlib'))
UTIL = 
File.join(LIB_DIR, 'util.R')
PLOT = 
File.join(LIB_DIR, 'plot.R')
SESSION = 
ENV["RServeSession"] || "Session-PID-" + Process.pid.to_s

Class Attribute Summary collapse

Class Method Summary collapse

Class Attribute Details

.model_dir ⇒ Object

Returns the value of attribute model_dir.



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# File 'lib/rbbt/util/R/model.rb', line 5

def model_dir
  @model_dir
end

Class Method Details

._eval(cmd) ⇒ Object 



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# File 'lib/rbbt/util/R/eval.rb', line 122

def self._eval(cmd)
  RbbtSemaphore.synchronize(semfile) do 
    times = 1
    begin
      instance.eval(cmd)
    rescue Rserve::Connection::EvalError
      times = times - 1
      if times > 0
        clear
        retry 
      else
        raise $!
      end
    end
  end
end

.clear ⇒ Object 



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# File 'lib/rbbt/util/R/eval.rb', line 43

def self.clear
  @@instance = nil
  if defined? @@instance_process and @@instance_process and Misc.pid_exists? @@instance_process
    Log.warn "Clearing Rserver session #{SESSION}, PID #{@@instance_process}"
    begin
      Process.kill :INT, @@instance_process
    rescue Exception
      Log.warn "Error killing Rserve (#{@@instance_process}): #{$!.message}"
    end
  end
  FileUtils.rm_rf pid_file if File.exist? pid_file
  FileUtils.rm_rf socket_file if File.exist? socket_file
  FileUtils.rm_rf lockfile if File.exist? lockfile
  FileUtils.rm_rf workdir if File.exist? workdir
end

.console(script, options = {}) ⇒ Object 



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# File 'lib/rbbt/util/R.rb', line 94

def self.console(script, options = {})
  TmpFile.with_file do |init_file|
     Open.write(init_file) do |f|
        f.puts "# Loading basic rbbt environment"
        f.puts "library(utils);\n"
        f.puts "source('#{R::UTIL}');\n"
        f.puts 
        f.puts script
      end

     pid = Process.fork do |ppid|
       ENV["R_PROFILE"] = init_file
       exec("R")
     end

     begin
       Process.waitpid pid
     rescue Interrupt
       if Misc.pid_exists? pid
         Process.kill "INT", pid
         retry
       else
         raise $!
       end
     rescue Exception
       Process.kill 9, pid if Misc.pid_exists? pid
       raise $!
     ensure
       Process.waitpid pid if Misc.pid_exists? pid
     end

  end
end

.eval(cmd) ⇒ Object 



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# File 'lib/rbbt/util/R/eval.rb', line 143

def self.eval(cmd)
  eval_a(cmd).first
end

.eval_a(cmd) ⇒ Object 



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# File 'lib/rbbt/util/R/eval.rb', line 139

def self.eval_a(cmd)
  _eval(cmd).payload
end

.eval_run(cmd) ⇒ Object 



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# File 'lib/rbbt/util/R/eval.rb', line 147

def self.eval_run(cmd)
  _eval(cmd)
end

.hash2Rargs(hash) ⇒ Object 



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# File 'lib/rbbt/util/R.rb', line 157

def self.hash2Rargs(hash)
  hash.collect do |k,v|
    [k.to_s, ruby2R(v)] * "="
  end * ", "
end

.instance ⇒ Object 



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# File 'lib/rbbt/util/R/eval.rb', line 59

def self.instance
  @@instance ||= begin

                   clear if File.exist? pid_file and ! Misc.pid_exists?(Open.read(pid_file).strip.to_i)

                   FileUtils.mkdir_p File.dirname(socket_file) unless File.directory?(File.dirname(socket_file))
                   FileUtils.mkdir_p workdir unless File.directory? workdir

                   at_exit do
                     self.clear
                   end unless defined? @@instance_process

                   begin

                     if not File.exist? socket_file

                       sh_pid = Process.fork do
                         args = %w(--quiet --no-save --RS-socket)
                         args << "'#{socket_file}'"
                         args << "--RS-workdir"
                         args << "'#{workdir}'"
                         args << "--RS-pidfile"
                         args << "'#{pid_file}'"

                         if ENV["R_HOME"]
                           bin_path = File.join(ENV["R_HOME"], "bin/Rserve") 
                         else
                           bin_path = "Rserve"
                         end
                         cmd = bin_path + " " + args*" "
                         $stdout.reopen File.new('/dev/null', 'w')
                         exec(ENV, cmd)
                       end

                       Misc.insist(10, 0.5, false) do
                         raise "Rserve did not start" unless File.exist? pid_file
                       end

                       @@instance_process = Open.read(pid_file).to_i
                       Log.info "New Rserver session stated with PID (#{sh_pid}) #{@@instance_process}: #{SESSION}"
                     end

                     i = Rserve::Connection.new :hostname => socket_file

                     begin
                      FileUtils.mkdir workdir unless File.exist? workdir
                      i.eval "setwd('#{workdir}');"
                      i.eval "source('#{UTIL}');" 
                      i
                     rescue Exception
                       Log.exception $!
                       raise TryAgain
                     end
                   rescue Exception
                     Log.exception $!
                     Process.kill :INT, @@instance_process if defined? @@instance_process and @@instance_process
                     FileUtils.rm socket_file if File.exist? socket_file
                     retry if TryAgain === $!
                     raise $!
                   end
                 end
end

.interactive(script, source = [], options = {}) ⇒ Object 



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# File 'lib/rbbt/util/R.rb', line 59

def self.interactive(script, source = [], options = {})
  TmpFile.with_file(script) do |script_file|
    TmpFile.with_file do |init_file|

      cmd = <<-EOF
# Loading basic rbbt environment"
library(utils, quietly=TRUE);
library(grDevices,quietly=TRUE)   
source('#{R::UTIL}');
EOF

  require_sources  = source.collect{|source|
    source = R::LIB_DIR["#{source.to_s}.R"] if R::LIB_DIR["#{source.to_s}.R"].exists?
    "source('#{source}')"
  } * ";\n" if Array === source and source.any?

  cmd << require_sources + "\n\n" if require_sources

      cmd += <<-EOF

rbbt.require('readr')
interactive.script.file = '#{script_file}'
interactive.script = read_file(interactive.script.file)

cat(interactive.script)

source(interactive.script.file)
      EOF

      Open.write init_file, cmd
      CMD.cmd("env R_PROFILE='#{init_file}' xterm \"$R_HOME/bin/R\"")
    end
  end
end

.lockfile ⇒ Object 



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# File 'lib/rbbt/util/R/eval.rb', line 21

def self.lockfile
  @@lockfile ||= socket_file + '.lock'
end

.pid_file ⇒ Object 



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# File 'lib/rbbt/util/R/eval.rb', line 39

def self.pid_file
  @@pidfile ||= File.join(workdir, 'pid')
end

.ruby2R(object) ⇒ Object 



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# File 'lib/rbbt/util/R.rb', line 128

def self.ruby2R(object)
  case object
  when Float::INFINITY
    "Inf"
  when nil
    "NULL"
  when ":NA"
    "NA"
  when TSV
    "matrix(#{R.ruby2R object.values},dimnames=list(#{R.ruby2R object.keys}, #{R.ruby2R object.fields}))"
  when Symbol
    "#{ object }"
  when String
    object[0] == ":" ? object[1..-1] : "'#{ object }'"
  when Numeric
    object
  when TrueClass
    "TRUE"
  when FalseClass
    "FALSE"
  when Array
    "c(#{object.collect{|e| ruby2R(e) } * ", "})"
  when Hash
    "list(" << object.collect{|k,v| [k, ruby2R(v)] * "="} * ", " << ")"
  else
    raise "Type of object not known: #{ object.inspect }"
  end
end

.run(command, source = nil, options = nil) ⇒ Object 



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# File 'lib/rbbt/util/R.rb', line 13

def self.run(command, source = nil, options = nil)
  source, options = nil, source if options.nil? and Hash === source
  options = {} if options.nil?
  monitor = options.delete :monitor

  cmd =<<-EOF
# Loading basic rbbt environment
source('#{UTIL}');

  EOF

  require_sources  = source.collect{|source|
    source = R::LIB_DIR["#{source.to_s}.R"] if R::LIB_DIR["#{source.to_s}.R"].exists?
    "source('#{source}')"
  } * ";\n" if Array === source and source.any?

  cmd << require_sources + "\n\n" if require_sources

  case
  when IO === command
    cmd << command.read
  when File.exist?(command)
    cmd << File.open(command, 'r') do |f| f.read end
  else
    cmd << command
  end

  Log.debug{"R Script:\n#{ cmd }"}

  if monitor
    #io = CMD.cmd('R --no-save --quiet', options.merge(:in => cmd, :pipe => true, :log => true))
    io = CMD.cmd('R --no-save --quiet', options.merge(:in => cmd, :pipe => true, :log => true, :xvfb => options[:xvfb]))
    while line = io.gets
      case monitor
      when Proc
        monitor.call line
      else
        Log.debug "R: " <<  line
      end
    end
    io.join if io.respond_to? :join
  else
    CMD.cmd('R --no-save --slave --quiet', options.merge(:in => cmd, :xvfb => options[:xvfb]))
  end
end

.semfile ⇒ Object 



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# File 'lib/rbbt/util/R/eval.rb', line 25

def self.semfile
  if defined? @@semfile and not @@semfile.nil?
    @@semfile 
  else
    @@semfile = File.basename(socket_file) + '.sem'
    RbbtSemaphore.create_semaphore(@@semfile,1) 
    @@semfile
  end
end

.socket_file ⇒ Object 



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# File 'lib/rbbt/util/R/eval.rb', line 17

def self.socket_file
  @@socket_file ||= Rbbt.tmp.R_sockets[R::SESSION].find
end

.tsv(file, options = {}) ⇒ Object 



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# File 'lib/rbbt/util/R.rb', line 163

def self.tsv(file, options = {})
  options = Misc.add_defaults :header_hash => '', :sep => / +/, :type => :list, :key_field => 'ID'
  key_field = Misc.process_options options, :key_field
  clean = CMD.cmd('grep -v WARNING', :in => file, :pipe => true)
  TSV.open(clean, options).tap{|tsv| tsv.key_field = key_field }
end

.workdir ⇒ Object 



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# File 'lib/rbbt/util/R/eval.rb', line 35

def self.workdir
  @@workdir ||= socket_file + '.wd'
end