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.



5
6
7
 
# File 'lib/rbbt/util/R/model.rb', line 5

def model_dir
  @model_dir
end

Class Method Details

._eval(cmd) ⇒ Object 



122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
 
# 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 



43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
 
# 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 



94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
 
# 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 



143
144
145
 
# File 'lib/rbbt/util/R/eval.rb', line 143

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

.eval_a(cmd) ⇒ Object 



139
140
141
 
# File 'lib/rbbt/util/R/eval.rb', line 139

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

.eval_run(cmd) ⇒ Object 



147
148
149
 
# File 'lib/rbbt/util/R/eval.rb', line 147

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

.hash2Rargs(hash) ⇒ Object 



157
158
159
160
161
 
# 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 



59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
 
# 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 



59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
 
# 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 



21
22
23
 
# File 'lib/rbbt/util/R/eval.rb', line 21

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

.pid_file ⇒ Object 



39
40
41
 
# File 'lib/rbbt/util/R/eval.rb', line 39

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

.ruby2R(object) ⇒ Object 



128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
 
# 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 



13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
 
# 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
    nil
  else
    CMD.cmd('R --no-save --slave --quiet', options.merge(:in => cmd, :xvfb => options[:xvfb]))
  end
end

.semfile ⇒ Object 



25
26
27
28
29
30
31
32
33
 
# 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 



17
18
19
 
# 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 



163
164
165
166
167
168
 
# 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 



35
36
37
 
# File 'lib/rbbt/util/R/eval.rb', line 35

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