From: Matt Maycock <ummaycoc@...>
Date: 2004-10-11T05:54:57+09:00
Subject: Re: TempFile

> Can you show us error reproducing "whole" script?
> I don't think of any reason of your problem from your code chunk.
> 
>                                                         matz.

You asked for it :-)

Here's the script, with all code it calls being included (thus, really
long post)

#------------------------------------------------------------#
#--- COMMAND LINE Script I Use        --- #
#--- requires ext/default_plotter and --- #
#---   ext/enum_from - they follow    --- #
# reads in a list of csv files that my boss gave me, and takes out
# some experiment data, and adds it into the default plotter to make
# graphs!  Not really that complicated.

ls *.csv | ruby -r ext/default_plotter -r ext/enum_from -ne '
  lines = File.readlines(chomp).map {|i| i.chomp.split(/\t/)}
  header = lines.shift

  plotter = `which gnuplot`.chomp

  lines.inject([]) {|arr, line|
    arr << header.inject(Hash.new) {|h, f| h[f] = line.shift; h}
  }.each {|row|
    id   = row["cloneid"].gsub(/\//, "_")
    file = "../../results/#{chomp.gsub(/\.csv$/, "")}/#{id}.png"
 
    Dir.mkdir(File.dirname(file)) unless FileTest.exists?(File.dirname(file))

    control, deprived = * %w{CON DEP}.map {|tag|
      [0, *[3,6,9,12].map {|i| row["#{i}_#{tag}"].to_f - row["0_CON"].to_f}]
    }

    xlabel, ylabel, xtics, ytics, xrange, yrange = nil
    xlabel = ["Gene Title", "Gene Symbol"].map {|k| "#{k}: #{row[k]}"}
    xlabel << ""
    table = [%w{Time Control Deprived}]
    [0, 3, 6, 9, 12].each_with_index {|e, i|
      table << [e.to_s.rjust(3), control[i], deprived[i]].map {|i| i.to_s}
    }

    frac = /^(-?\d*)(\.?\d*)$/
    ilens = (1..2).map {|i|
      table.map {|a| a[i] =~ frac ? $1.length : 0}.max
    }
    flens = (1..2).map {|i|
      table.map {|a| a[i] =~ frac ? $2.length : 0}.max
    }

    (1..2).each {|i|
      table.each {|a|
        a[i] = "#{$1.rjust(ilens[i-1])}#{$2.ljust(flens[i-1])}" if a[i] =~ frac
      }
    }

    lens  = (0...(table[0].length)).map {|i| table.map {|a| a[i].length}.max}
    dlens = (0...(table[0].length)).map {|i| table.from(1).map {|a|
a[i].length}.max}
    table.each_with_index {|arr, ai|
      index = 0
      if ai == 0 then
        xlabel << arr.map {|item|
          actualmax = lens[index]
          item.center(actualmax+2)
        }.join("  ")
        next
      end

      xlabel << arr.map {|item|
        actualmax = lens[index]
        datamax   = dlens[index]
        v = item.rjust(datamax+1)
        v.center(actualmax+1)
        index += 1
        v
      }.join("  ")
    }

    xlabel = xlabel.join("\\n")

    DefaultPlotter.data {|files|
      [control, deprived].each {|arr|
        files.add {|filehandle|
          arr.each_with_index {|e, i|
            filehandle.puts(e, i*3)
          }
        }
      }

      DefaultPlotter.plot(file, plotter, id, xlabel, ylabel, xtics,
ytics, xrange, yrange, "png") {|plot|
        files.each_path_with_index {|path, idx|
          plot.add(File.expand_path(path), %w{Control Deprived}[idx],
"lines", "2:1")
        }
      }
    }
  }
'

#------------------------------------------------------------#
#--- ext/enum_from --- #
# Allows you to take a nth tail...
module Enumerable
  def from(index)
    result = []
    self.each_with_index {|e, i|
      next unless i >= index
      yield e if block_given?
      result << e
    }

    result
  end
end

#------------------------------------------------------------#
#--- ext/default_plotter ---#
#--- requires ext/gnuplot - which follows ---#
# Just an alias for a `plotting' object.
require "ext/gnuplot"
DefaultPlotter = GnuPlot

#------------------------------------------------------------#
#--- ext/gnuplot ---#
#--- requires ext/plot and ext/singleton_class - which follow ---#
# Set up to use gnuplot to make wonderful graphs.
require 'ext/plot'
require 'ext/singleton_class'
require 'tempfile'

module GnuPlot
end

# Take an output (`file' to write to, basically)
#      a  title  (what to call graph)
#      an xlabel (what to call x-axis)
#      a  ylabel (what to call y-axis)
#      an xtics  (how to mark x-axis)
#      a  ytics  (how to mark y-axis)
#      an xrange (what part of x-axis to show)
#      a  yrange (what part of y-axis to show)
#      a  format (what to write `as' - png, gif, eps, etc)
#      block - takes the `plot' object and interacts with it.
#
#  the plot object the block gets has the following methods:
#    close :  closes the plot command file - now useable for making gnuplots!
#    add(path, title, style, use) :  add the data from the file with
path, use title and style, with columns use
#    path :  gives the path of the file containing the gnuplot commands
def GnuPlot.plotter(output, title=nil, xlabel=nil, ylabel=nil,
xtics=nil, ytics=nil, xrange=nil, yrange=nil, format=nil, &block)
  raise ArgumentException, "No block given" if block.nil?

  if Hash === output then
    h = output
    syms = [:output, :title, :xlabel, :ylabel, :xtics, :ytics,
:xrange, :yrange, :format]
    make_gnuplot(*syms.map {|sym| h[sym]}, &block)
  end
  raise ArgumentException, "Cannot accept nil output destination." if
output.nil?

  gpcmd = Tempfile.new('run_gnuplot_cmds_script')
  [["set terminal #{format}",      false],
   ["set output \"#{output}\"",    false],
   ["set pointsize 1.4",           false],
   ["set title \"#{title}\"",      title.nil?],
   ["set xlabel \"#{xlabel}\"",    xlabel.nil?],
   ["set ylabel \"#{ylabel}\"",    ylabel.nil?],
   ["set xrange [#{xrange}]",      xrange.nil?],
   ["set yrange [#{yrange}]",      yrange.nil?],
   ["set xtics (#{xtics})",        xtics.nil?],
   ["set ytics (#{ytics})",        ytics.nil?]].each {|str, skip|
    gpcmd.puts str unless skip
  }

  handle = Object.new
  closed = false
  gpcmds = []

  handle.singleton_def(:close) {
    next if closed
    closed = true

    index = 0
    space = ' ' * 'plot'.length

    cmds = []
    gpcmds.each_with_index {|c, i|
      cmds << "#{i == 0 ? 'plot' : space} #{c}"
    }

    gpcmd.puts cmds.join(",\\\n")
    gpcmd.close
  }

  handle.singleton_def(:add) {|path, title, style, using|
    cmd = path.inspect
    if using.nil? then
      cmd += ' using 1:2'
    else
      cmd += " using #{using}"
    end

    if title.nil? then
      cmd += ' notitle'
    else
      cmd += " title #{title.inspect}"
    end

    cmd += " with #{style}" unless style.nil?
    gpcmds << cmd
  }
  
  handle.singleton_def(:path) {
    gpcmd.path
  }

  result = nil
  begin
    result = block[handle]
    gpcmd.unlink
  rescue Exception
    begin
      gpcmd.unlink
    rescue Exception
    end
    raise
  end
  result
end

# Turns a set of points into something gnuplot understands as separate
coordinates.
def GnuPlot.make_point(*points)
  points.join("\t")
end

# Make GnuPlot a plot!
GnuPlot.extend(Plot)

# Make a gnuplot range!  here, we have a name for the range (x?, y?),
and the ends.
# the ends can be numbers, or nolow nohigh...
def GnuPlot.make_range(name, a, b, errorp=nil)
  error = errorp.nil? ? Proc.new{|exc, msg|
    raise exc, msg
  } : Proc.new {|exc, msg|
    errorp[exc, msg]
    return
  }

  a = a.strip.downcase
  b = b.strip.downcase
  error[ArgumentError, "#{name}:  both points are #{a.upcase}."]  if a
=~ /^no(low|high)$/ && a == b
  return make_range[name, b, a] if b == 'nolow' || a == 'nohigh'

  floata, floatb = *[a, b].map {|c|
!(/^(-|\+)?(\d+)?\.?(\d+)?$/.match(c).nil? || /\d/.match(c).nil?)}
  noa, nob       = *[a, b].map {|c| ['nolow', 'nohigh'].include?(c)}
  error[ArgumentError, "Invalid points: #{a}, #{b}."] if !(floata ||
noa) && !(floatb || nob)
  a = (a == 'nolow') ? '' : a.to_f
  b = (b == 'nohigh') ? '' : b.to_f
  a, b = b, a if Float === a && Float === b && b < a
  a, b = a.to_s, b.to_s
  "#{a}:#{b}"
end

#------------------------------------------------------------#
#--- ext/plot ---#
#--- requires ext/singleton_class - which follows ---#
require 'tempfile'
require 'ext/singleton_class'

module Plot
  # Output is `where' to go with the graph (file)
  # plotter is the actual command to invoke.
  # the rest, except errorp and debugp are the same as gnuplot.plotter args
  # errorp and debugp are procs toc all with error and debug information.
  #
  # Needs a block - that block is passed a plot object who's sole method is add,
  # which is the same as the add method from the object yieled by
plotter's block.
  def plot(output, plotter, title=nil, xlabel=nil, ylabel=nil,
xtics=nil, ytics=nil, xrange=nil, yrange=nil, format=nil, errorp=nil,
debugp=nil)
    error = errorp.nil? ? Proc.new{|exc, msg|
      raise exc, msg
    } : Proc.new {|exc, msg|
      errorp[exc, msg]
      return
    }
    debug = debugp.nil? ? Proc.new {} : debugp

    error[ArgumentError, 'Block not given for Plot # plot.  A block is
required.'] unless block_given?
      
    plotargs  = [output, title, xlabel, ylabel, xtics, ytics, xrange,
yrange, format]
    plotblock = Proc.new {|plot_handle|
      yield(Object.new.singleton_def(:add) {|*args| plot_handle.add(*args)})
      plot_handle.close

      debug[:command_file, File.readlines(plot_handle.path).map {|i| i.chomp}]

      `#{plotter} #{plot_handle.path}`
    }

    plotter(*plotargs, &plotblock)
  end

  # Basically, make an object that is a database of plotting files.
  # errorp and debugp are the same as above.
  # Takes a block - this block gets the `database'
  # this database has the following methods:
  #    add - calling this gets you a filehandle back in the block add gets
  #          this filehandle can be given points to add, and when the block
  #          is done, the file gets added to the end of the list of data files
  #    use_file(fname) - adds fname to the end of the list of data files
  #    each_path_with_index - use block to go over each file in the list of
  #          of data files and have the index in the list, too
  #    each_path - same as above, no index
  # at the end of the block, the database's files are `cleared'
  def data(errorp=nil, debugp=nil)
    error = errorp.nil? ? Proc.new{|exc, msg|
      raise exc, msg
    } : Proc.new {|exc, msg|
      errorp[exc, msg]
      return
    }
    debug = debugp.nil? ? Proc.new {} : debugp
    
    error[ArgumentError, 'Block not given for Plot # data.  A block is
required.'] unless block_given?
    handle = Object.new

    files = []

    done  = Proc.new {files.each {|f| f.unlink}}
    add   = Proc.new {|file| files << file}
    enum  = Proc.new {|block, index|
      files.each_with_index {|f, i|
        block[f.path, i] if index
        block[f.path]    unless index
      }
    }
    point = Proc.new {|*args| make_point(*args)}

    handle.instance_eval {
      @done,  @add,   @enum,
      @error, @debug, @point = done,  add,   enum,
                               error, debug, point
    }

    def handle.add
      unless block_given? then
        @done[]
        @error[ArgumentError, 'Block not given for Plot # data #
handle.add.  A block is required.']
      end

      file       = Tempfile.new('plotdata')
      filehandle, point = Object.new, @point
      filehandle.singleton_def(:puts) {|*points|
        file.puts(point[*points])
      }

      yield filehandle
      file.close(false)

      @debug[:data_file, File.readlines(file.path).map {|l| l.chomp}]
      @add[file]
    end

    def handle.use_file(fname)
      @error[ArgumentError, "File #{fname} does not exist."] unless
FileTest.exists?(fname)
      @error[ArgumentError, "File #{fname} isn't a file."]   unless
FileTest.file?(fname)
      @error[ArgumentError, "File #{fname} isn't readable."] unless
FileTest.readable?(fname)
      @add[File.open(fname).singleton_def(:unlink) {self.close}]
    end

    def handle.each_path_with_index(&block)
      if block.nil? then
        @done[]
        @error[ArgumentError, 'Block not given for Plot # data #
handle.each_path_with_index.  A block is required']
      end

      @enum[block, true]
    end

    def handle.each_path(&block)
      if block.nil? then
        @done[]
        @error[ArgumentError, 'Block not given for Plot # data #
handle.each_path.  A block is required']
      end

      @enum[block, false]
    end

    yield handle

    files.each {|f| f.unlink}
    files.clear

    nil
  end
end

#------------------------------------------------------------#
#--- ext/singleton_class ---#
class Object
  def singleton_class
    class << self
      self
    end
  end
  
  def singleton_def(sym, &block)
    self.singleton_class.send(:define_method, sym, &block)
    self
  end
end

-- 
There's no word in the English language for what you do to a dead
thing to make it stop chasing you.