Module: CMD

Defined in:
lib/rbbt/util/cmd.rb

Constant Summary collapse

TOOLS = 
IndiferentHash.setup({})

Class Method Summary collapse

Class Method Details

.bash(cmd) ⇒ Object 



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# File 'lib/rbbt/util/cmd.rb', line 73

def self.bash(cmd)
  %Q(bash <<EOF\n#{cmd}\nEOF\n)
end

.cmd(tool, cmd = nil, options = {}, &block) ⇒ Object 



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# File 'lib/rbbt/util/cmd.rb', line 105

def self.cmd(tool, cmd = nil, options = {}, &block)
  options, cmd = cmd, nil if Hash === cmd

  options = Misc.add_defaults options, :stderr => Log::DEBUG
  in_content = options.delete(:in)
  stderr     = options.delete(:stderr)
  pipe       = options.delete(:pipe)
  post       = options.delete(:post)
  log        = options.delete(:log)
  no_fail    = options.delete(:no_fail)
  no_fail    = options.delete(:nofail) if no_fail.nil?
  no_wait    = options.delete(:no_wait)
  xvfb       = options.delete(:xvfb)
  bar        = options.delete(:progress_bar)
  save_stderr = options.delete(:save_stderr)

  dont_close_in  = options.delete(:dont_close_in)

  log = true if log.nil?
  
  if cmd.nil? && ! Symbol === tool 
    cmd = tool
  else
    tool = get_tool(tool)
    if cmd.nil?
      cmd = tool
    else
      cmd = tool + ' ' + cmd
    end

  end

  case xvfb
  when TrueClass
    cmd = "xvfb-run --server-args='-screen 0 1024x768x24' --auto-servernum #{cmd}"
  when String
    cmd = "xvfb-run --server-args='#{xvfb}' --auto-servernum --server-num=1 #{cmd}"
  when String
  end

  if stderr == true
    stderr = Log::HIGH
  end

  cmd_options = process_cmd_options options
  if cmd =~ /'\{opt\}'/
    cmd.sub!('\'{opt}\'', cmd_options) 
  else
    cmd << " " << cmd_options
  end

  in_content = StringIO.new in_content if String === in_content

  sin, sout, serr, wait_thr = begin
                                Open3.popen3(ENV, cmd)
                              rescue
                                Log.warn $!.message
                                raise ProcessFailed, nil, cmd unless no_fail
                                return
                              end
  pid = wait_thr.pid

  Log.debug{"CMD: [#{pid}] #{cmd}" if log}

  if in_content.respond_to?(:read)
    in_thread = Thread.new(Thread.current) do |parent|
      Thread.current.report_on_exception = false if no_fail
      begin
        begin
          while c = in_content.readpartial(Misc::BLOCK_SIZE)
            sin << c 
          end
        rescue EOFError
        end
        sin.close  unless sin.closed?

        unless dont_close_in
          in_content.close unless in_content.closed? 
          in_content.join if in_content.respond_to? :join 
        end
      rescue
        Log.error "Error in CMD  [#{pid}] #{cmd}: #{$!.message}" unless no_fail
        raise $!
      end
    end
  else
    in_thread = nil
    sin.close
  end

  pids = [pid]

  if pipe

    ConcurrentStream.setup sout, :pids => pids, :autojoin => no_wait, :no_fail => no_fail 

    if (Integer === stderr and log) || bar
      err_thread = Thread.new do
        while line = serr.gets
          bar.process(line) if bar
          sout.log = line
          sout.std_err << line if save_stderr
          Log.log "STDERR [#{pid}]: " +  line, stderr if log
        end 
        serr.close
      end
    else
      err_thread = Misc.consume_stream(serr, true)
    end

    sout.threads = [in_thread, err_thread, wait_thr].compact

    sout
  else

    if bar
      err = ""
      err_thread = Thread.new do
        while not serr.eof?
          line = serr.gets 
          bar.process(line) 
          err << line if Integer === stderr and log
        end
        serr.close
      end
    elsif log and Integer === stderr
      err = ""
      err_thread = Thread.new do
        while not serr.eof?
          err << serr.gets 
        end
        serr.close
      end
    else
      Misc.consume_stream(serr, true)
      #serr.close 
      err_thread = nil
      err = ""
    end

    ConcurrentStream.setup sout, :pids => pids, :threads => [in_thread, err_thread].compact, :autojoin => no_wait, :no_fail => no_fail 

    out = StringIO.new sout.read
    sout.close unless sout.closed?

    status = wait_thr.value
    if not status.success? and not no_fail
      if !err.empty?
        raise ProcessFailed.new pid, "#{cmd} failed with error status #{status.exitstatus}.\n#{err}"
      else
        raise ProcessFailed.new pid, "#{cmd} failed with error status #{status.exitstatus}"
      end
    else
      Log.log err, stderr if Integer === stderr and log
    end

    out
  end
end

.cmd_log(*args) ⇒ Object 



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# File 'lib/rbbt/util/cmd.rb', line 313

def self.cmd_log(*args)
  cmd_pid(*args)
  nil
end

.cmd_pid(*args) ⇒ Object 



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# File 'lib/rbbt/util/cmd.rb', line 265

def self.cmd_pid(*args)
  all_args = *args

  bar = all_args.last[:progress_bar] if Hash === all_args.last

  all_args << {} unless Hash === all_args.last

  level = all_args.last[:log] || 0
  level = 0 if TrueClass === level
  level = 10 if FalseClass === level
  level = level.to_i

  all_args.last[:log] = true
  all_args.last[:pipe] = true

  io = cmd(*all_args)
  pid = io.pids.first

  line = "" if bar
  starting = true
  while c = io.getc
    if starting
      if pid
        Log.logn "STDOUT [#{pid}]: ", level
      else
        Log.logn "STDOUT: ", level
      end
      starting = false
    end
    STDERR << c if Log.severity <= level
    line << c if bar
    if c == "\n"
      bar.process(line) if bar
      starting = true
      line = "" if bar
    end
  end 
  begin
    io.join
    bar.remove if bar
  rescue
    bar.remove(true) if bar
    raise $!
  end

  nil
end

.conda(tool, env = nil, channel = 'bioconda') ⇒ Object 



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

def self.conda(tool, env = nil, channel = 'bioconda')
  if env
    CMD.cmd("bash -l -c '(conda activate #{env} && conda install #{tool} -c #{channel})'")      
  else
    CMD.cmd("bash -l -c 'conda install #{tool} -c #{channel}'")      
  end
end

.get_tool(tool) ⇒ Object 



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

def self.get_tool(tool)
  return tool.to_s unless TOOLS[tool]

  @@init_cmd_tool ||= IndiferentHash.setup({})

  claim, test, block, cmd = TOOLS[tool]
  cmd = tool.to_s if cmd.nil?

  if !@@init_cmd_tool[tool]

    begin
      if test
        CMD.cmd(test + " ")
      else
        CMD.cmd("#{cmd} --help")
      end
    rescue
      if claim
        claim.produce
      else
        block.call
      end
    end
    version_txt = ""
    version = nil
    ["--version", "-version", "--help", ""].each do |f|
      begin
        version_txt += CMD.cmd("#{cmd} #{f} 2>&1", :nofail => true).read
        version = Misc.scan_version_text(version_txt, tool)
        break if version
      rescue
        Log.exception $!
      end
    end

    @@init_cmd_tool[tool] = version || true

    return cmd if cmd
  end

  cmd
end

.gzip_pipe(file) ⇒ Object 



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# File 'lib/rbbt/util/cmd.rb', line 69

def self.gzip_pipe(file)
  Open.gzip?(file) ? "<(gunzip -c '#{file}')" : "'#{file}'"
end

.process_cmd_options(options = {}) ⇒ Object 



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# File 'lib/rbbt/util/cmd.rb', line 77

def self.process_cmd_options(options = {})
  add_dashes = Misc.process_options options, :add_option_dashes

  string = ""
  options.each do |option, value|
    raise "Invalid option key: #{option.inspect}" if option.to_s !~ /^[a-z_0-9\-=.]+$/i
    #raise "Invalid option value: #{value.inspect}" if value.to_s.include? "'"
    value = value.gsub("'","\\'") if value.to_s.include? "'"

    option = "--" << option.to_s if add_dashes and option.to_s[0] != '-'

    case 
    when value.nil? || FalseClass === value 
      next
    when TrueClass === value
      string << "#{option} "
    else
      if option.to_s.chars.to_a.last == "="
        string << "#{option}'#{value}' "
      else
        string << "#{option} '#{value}' "
      end
    end
  end

  string.strip
end

.tool(tool, claim = nil, test = nil, cmd = nil, &block) ⇒ Object 



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# File 'lib/rbbt/util/cmd.rb', line 9

def self.tool(tool, claim = nil, test = nil, cmd = nil, &block)
  TOOLS[tool] = [claim, test, block, cmd]
end

.versions ⇒ Object 



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# File 'lib/rbbt/util/cmd.rb', line 64

def self.versions
  return {} unless defined? @@init_cmd_tool
  @@init_cmd_tool.select{|k,v| v =~ /\d+\./ }
end