Module: Open

Defined in:
lib/scout/open.rb,
lib/scout/open/lock.rb,
lib/scout/open/util.rb,
lib/scout/open/remote.rb,
lib/scout/open/stream.rb,
lib/scout/persist/open.rb

Defined Under Namespace

Modules: NamedStream

Constant Summary collapse

GREP_CMD = 
begin
  if ENV["GREP_CMD"] 
    ENV["GREP_CMD"]
  elsif File.exist?('/bin/grep')
    "/bin/grep"
  elsif File.exist?('/usr/bin/grep')
    "/usr/bin/grep"
  else
    "grep"
  end
end
BLOCK_SIZE = 
1024 * 8
PIPE_MUTEX = 
Mutex.new
OPEN_PIPE_IN = 
[]

Class Attribute Summary collapse

Class Method Summary collapse

Class Attribute Details

.remote_cache_dir ⇒ Object

Returns the value of attribute remote_cache_dir.



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# File 'lib/scout/open/remote.rb', line 7

def remote_cache_dir
  @remote_cache_dir
end

.sensible_write_dir ⇒ Object

Returns the value of attribute sensible_write_dir.



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# File 'lib/scout/open/stream.rb', line 13

def sensible_write_dir
  @sensible_write_dir
end

.sensible_write_lock_dir ⇒ Object

Returns the value of attribute sensible_write_lock_dir.



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# File 'lib/scout/open/stream.rb', line 5

def sensible_write_lock_dir
  @sensible_write_lock_dir
end

Class Method Details

._just_open ⇒ Object 



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# File 'lib/scout/resource/open.rb', line 2

def self.open(file, options = {})
  if IO === file || StringIO === file
    if block_given?
      res = yield file, options
      file.close
      return res
    else
      return file
    end
  end

  options = IndiferentHash.add_defaults options, :noz => false, :mode => 'r'

  mode = IndiferentHash.process_options options, :mode

  options[:noz] = true if mode.include? "w"

  io = file_open(file, options[:grep], mode, options[:invert_grep], options)

  io = unzip(io)   if ((String === file and zip?(file))   and not options[:noz]) or options[:zip]
  io = gunzip(io)  if ((String === file and gzip?(file))  and not options[:noz]) or options[:gzip]
  io = bgunzip(io) if ((String === file and bgzip?(file)) and not options[:noz]) or options[:bgzip]

  io.extend NamedStream
  io.filename = file

  if block_given?
    res = nil
    begin
      res = yield(io)
    rescue DontClose
      res = $!.payload
    rescue Exception
      io.abort $! if io.respond_to? :abort
      io.join if io.respond_to? :join
      raise $!
    ensure
      io.close if io.respond_to? :close and not io.closed?
      io.join if io.respond_to? :join
    end
    res
  else
    io
  end
end

.add_cache(url, data, options = {}) ⇒ Object 



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# File 'lib/scout/open/remote.rb', line 120

def self.add_cache(url, data, options = {})
  filename = cache_file(url, options)
  Open.sensible_write(filename, data, :force => true)
end

.bgunzip(stream) ⇒ Object 



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# File 'lib/scout/open/util.rb', line 33

def self.bgunzip(stream)
  Bgzf.setup stream
end

.bgzip(stream) ⇒ Object 



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# File 'lib/scout/open/util.rb', line 45

def self.bgzip(stream)
  CMD.cmd('bgzip', :in => stream, :pipe => true, :no_fail => true, :no_wait => true)
end

.bgzip?(file) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/scout/open/util.rb', line 61

def self.bgzip?(file)
  file = file.find if Path === file
  !! (file =~ /\.bgz$/)
end

.broken_link?(path) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/scout/open/util.rb', line 102

def self.broken_link?(path)
  File.symlink?(path) && ! File.exist?(File.readlink(path))
end

.cache_file(url, options) ⇒ Object 



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# File 'lib/scout/open/remote.rb', line 98

def self.cache_file(url, options)
  File.join(self.remote_cache_dir, digest_url(url, options))
end

.collapse_stream(s, line: nil, sep: "\t", header: nil, &block) ⇒ Object

def self.sort_stream(stream, header_hash = “#”, cmd_args = “-u”)

StringIO.new stream.read.split("\n").sort.uniq * "\n"

end



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# File 'lib/scout/open/stream.rb', line 439

def self.collapse_stream(s, line: nil, sep: "\t", header: nil, &block)
  sep ||= "\t"
  Open.open_pipe do |sin|

    sin.puts header if header

    line ||= s.gets

    current_parts = []
    while line
      key, *parts = line.chomp.split(sep, -1)
      case
      when key.nil?
      when current_parts.nil?
        current_parts = parts
        current_key = key
      when current_key == key
        parts.each_with_index do |part,i|
          if current_parts[i].nil?
            current_parts[i] = "|" << part
          else
            current_parts[i] = current_parts[i] << "|" << part
          end
        end

        (parts.length..current_parts.length-1).to_a.each do |pos|
          current_parts[pos] = current_parts[pos] << "|" << ""
        end
      when current_key.nil?
        current_key = key
        current_parts = parts
      when current_key != key
        if block_given?
          res = block.call(current_parts)
          sin.puts [current_key, res] * sep
        else
          sin.puts [current_key, current_parts].flatten * sep
        end
        current_key = key
        current_parts = parts
      end
      line = s.gets
    end

    if block_given?
      res = block.call(current_parts)
      sin.puts [current_key, res] * sep
    else
      sin.puts [current_key, current_parts].flatten * sep
    end unless current_key.nil?
  end
end

.consume_stream(io, in_thread = false, into = nil, into_close = true, &block) ⇒ Object 



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# File 'lib/scout/open/stream.rb', line 19

def self.consume_stream(io, in_thread = false, into = nil, into_close = true, &block)
  return if Path === io
  return unless io.respond_to? :read

  if io.respond_to? :closed? and io.closed?
    io.join if io.respond_to? :join
    return
  end

  if in_thread
    consumer_thread = Thread.new(Thread.current) do |parent|
      Thread.current["name"] = "Consumer #{Log.fingerprint io}"
      Thread.current.report_on_exception = false
      consume_stream(io, false, into, into_close)
    end

    io.threads.push(consumer_thread) if io.respond_to?(:threads)
    Thread.pass until consumer_thread["name"]

    consumer_thread
  else
    if into
      Log.low "Consuming stream #{Log.fingerprint io} -> #{Log.fingerprint into}"
    else
      Log.low "Consuming stream #{Log.fingerprint io}"
    end

    begin
      into = into.find if Path === into

      if String === into
        dir = File.dirname(into)
        Open.mkdir dir unless File.exist?(dir)
        into_path, into = into, File.open(into, 'w')
      end

      into_close = false unless into.respond_to? :close

      while c = io.read(BLOCK_SIZE)
        into << c if into
        last_c = c if c
        break if io.closed?
      end

      io.join if io.respond_to? :join
      io.close unless io.closed?
      into.join if into and into_close and into.respond_to?(:joined?) and not into.joined?
      into.close if into and into_close and not into.closed?
      block.call if block_given?

      last_c
    rescue Aborted
      Thread.current["exception"] = true
      Log.low "Consume stream Aborted #{Log.fingerprint io} into #{into_path || into}"
      io.abort $! if io.respond_to? :abort
      into.close if into.respond_to?(:closed?) && ! into.closed?
      FileUtils.rm into_path if into_path and File.exist?(into_path)
    rescue Exception
      Thread.current["exception"] = true
      Log.low "Consume stream Exception reading #{Log.fingerprint io} into #{into_path || into} - #{$!.message}"
      exception = (io.respond_to?(:stream_exception) && io.stream_exception) ? io.stream_exception : $!
      io.abort exception if io.respond_to? :abort
      into.close if into.respond_to?(:closed?) && ! into.closed?
      into_path = into if into_path.nil? && String === into
      if into_path and File.exist?(into_path)
        FileUtils.rm into_path
      end
      raise exception
    end
  end
end

.cp(source, target, options = {}) ⇒ Object 



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# File 'lib/scout/open/util.rb', line 189

def self.cp(source, target, options = {})
  source = source.find if Path === source
  target = target.find if Path === target

  FileUtils.mkdir_p File.dirname(target) unless File.exist?(File.dirname(target))
  FileUtils.rm_rf target if File.exist?(target)
  FileUtils.cp_r source, target
end

.ctime(file) ⇒ Object 



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# File 'lib/scout/open/util.rb', line 161

def self.ctime(file)
  file = file.find if Path === file
  File.ctime(file)
end

.digest_url(url, options = {}) ⇒ Object 



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# File 'lib/scout/open/remote.rb', line 93

def self.digest_url(url, options = {})
  params = [url, options.values_at("--post-data", "--post-data="), (options.include?("--post-file")? Open.read(options["--post-file"]).split("\n").sort * "\n" : "")]
  Misc.digest([url, params])
end

.directory?(file) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/scout/open/util.rb', line 106

def self.directory?(file)
  file = file.find if Path === file
  File.directory?(file)
end

.download(url, file) ⇒ Object 



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# File 'lib/scout/open/remote.rb', line 89

def self.download(url, file)
  CMD.cmd_log(:wget, "'#{url}' -O '#{file}'")
end

.exist_or_link?(file) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/scout/open/util.rb', line 117

def self.exist_or_link?(file)
  self.exists?(file) || File.symlink?(file)
end

.exists?(file) ⇒ Boolean Also known as: exist?

Returns:

  • (Boolean) 


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# File 'lib/scout/open/util.rb', line 111

def self.exists?(file)
  file = file.find if Path === file
  File.exist?(file)
end

.file_open(file, grep = false, mode = 'r', invert_grep = false, options = {}) ⇒ Object 



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# File 'lib/scout/open.rb', line 34

def self.file_open(file, grep = false, mode = 'r', invert_grep = false, options = {})
  Open.mkdir File.dirname(file) if mode.include? 'w'

  stream = get_stream(file, mode, options)

  if grep
    grep(stream, grep, invert_grep)
  else
    stream
  end
end

.file_write(file, content, mode = 'w') ⇒ Object 



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# File 'lib/scout/open.rb', line 46

def self.file_write(file, content, mode = 'w')
  File.open(file, mode) do |f|
    begin
      f.flock(File::LOCK_EX)
      f.write content 
      f.flock(File::LOCK_UN)
    ensure
      f.close unless f.closed?
    end
  end
end

.get_stream(file, mode = 'r', options = {}) ⇒ Object 



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# File 'lib/scout/open.rb', line 23

def self.get_stream(file, mode = 'r', options = {})
  return file if Open.is_stream?(file)
  return file.stream if Open.has_stream?(file)
  file = file.find if Path === file

  return Open.ssh(file, options) if Open.ssh?(file)
  return Open.wget(file, options) if Open.remote?(file)

  File.open(file, mode)
end

.grep(stream, grep, invert = false, fixed = nil) ⇒ Object 



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# File 'lib/scout/open/util.rb', line 14

def self.grep(stream, grep, invert = false, fixed = nil)
  case 
  when Array === grep
    TmpFile.with_file(grep * "\n", false) do |f|
      if FalseClass === fixed
        CMD.cmd("#{GREP_CMD} #{invert ? '-v' : ''} -", "-f" => f, :in => stream, :pipe => true, :post => proc{FileUtils.rm f})
      else
        CMD.cmd("#{GREP_CMD} #{invert ? '-v' : ''} -", "-w" => true, "-F" => true, "-f" => f, :in => stream, :pipe => true, :post => proc{FileUtils.rm f})
      end
    end
  else
    CMD.cmd("#{GREP_CMD} #{invert ? '-v ' : ''} '#{grep}' -", :in => stream, :pipe => true, :post => proc{begin stream.force_close; rescue Exception; end if stream.respond_to?(:force_close)})
  end
end

.gunzip(stream) ⇒ Object 



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# File 'lib/scout/open/util.rb', line 37

def self.gunzip(stream)
  CMD.cmd('zcat', :in => stream, :pipe => true, :no_fail => true, :no_wait => true)
end

.gzip(stream) ⇒ Object 



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# File 'lib/scout/open/util.rb', line 41

def self.gzip(stream)
  CMD.cmd('gzip', :in => stream, :pipe => true, :no_fail => true, :no_wait => true)
end

.gzip?(file) ⇒ Boolean

Questions

Returns:

  • (Boolean) 


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# File 'lib/scout/open/util.rb', line 56

def self.gzip?(file)
  file = file.find if Path === file
  !! (file =~ /\.gz$/)
end

.gzip_pipe(file) ⇒ Object 



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# File 'lib/scout/open/util.rb', line 29

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

.has_stream?(obj) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/scout/open/util.rb', line 75

def self.has_stream?(obj)
  obj.respond_to?(:stream)
end

.in_cache(url, options = {}) ⇒ Object 



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# File 'lib/scout/open/remote.rb', line 102

def self.in_cache(url, options = {})
  filename = cache_file(url, options)
  if File.exist? filename
    return filename 
  else
    nil
  end
end

.init_lock ⇒ Object 



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# File 'lib/scout/open/lock.rb', line 7

def self.init_lock
  Lockfile.refresh = 2 
  Lockfile.max_age = 30
  Lockfile.suspend = 4
end

.is_stream?(obj) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/scout/open/util.rb', line 71

def self.is_stream?(obj)
  IO === obj || StringIO === obj
end

.json(file) ⇒ Object 



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# File 'lib/scout/persist/open.rb', line 6

def self.json(file)
  Open.open(file){|f| JSON.load(f) }
end

.link(source, target, options = {}) ⇒ Object 



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# File 'lib/scout/open/util.rb', line 235

def self.link(source, target, options = {})
  begin
    Open.ln(source, target, options)
  rescue
    Open.ln_s(source, target, options)
  end
  nil
end

.list(file) ⇒ Object 



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# File 'lib/scout/open/util.rb', line 244

def self.list(file)
  file = file.produce_and_find if Path === file
  Open.read(file).split("\n")
end

.ln(source, target, options = {}) ⇒ Object 



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# File 'lib/scout/open/util.rb', line 210

def self.ln(source, target, options = {})
  source = source.find if Path === source
  target = target.find if Path === target
  source = File.realpath(source) if File.symlink?(source)

  FileUtils.mkdir_p File.dirname(target) unless File.exist?(File.dirname(target))
  FileUtils.rm target if File.exist?(target)
  FileUtils.rm target if File.symlink?(target)
  FileUtils.ln source, target
end

.ln_h(source, target, options = {}) ⇒ Object 



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# File 'lib/scout/open/util.rb', line 221

def self.ln_h(source, target, options = {})
  source = source.find if Path === source
  target = target.find if Path === target

  FileUtils.mkdir_p File.dirname(target) unless File.exist?(File.dirname(target))
  FileUtils.rm target if File.exist?(target)
  begin
    CMD.cmd("ln -L '#{ source }' '#{ target }'")
  rescue ProcessFailed
    Log.debug "Could not hard link #{source} and #{target}: #{$!.message.gsub("\n", '. ')}"
    CMD.cmd("cp -L '#{ source }' '#{ target }'")
  end
end

.ln_s(source, target, options = {}) ⇒ Object 



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# File 'lib/scout/open/util.rb', line 199

def self.ln_s(source, target, options = {})
  source = source.find if Path === source
  target = target.find if Path === target

  target = File.join(target, File.basename(source)) if File.directory? target
  FileUtils.mkdir_p File.dirname(target) unless File.exist?(File.dirname(target))
  FileUtils.rm target if File.exist?(target)
  FileUtils.rm target if File.symlink?(target)
  FileUtils.ln_s source, target
end

.lock(file, unlock = true, options = {}) ⇒ Object 



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# File 'lib/scout/open/lock.rb', line 15

def self.lock(file, unlock = true, options = {})
  unlock, options = true, unlock if Hash === unlock
  return yield if file.nil? and not Lockfile === options[:lock]

  if Lockfile === file
    lockfile = file
  else
    file = file.find if Path === file
    FileUtils.mkdir_p File.dirname(File.expand_path(file)) unless File.exist? File.dirname(File.expand_path(file))

    case options[:lock]
    when Lockfile
      lockfile = options[:lock]
    when FalseClass
      lockfile = nil
      unlock = false
    when Path, String
      lock_path = options[:lock].find
      lockfile = Lockfile.new(lock_path, options)
    else
      lock_path = File.expand_path(file + '.lock')
      lockfile = Lockfile.new(lock_path, options)
    end
  end

  begin
    lockfile.lock unless lockfile.nil? || lockfile.locked?
  rescue Aborted, Interrupt
    raise LockInterrupted
  end

  res = nil

  begin
    res = yield lockfile
  rescue KeepLocked
    unlock = false
    res = $!.payload
  ensure
    if unlock 
      begin
        if lockfile.locked?
          lockfile.unlock 
        end
      rescue Exception
        Log.warn "Exception unlocking: #{lockfile.path}"
        Log.exception $!
      end
    end
  end

  res
end

.marshal(file) ⇒ Object 



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# File 'lib/scout/persist/open.rb', line 14

def self.marshal(file)
  Open.open(file){|f| Marshal.load(f) }
end

.mkdir(target) ⇒ Object 



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# File 'lib/scout/open/util.rb', line 143

def self.mkdir(target)
  target = target.find if Path === target
  if ! File.exist?(target)
    FileUtils.mkdir_p target
  end
end

.mtime(file) ⇒ Object 



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# File 'lib/scout/open/util.rb', line 171

def self.mtime(file)
  file = file.find if Path === file
  begin
    if File.symlink?(file) || File.stat(file).nlink > 1
      if File.exist?(file + '.info') && defined?(Step)
        done = Persist.load(file + '.info', Step::SERIALIZER)[:done]
        return done if done
      end

      file = Pathname.new(file).realpath.to_s 
    end
    return nil unless File.exist?(file)
    File.mtime(file)
  rescue
    nil
  end
end

.mv(source, target, options = {}) ⇒ Object 



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# File 'lib/scout/open/util.rb', line 121

def self.mv(source, target, options = {})
  target = target.find if Path === target
  source = source.find if Path === source
  FileUtils.mkdir_p File.dirname(target) unless File.exist?(File.dirname(target))
  tmp_target = File.join(File.dirname(target), '.tmp_mv.' + File.basename(target))
  FileUtils.mv source, tmp_target
  FileUtils.mv tmp_target, target
  return nil
end

.notify_write(file) ⇒ Object 



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# File 'lib/scout/open/util.rb', line 80

def self.notify_write(file)
  begin
    notification_file = file + '.notify'
    if Open.exists? notification_file
      key = Open.read(notification_file).strip
      key = nil if key.empty?
      if key && key.include?("@")
        to = from = key
        subject = "Wrote " << file
        message = "Content attached"
        Misc.send_email(from, to, subject, message, :files => [file])
      else
        Misc.notify("Wrote " << file, nil, key)
      end
      Open.rm notification_file
    end
  rescue
    Log.exception $!
    Log.warn "Error notifying write of #{ file }"
  end
end

.open(file, *args, **kwargs, &block) ⇒ Object 



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# File 'lib/scout/open.rb', line 58

def self.open(file, options = {})
  if IO === file || StringIO === file
    if block_given?
      res = yield file, options
      file.close
      return res
    else
      return file
    end
  end

  options = IndiferentHash.add_defaults options, :noz => false, :mode => 'r'

  mode = IndiferentHash.process_options options, :mode

  options[:noz] = true if mode.include? "w"

  io = file_open(file, options[:grep], mode, options[:invert_grep], options)

  io = unzip(io)   if ((String === file and zip?(file))   and not options[:noz]) or options[:zip]
  io = gunzip(io)  if ((String === file and gzip?(file))  and not options[:noz]) or options[:gzip]
  io = bgunzip(io) if ((String === file and bgzip?(file)) and not options[:noz]) or options[:bgzip]

  io.extend NamedStream
  io.filename = file

  if block_given?
    res = nil
    begin
      res = yield(io)
    rescue DontClose
      res = $!.payload
    rescue Exception
      io.abort $! if io.respond_to? :abort
      io.join if io.respond_to? :join
      raise $!
    ensure
      io.close if io.respond_to? :close and not io.closed?
      io.join if io.respond_to? :join
    end
    res
  else
    io
  end
end

.open_cache(url, options = {}) ⇒ Object 



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# File 'lib/scout/open/remote.rb', line 125

def self.open_cache(url, options = {})
  filename = cache_file(url, options)
  Open.open(filename)
end

.open_pipe(do_fork = false, close = true) ⇒ Object 



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# File 'lib/scout/open/stream.rb', line 210

def self.open_pipe(do_fork = false, close = true)
  raise "No block given" unless block_given?

  sout, sin = Open.pipe

  if do_fork

    pid = Process.fork {
      begin
        purge_pipes(sin)
        sout.close

        yield sin
        sin.close if close and not sin.closed?

      rescue Exception
        Log.exception $!
        Kernel.exit!(-1)
      end
      Kernel.exit! 0
    }
    sin.close

    ConcurrentStream.setup sout, :pids => [pid]
  else

    ConcurrentStream.setup sin, :pair => sout
    ConcurrentStream.setup sout, :pair => sin

    thread = Thread.new do
      begin
        ConcurrentStream.process_stream(sin, :message => "Open pipe") do
          Thread.current.report_on_exception = false
          Thread.current["name"] = "Pipe input #{Log.fingerprint sin} => #{Log.fingerprint sout}"

          yield sin
        end
      end
    end

    sin.threads = [thread]
    sout.threads = [thread]

    Thread.pass until thread["name"]
  end

  sout
end

.pipe ⇒ Object 



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# File 'lib/scout/open/stream.rb', line 169

def self.pipe
  OPEN_PIPE_IN.delete_if{|pipe| pipe.closed? }
  res = PIPE_MUTEX.synchronize do
    sout, sin = IO.pipe
    OPEN_PIPE_IN << sin

    [sout, sin]
  end
  Log.low{"Creating pipe #{[Log.fingerprint(res.last), Log.fingerprint(res.first)] * " -> "}"}
  res
end

.purge_pipes(*save) ⇒ Object 



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# File 'lib/scout/open/stream.rb', line 201

def self.purge_pipes(*save)
  PIPE_MUTEX.synchronize do
    OPEN_PIPE_IN.each do |pipe|
      next if save.include? pipe
      pipe.close unless pipe.closed?
    end
  end
end

.read(file, options = {}, &block) ⇒ Object 



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# File 'lib/scout/open.rb', line 104

def self.read(file, options = {}, &block)
  open(file, options) do |f|
    if block_given?
      res = []
      while not f.eof?
        l = f.gets
        l = Misc.fixutf8(l) unless options[:nofix]
        res << yield(l)
      end
      res
    else
      if options[:nofix]
        f.read
      else
        Misc.fixutf8(f.read)
      end
    end
  end
end

.read_stream(stream, size) ⇒ Object 



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# File 'lib/scout/open/stream.rb', line 377

def self.read_stream(stream, size)
  str = nil
  Thread.pass while IO.select([stream],nil,nil,1).nil?
  while not str = stream.read(size)
    IO.select([stream],nil,nil,1)
    Thread.pass
    raise ClosedStream if stream.eof?
  end

  while str.length < size
    raise ClosedStream if stream.eof?
    IO.select([stream],nil,nil,1)
    if new = stream.read(size-str.length)
      str << new
    end
  end
  str
end

.realpath(file) ⇒ Object 



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# File 'lib/scout/open/util.rb', line 166

def self.realpath(file)
  file = file.find if Path === file
  Pathname.new(File.expand_path(file)).realpath.to_s 
end

.release_pipes(*pipes) ⇒ Object 



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# File 'lib/scout/open/stream.rb', line 193

def self.release_pipes(*pipes)
  PIPE_MUTEX.synchronize do
    pipes.flatten.each do |pipe|
      pipe.close unless pipe.closed?
    end
  end
end

.remote?(file) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/scout/open/remote.rb', line 14

def self.remote?(file)
  !! (file =~ /^(?:https?|ftp|ssh):\/\//)
end

.remove_from_cache(url, options = {}) ⇒ Object 



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# File 'lib/scout/open/remote.rb', line 111

def self.remove_from_cache(url, options = {})
  filename = cache_file(url, options)
  if File.exist? filename
    FileUtils.rm filename 
  else
    nil
  end
end

.rm(file) ⇒ Object 



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# File 'lib/scout/open/util.rb', line 131

def self.rm(file)
  FileUtils.rm(file) if File.exist?(file) || Open.broken_link?(file)
end

.rm_rf(file) ⇒ Object 



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# File 'lib/scout/open/util.rb', line 135

def self.rm_rf(file)
  FileUtils.rm_rf(file)
end

.scp(source_file, target_file, target: nil, source: nil) ⇒ Object 



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# File 'lib/scout/open/remote.rb', line 130

def self.scp(source_file, target_file, target: nil, source: nil)
  CMD.cmd_log("ssh #{target} mkdir -p #{File.dirname(target_file)}")
  target_file = [target, target_file] * ":" if target && ! target_file.start_with?(target+":")
  source_file = [source, source_file] * ":" if source && ! source_file.start_with?(source+":")
  CMD.cmd_log("scp -r '#{ source_file }' #{target_file}")
end

.sensible_write(path, content = nil, options = {}, &block) ⇒ Object 



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# File 'lib/scout/open/stream.rb', line 91

def self.sensible_write(path, content = nil, options = {}, &block)
  force = IndiferentHash.process_options options, :force

  if File.exist?(path) and not force
    Open.consume_stream content
    return
  end

  lock_options = IndiferentHash.pull_keys options.dup, :lock
  lock_options = lock_options[:lock] if Hash === lock_options[:lock]
  tmp_path = TmpFile.tmp_for_file(path, {:dir => Open.sensible_write_dir})
  tmp_path_lock = TmpFile.tmp_for_file(path, {:dir => Open.sensible_write_lock_dir})

  tmp_path_lock = nil if FalseClass === options[:lock]

  Open.lock tmp_path_lock, lock_options do

    if File.exist? path and not force
      Log.warn "Path exists in sensible_write, not forcing update: #{ path }"
      Open.consume_stream content
    else
      FileUtils.mkdir_p File.dirname(tmp_path) unless File.directory?(File.dirname(tmp_path))
      FileUtils.rm_f tmp_path if File.exist? tmp_path
      Log.low "Sensible write stream #{Log.fingerprint content} -> #{Log.fingerprint path}" if IO === content
      begin
        case
        when block_given?
          File.open(tmp_path, 'wb', &block)
        when String === content
          File.open(tmp_path, 'wb') do |f| f.write content end
        when (IO === content or StringIO === content or File === content)
          Open.write(tmp_path) do |f|
            while block = content.read(BLOCK_SIZE)
              f.write block
              break if content.closed?
            end
          end
        else
          File.open(tmp_path, 'wb') do |f|  end
        end

        begin
          Misc.insist do
            Open.mv tmp_path, path, lock_options
          end
        rescue Exception
          raise $! unless File.exist? path
        end

        Open.touch path if File.exist? path
        content.join if content.respond_to?(:join) and not Path === content and not (content.respond_to?(:joined?) && content.joined?)

        Open.notify_write(path)
      rescue Aborted
        Log.low "Aborted sensible_write -- #{ Log.reset << path }"
        content.abort if content.respond_to? :abort
        Open.rm path if File.exist? path
      rescue Exception
        exception = (AbortedStream === content and content.exception) ? content.exception : $!
        Log.low "Exception in sensible_write: [#{Process.pid}] #{exception.message} -- #{ path }"
        content.abort(exception) if content.respond_to? :abort
        Open.rm path if File.exist? path
        raise exception
      rescue
        raise $!
      ensure
        FileUtils.rm_f tmp_path if File.exist? tmp_path
        if Lockfile === lock_options[:lock] and lock_options[:lock].locked?
          lock_options[:lock].unlock
        end
      end
    end
  end
end

.sort_stream(stream, header_hash: "#", cmd_args: "-u", memory: false) ⇒ Object 



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# File 'lib/scout/open/stream.rb', line 406

def self.sort_stream(stream, header_hash: "#", cmd_args: "-u", memory: false)
  sout = Open.open_pipe do |sin|
    ConcurrentStream.process_stream(stream) do
      line = stream.gets
      while line && line.start_with?(header_hash) do
        sin.puts line
        line = stream.gets
      end

      line_stream = Open.open_pipe do |line_stream_in|
        line_stream_in.puts line if line
        Open.consume_stream(stream, false, line_stream_in)
      end
      Log.low "Sub-sort stream #{Log.fingerprint stream} -> #{Log.fingerprint line_stream}"

      if memory
        line_stream.read.split("\n").sort.each do |line|
          sin.puts line
        end
      else
        io = CMD.cmd("env LC_ALL=C sort #{cmd_args || ""}", :in => line_stream, :pipe => true)
        Open.consume_stream(io, false, sin)
      end
    end
  end
  Log.low "Sort #{Log.fingerprint stream} -> #{Log.fingerprint sout}"
  sout
end

.ssh(file, options = {}) ⇒ Object 



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# File 'lib/scout/open/remote.rb', line 22

def self.ssh(file, options = {})
  m = file.match(/ssh:\/\/([^:]+):(.*)/)
  server = m[1]
  file = m[2]
  if server == 'localhost'
    Open.open(file)
  else
    CMD.cmd("ssh '#{server}' cat '#{file}'", :pipe => true, :autojoin => true)
  end
end

.ssh?(file) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/scout/open/remote.rb', line 18

def self.ssh?(file)
  !! (file =~ /^ssh:\/\//)
end

.tee_stream(stream) ⇒ Object 



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# File 'lib/scout/open/stream.rb', line 373

def self.tee_stream(stream)
  tee_stream_thread(stream)
end

.tee_stream_thread(stream) ⇒ Object 



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# File 'lib/scout/open/stream.rb', line 369

def self.tee_stream_thread(stream)
  tee_stream_thread_multiple(stream, 2)
end

.tee_stream_thread_multiple(stream, num = 2) ⇒ Object 



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# File 'lib/scout/open/stream.rb', line 259

def self.tee_stream_thread_multiple(stream, num = 2)
  in_pipes = []
  out_pipes = []
  num.times do
    sout, sin = Open.pipe
    in_pipes << sin
    out_pipes << sout
  end

  Log.low("Tee stream #{Log.fingerprint stream} -> #{Log.fingerprint out_pipes}")

  filename = stream.filename if stream.respond_to? :filename

  splitter_thread = Thread.new(Thread.current) do |parent|
    begin
      Thread.current.report_on_exception = false
      Thread.current["name"] = "Splitter #{Log.fingerprint stream}"

      skip = [false] * num
      while block = stream.read(BLOCK_SIZE)

        in_pipes.each_with_index do |sin,i|
          begin
            sin.write block
          rescue IOError
            Log.warn("Tee stream #{i} #{Log.fingerprint stream} IOError: #{$!.message} (#{Log.fingerprint sin})");
            skip[i] = true
          rescue
            Log.warn("Tee stream #{i} #{Log.fingerprint stream} Exception: #{$!.message} (#{Log.fingerprint sin})");
            raise $!
          end unless skip[i]
        end
        break if stream.closed?
      end

      stream.join if stream.respond_to? :join
      in_pipes.first.close unless in_pipes.first.closed?
    rescue Aborted, Interrupt
      stream.abort if stream.respond_to?(:abort) && ! stream.aborted?
      out_pipes.reverse.each do |sout|
        sout.threads.delete(Thread.current)
        begin
          sout.abort($!) if sout.respond_to?(:abort) && ! sout.aborted?
        rescue
        end
      end
      in_pipes.each do |sin|
        sin.close unless sin.closed?
      end
      Log.low "Tee aborting #{Log.fingerprint stream}"
      raise $!
    rescue Exception
      begin
        stream.abort($!) if stream.respond_to?(:abort) && ! stream.aborted?
        out_pipes.reverse.each do |sout|
          sout.threads.delete(Thread.current)
          begin
            sout.abort($!) if sout.respond_to?(:abort) && ! sout.aborted?
          rescue
          end
        end
        in_pipes.each do |sin|
          sin.close unless sin.closed?
        end
        Log.low "Tee exception #{Log.fingerprint stream}"
      rescue
      ensure
        begin
          in_pipes.each do |sin|
            sin.close unless sin.closed?
          end
        ensure
          raise $!
        end
      end
    end
  end

  Thread.pass until splitter_thread["name"]

  main_pipe = out_pipes.first

  ConcurrentStream.setup(main_pipe, :threads => [splitter_thread], :filename => filename, :autojoin => true)

  out_pipes[1..-1].each do |sout|
    ConcurrentStream.setup sout, :filename => filename, :threads => [splitter_thread]
  end

  main_pipe.callback = proc do
    begin
      stream.join if stream.respond_to?(:join) && ! stream.joined?
      in_pipes[1..-1].each do |sin|
        sin.close unless sin.closed?
      end
    rescue
      main_pipe.abort_callback.call($!)
      raise $!
    end
  end

  main_pipe.abort_callback = proc do |exception|
    stream.abort(exception)
    out_pipes[1..-1].each do |sout|
      sout.abort(exception)
    end
  end

  out_pipes
end

.touch(file) ⇒ Object 



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# File 'lib/scout/open/util.rb', line 139

def self.touch(file)
  FileUtils.touch(file)
end

.unzip(stream) ⇒ Object 



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# File 'lib/scout/open/util.rb', line 49

def self.unzip(stream)
  TmpFile.with_file(stream.read) do |filename|
    StringIO.new(CMD.cmd("unzip '{opt}' #{filename}", "-p" => true, :pipe => true).read)
  end
end

.wget(url, options = {}) ⇒ Object 



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# File 'lib/scout/open/remote.rb', line 33

def self.wget(url, options = {})
  options = options[:wget_options] if options.include?(:wget_options)
  if ! (options[:force] || options[:nocache]) && cache_file = in_cache(url, options)
    return file_open(cache_file)
  end

  Log.low "WGET:\n -URL: #{ url }\n -OPTIONS: #{options.inspect}"
  options = IndiferentHash.add_defaults options, "--user-agent=" => 'rbbt', :pipe => true, :autojoin => true

  wait(options[:nice], options[:nice_key]) if options[:nice]
  options.delete(:nice)
  options.delete(:nice_key)

  pipe  = options.delete(:pipe)
  quiet = options.delete(:quiet)
  post  = options.delete(:post)
  cookies = options.delete(:cookies)
  nocache = options.delete(:nocache)

  options["--quiet"]     = quiet if options["--quiet"].nil?
  options["--post-data="] ||= post if post

  if cookies
    options["--save-cookies"] = cookies
    options["--load-cookies"] = cookies
    options["--keep-session-cookies"] = true
  end

  stderr = case
           when options['stderr']
             options['stderr'] 
           when options['--quiet']
             false
           else
             nil
           end

  begin
    wget_options = options.dup
    wget_options = wget_options.merge( '-O' => '-') unless options.include?('--output-document')
    wget_options[:pipe] = pipe unless pipe.nil?
    wget_options[:stderr] = stderr unless stderr.nil?

    io = CMD.cmd("wget '#{ url }'", wget_options)
    if nocache && nocache.to_s != 'update'
      io
    else
      add_cache(url, io, options)
      open_cache(url, options)
    end
  rescue
   STDERR.puts $!.backtrace.inspect
   raise OpenURLError, "Error reading remote url: #{ url }.\n#{$!.message}"
  end
end

.with_fifo(path = nil, clean = true, &block) ⇒ Object 



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# File 'lib/scout/open/stream.rb', line 181

def self.with_fifo(path = nil, clean = true, &block)
  begin
    erase = path.nil?
    path = TmpFile.tmp_file if path.nil?
    File.rm path if clean && File.exist?(path)
    File.mkfifo path
    yield path
  ensure
    FileUtils.rm path if erase && File.exist?(path)
  end
end

.writable?(path) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/scout/open/util.rb', line 150

def self.writable?(path)
  path = path.find if Path === path
  if File.symlink?(path)
    File.writable?(File.dirname(path))
  elsif File.exist?(path)
    File.writable?(path)
  else
    File.writable?(File.dirname(File.expand_path(path)))
  end
end

.write(file, content = nil, options = {}) ⇒ Object 



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# File 'lib/scout/open.rb', line 124

def self.write(file, content = nil, options = {})
  options = IndiferentHash.add_defaults options, :mode => 'w'

  file = file.find(options[:where]) if Path === file
  mode = IndiferentHash.process_options options, :mode

  FileUtils.mkdir_p File.dirname(file)

  case
  when block_given?
    begin
      f = File.open(file, mode)
      begin
        yield f
      ensure
        f.close unless f.closed?
      end
    rescue Exception
      FileUtils.rm file if File.exist? file
      raise $!
    end
  when content.nil?
    file_write(file, "", mode)
  when String === content
    file_write(file, content, mode)
  when (IO === content || StringIO === content)
    begin
      File.open(file, mode) do |f| 
        f.flock(File::LOCK_EX)
        while block = content.read(Open::BLOCK_SIZE)
          f.write block
        end
        f.flock(File::LOCK_UN)
      end
    rescue Exception
      FileUtils.rm_rf file if File.exist? file
      raise $!
    end
    content.close unless content.closed?
    content.join if content.respond_to? :join
  else
    raise "Content unknown #{Log.fingerprint content}"
  end

  notify_write(file)
end

.yaml(file) ⇒ Object 



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# File 'lib/scout/persist/open.rb', line 10

def self.yaml(file)
  Open.open(file){|f| YAML.load(f) }
end

.zip?(file) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/scout/open/util.rb', line 66

def self.zip?(file)
  file = file.find if Path === file
  !! (file =~ /\.zip$/)
end