Class: Step

Inherits:
Object
  • Object
show all
Defined in:
lib/rbbt/workflow/step.rb,
lib/rbbt/workflow/accessor.rb,
lib/rbbt/workflow/step/run.rb

Constant Summary collapse

INFO_SERIALIAZER = 
Marshal
STREAM_CACHE = 
{}
STREAM_CACHE_MUTEX = 
Mutex.new

Class Attribute Summary collapse

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(path, task = nil, inputs = nil, dependencies = nil, bindings = nil, clean_name = nil) ⇒ Step

Returns a new instance of Step.



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# File 'lib/rbbt/workflow/step.rb', line 31

def initialize(path, task = nil, inputs = nil, dependencies = nil, bindings = nil, clean_name = nil)
  path = Path.setup(Misc.sanitize_filename(path)) if String === path
  path = path.call if Proc === path

  @path = path
  @task = task
  @bindings = bindings
  @dependencies = case
                  when dependencies.nil? 
                    []
                  when Array === dependencies
                    dependencies
                  else
                    [dependencies]
                  end
  @mutex = Mutex.new
  @info_mutex = Mutex.new
  @inputs = inputs || []
  NamedArray.setup @inputs, task.inputs.collect{|s| s.to_s} if task and task.respond_to? :inputs and task.inputs
end

Class Attribute Details

.lock_dir ⇒ Object

Returns the value of attribute lock_dir.



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# File 'lib/rbbt/workflow/step.rb', line 14

def lock_dir
  @lock_dir
end

.log_relay_step ⇒ Object

Returns the value of attribute log_relay_step.



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# File 'lib/rbbt/workflow/step.rb', line 74

def log_relay_step
  @log_relay_step
end

Instance Attribute Details

#bindings ⇒ Object

Returns the value of attribute bindings.



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# File 'lib/rbbt/workflow/step.rb', line 8

def bindings
  @bindings
end

#clean_name ⇒ Object

Returns the value of attribute clean_name.



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# File 'lib/rbbt/workflow/step.rb', line 8

def clean_name
  @clean_name
end

#dependencies ⇒ Object

Returns the value of attribute dependencies.



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# File 'lib/rbbt/workflow/step.rb', line 8

def dependencies
  @dependencies
end

#dupped ⇒ Object (readonly)

Returns the value of attribute dupped.



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# File 'lib/rbbt/workflow/step/run.rb', line 3

def dupped
  @dupped
end

#exec(no_load = false) ⇒ Object

Returns the value of attribute exec.



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# File 'lib/rbbt/workflow/step.rb', line 10

def exec
  @exec
end

#inputs ⇒ Object

Returns the value of attribute inputs.



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# File 'lib/rbbt/workflow/step.rb', line 8

def inputs
  @inputs
end

#mutex ⇒ Object

Returns the value of attribute mutex.



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# File 'lib/rbbt/workflow/step.rb', line 11

def mutex
  @mutex
end

#path ⇒ Object

Returns the value of attribute path.



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# File 'lib/rbbt/workflow/step.rb', line 8

def path
  @path
end

#pid ⇒ Object

Returns the value of attribute pid.



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# File 'lib/rbbt/workflow/step.rb', line 9

def pid
  @pid
end

#result ⇒ Object

Returns the value of attribute result.



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# File 'lib/rbbt/workflow/step.rb', line 11

def result
  @result
end

#saved_stream ⇒ Object (readonly)

Returns the value of attribute saved_stream.



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# File 'lib/rbbt/workflow/step/run.rb', line 3

def saved_stream
  @saved_stream
end

#seen ⇒ Object

Returns the value of attribute seen.



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# File 'lib/rbbt/workflow/step.rb', line 11

def seen
  @seen
end

#stream ⇒ Object (readonly)

Returns the value of attribute stream.



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# File 'lib/rbbt/workflow/step/run.rb', line 3

def stream
  @stream
end

#task ⇒ Object

Returns the value of attribute task.



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# File 'lib/rbbt/workflow/step.rb', line 8

def task
  @task
end

Class Method Details

.clean(path) ⇒ Object 



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# File 'lib/rbbt/workflow/step.rb', line 158

def self.clean(path)
  info_file = Step.info_file path
  files_dir = Step.files_dir path
  if Open.exists?(path) or Open.exists?(info_file)
    begin
      self.abort if self.running?
    rescue Exception
    end

    @result = nil
    @pid = nil

    Misc.insist do
      Open.rm info_file if Open.exists? info_file
      Open.rm info_file + '.lock' if Open.exists? info_file + '.lock'
      Open.rm path if Open.exists? path
      Open.rm path + '.lock' if Open.exists? path + '.lock'
      Open.rm_rf files_dir if Open.exists? files_dir
    end
  end
end

.dup_stream(stream) ⇒ Object 



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# File 'lib/rbbt/workflow/step/run.rb', line 7

def self.dup_stream(stream)
  case stream
  when IO, File
    return stream if stream.closed?

    STREAM_CACHE_MUTEX.synchronize do
      case current = STREAM_CACHE[stream]
      when nil
        Log.medium "Not duplicating stream #{ Misc.fingerprint(stream) }"
        STREAM_CACHE[stream] = stream
      when File
        if Open.exists? current.path 
          Log.medium "Reopening file #{ Misc.fingerprint(current) }"
          Open.open(current.path)
        else
          Log.medium "Duplicating file #{ Misc.fingerprint(current) } #{current.inspect}"
          Misc.dup_stream(current)
        end

      else
        Log.medium "Duplicating stream #{ Misc.fingerprint(stream) }"
        Misc.dup_stream(current)
      end
    end
  when TSV::Dumper#, TSV::Parser
    stream = stream.stream
    return stream if stream.closed?

    STREAM_CACHE_MUTEX.synchronize do
      if STREAM_CACHE[stream].nil?
        Log.high "Not duplicating dumper #{ stream.inspect }"
        STREAM_CACHE[stream] = stream
      else
        new = Misc.dup_stream(STREAM_CACHE[stream])
        Log.high "Duplicating dumper #{ stream.inspect } into #{new.inspect}"
        new
      end
    end
  else
    stream
  end
end

.files_dir(path) ⇒ Object 



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# File 'lib/rbbt/workflow/accessor.rb', line 26

def self.files_dir(path)
  path.nil? ? nil : path + '.files'
end

.info_file(path) ⇒ Object 



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# File 'lib/rbbt/workflow/accessor.rb', line 30

def self.info_file(path)
  path.nil? ? nil : path + '.info'
end

.job_name_for_info_file(info_file, extension = nil) ⇒ Object 



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# File 'lib/rbbt/workflow/accessor.rb', line 45

def self.job_name_for_info_file(info_file, extension = nil)
  if extension and not extension.empty?
    info_file.sub(/\.#{extension}\.info$/,'')
  else
    info_file.sub(/\.info$/,'')
  end
end

.log(status, message, path, &block) ⇒ Object 



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# File 'lib/rbbt/workflow/accessor.rb', line 225

def self.log(status, message, path, &block)
  if block
    if Hash === message
      log_progress(status, message, path, &block)
    else
      log_block(status, message, path, &block)
    end
  else
    log_string(status, message, path)
  end
end

.log_block(staus, message, path, &block) ⇒ Object 



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# File 'lib/rbbt/workflow/accessor.rb', line 170

def self.log_block(staus, message, path, &block)
  start = Time.now
  status = status.to_s
  status_color = self.status_color status

  Log.info do 
    now = Time.now
    str = Log.color :reset
    str << "#{ Log.color status_color, status}"
    str << ": #{ message }" if message
    str << " -- #{Log.color :blue, path.to_s}" if path
    str << " #{Log.color :yellow, Process.pid}"
    str
  end
  res = yield
  eend = Time.now
  Log.info do 
    now = Time.now
    str = "#{ Log.color :cyan, status.to_s } +#{Log.color :green, "%.1g" % (eend - start)}"
    str << " -- #{Log.color :blue, path.to_s}" if path
    str << " #{Log.color :yellow, Process.pid}"
    str
  end
  res
end

.log_progress(status, options, path, &block) ⇒ Object 



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# File 'lib/rbbt/workflow/accessor.rb', line 211

def self.log_progress(status, options, path, &block)
  options = Misc.add_defaults options, :severity => Log::INFO
  max = Misc.process_options options, :max
  Log::ProgressBar.with_bar(max, options) do |bar|
    begin
      res = yield bar
      raise KeepBar.new res if IO === res
      res
    rescue
      Log.exception $!
    end
  end
end

.log_string(status, message, path) ⇒ Object 



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# File 'lib/rbbt/workflow/accessor.rb', line 196

def self.log_string(status, message, path)
  Log.info do 

    status = status.to_s
    status_color = self.status_color status

    str = Log.color :reset
    str << "#{ Log.color status_color, status}"
    str << ": #{ message }" if message
    str << " -- #{Log.color :blue, path.to_s}" if path
    str << " #{Log.color :yellow, Process.pid}"
    str
  end
end

.purge_stream_cache ⇒ Object 



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# File 'lib/rbbt/workflow/step/run.rb', line 50

def self.purge_stream_cache
  return
  STREAM_CACHE_MUTEX.synchronize do
    STREAM_CACHE.collect{|k,s| 
      Thread.new do
        Misc.consume_stream s
      end
    }
    STREAM_CACHE.clear
  end
end

.started? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rbbt/workflow/accessor.rb', line 9

def self.started?
  info_file.exists?
end

.status_color(status) ⇒ Object 



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# File 'lib/rbbt/workflow/accessor.rb', line 156

def self.status_color(status)
  status = status.split(">").last
  case status
  when "starting"
    :yellow
  when "error", "aborted"
    :red
  when "done"
    :green
  else
    :cyan
  end
end

.step_info(path) ⇒ Object 



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# File 'lib/rbbt/workflow/accessor.rb', line 34

def self.step_info(path)
  begin
    Open.open(info_file(path)) do |f|
      INFO_SERIALIAZER.load(f)
    end
  rescue Exception
    Log.exception $!
    {}
  end
end

.wait_for_jobs(jobs) ⇒ Object 



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# File 'lib/rbbt/workflow/accessor.rb', line 13

def self.wait_for_jobs(jobs)
  jobs = [jobs] if Step === jobs
  begin
    threads = []
    jobs.each do |j| threads << Thread.new{j.join} end
    threads.each{|t| t.join }
  rescue Exception
    threads.each{|t| t.exit }
    jobs.each do |j| j.abort end
    raise $!
  end
end

Instance Method Details

#_abort ⇒ Object 



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# File 'lib/rbbt/workflow/step/run.rb', line 375

def _abort
  return if @aborted
  @aborted = true
  return if done?
  Log.medium{"#{Log.color :red, "Aborting"} #{Log.color :blue, path}"}
  begin
    stop_dependencies
    abort_stream
    abort_pid
  rescue Aborted
    Log.medium{"#{Log.color :red, "Aborting ABORTED RETRY"} #{Log.color :blue, path}"}
    retry
  rescue Exception
    retry
  ensure
    if Open.exists? path
      Log.warn "Aborted job had finished. Removing result -- #{ path }"
      begin
        Open.rm path
      rescue Exception
        Log.warn "Exception removing result of aborted job: #{$!.message}"
      end
    end
  end
  Log.medium{"#{Log.color :red, "Aborted"} #{Log.color :blue, path}"}
end

#_exec ⇒ Object 



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# File 'lib/rbbt/workflow/step/run.rb', line 83

def _exec
  @exec = true if @exec.nil?
  @task.exec_in((bindings ? bindings : self), *@inputs)
end

#abort ⇒ Object 



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# File 'lib/rbbt/workflow/step/run.rb', line 402

def abort
  _abort
  log(:aborted, "Job aborted") unless aborted? or error?
end

#abort_pid ⇒ Object 



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# File 'lib/rbbt/workflow/step/run.rb', line 336

def abort_pid
  @pid ||= info[:pid]

  case @pid
  when nil
    Log.medium "Could not abort #{path}: no pid"
    false
  when Process.pid
    Log.medium "Could not abort #{path}: same process"
    false
  else
    Log.medium "Aborting #{path}: #{ @pid }"
    begin
      Process.kill("KILL", @pid)
      Process.waitpid @pid
    rescue Exception
      Log.debug("Aborted job #{@pid} was not killed: #{$!.message}")
    end
    true
  end
end

#abort_stream ⇒ Object 



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# File 'lib/rbbt/workflow/step/run.rb', line 358

def abort_stream
  stream = get_stream if @result
  stream ||= @saved_stream 
  @saved_stream = nil
  if stream and stream.respond_to? :abort and not stream.aborted?
    begin
      Log.medium "Aborting job stream #{stream.inspect} -- #{Log.color :blue, path}"
      stream.abort 
      #stream.close unless stream.closed?
    rescue Aborted
      Log.medium "Aborting job stream #{stream.inspect} ABORTED RETRY -- #{Log.color :blue, path}"
      Log.exception $!
      retry
    end
  end
end

#aborted? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rbbt/workflow/accessor.rb', line 279

def aborted?
  @aborted || status == :aborted
end

#checks ⇒ Object 



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# File 'lib/rbbt/workflow/step/run.rb', line 98

def checks
  rec_dependencies.collect{|dependency| dependency.path }.uniq
end

#child(&block) ⇒ Object 



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# File 'lib/rbbt/workflow/step.rb', line 137

def child(&block)
  child_pid = Process.fork &block
  children_pids = info[:children_pids]
  if children_pids.nil?
    children_pids = [child_pid]
  else
    children_pids << child_pid
  end
  #Process.detach(child_pid)
  set_info :children_pids, children_pids
  child_pid
end

#clean ⇒ Object 



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# File 'lib/rbbt/workflow/step.rb', line 180

def clean
  Step.clean(path)
  self
end

#done? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rbbt/workflow/accessor.rb', line 259

def done?
  path and File.exists? path
end

#dup_inputs ⇒ Object 



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# File 'lib/rbbt/workflow/step/run.rb', line 75

def dup_inputs
  return if @dupped or ENV["RBBT_NO_STREAM"] == 'true'
  @inputs = @inputs.collect do |input|
    Step.dup_stream input
  end
  @dupped = true
end

#error? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rbbt/workflow/accessor.rb', line 275

def error?
  status == :error
end

#exception(ex, msg = nil) ⇒ Object 



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# File 'lib/rbbt/workflow/accessor.rb', line 243

def exception(ex, msg = nil)
  self._abort
  ex_class = ex.class.to_s
  set_info :backtrace, ex.backtrace
  set_info :exception, {:class => ex_class, :message => ex.message, :backtrace => ex.backtrace}
  if msg.nil?
    log :error, "#{ex_class} -- #{ex.message}"
  else
    log :error, "#{msg} -- #{ex.message}"
  end
end

#file(name) ⇒ Object 



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# File 'lib/rbbt/workflow/accessor.rb', line 296

def file(name)
  Path.setup(File.join(files_dir, name.to_s))
end

#files ⇒ Object 



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# File 'lib/rbbt/workflow/accessor.rb', line 289

def files
  files = Dir.glob(File.join(files_dir, '**', '*')).reject{|path| File.directory? path}.collect do |path| 
    Misc.path_relative_to(files_dir, path) 
  end
  files
end

#files_dir ⇒ Object

{{{ INFO



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# File 'lib/rbbt/workflow/accessor.rb', line 285

def files_dir
  @files_dir ||= Step.files_dir path
end

#fork(semaphore = nil) ⇒ Object 



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# File 'lib/rbbt/workflow/step/run.rb', line 279

def fork(semaphore = nil)
  raise "Can not fork: Step is waiting for proces #{@pid} to finish" if not @pid.nil? and not Process.pid == @pid and Misc.pid_exists?(@pid) and not done? and info[:forked]
  @pid = Process.fork do
    Misc.pre_fork
    begin
      RbbtSemaphore.wait_semaphore(semaphore) if semaphore
      FileUtils.mkdir_p File.dirname(path) unless File.exists? File.dirname(path)
      begin
        res = run true
        set_info :forked, true
      rescue Aborted
        Log.debug{"Forked process aborted: #{path}"}
        log :aborted, "Job aborted (#{Process.pid})"
        raise $!
      rescue Exception
        Log.debug("Exception '#{$!.message}' caught on forked process: #{path}")
        raise $!
      ensure
        join_stream
      end

      begin
        children_pids = info[:children_pids]
        if children_pids
          children_pids.each do |pid|
            if Misc.pid_exists? pid
              begin
                Process.waitpid pid
              rescue Errno::ECHILD
                Log.low "Waiting on #{ pid } failed: #{$!.message}"
              end
            end
          end
          set_info :children_done, Time.now
        end
      rescue Exception
        Log.debug("Exception waiting for children: #{$!.message}")
        RbbtSemaphore.post_semaphore(semaphore) if semaphore
        Kernel.exit! -1
      end
      set_info :pid, nil
    ensure
      RbbtSemaphore.post_semaphore(semaphore) if semaphore
      Kernel.exit! 0
    end
  end
  Process.detach(@pid)
  self
end

#get_stream ⇒ Object 



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# File 'lib/rbbt/workflow/step/run.rb', line 62

def get_stream
  @mutex.synchronize do
    begin
      return nil if @saved_stream
      if IO === @result 
        @saved_stream = @result 
      else 
        nil
      end
    end
  end
end

#grace ⇒ Object 



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# File 'lib/rbbt/workflow/step/run.rb', line 421

def grace
  until done? or result or error? or aborted? or streaming? 
    sleep 1 
  end
  self
end

#info(check_lock = true) ⇒ Object 



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# File 'lib/rbbt/workflow/accessor.rb', line 74

def info(check_lock = true)
  return {} if info_file.nil? or not Open.exists? info_file
  begin
    begin
      return @info_cache if @info_cache and File.ctime(info_file) < @info_cache_time
    rescue Exception
      raise $!
    end

    begin
      @info_cache = Misc.insist(2, 3, info_file) do
        Misc.insist(2, 1, info_file) do
          Misc.insist(3, 0.2, info_file) do
            raise TryAgain, "Info locked" if check_lock and info_lock.locked?
            Open.open(info_file) do |file|
              INFO_SERIALIAZER.load(file) #|| {}
            end
          end
        end
      end
      @info_cache_time = Time.now
      @info_cache
    end
  rescue Exception
    Log.debug{"Error loading info file: " + info_file}
    Log.exception $!
    Open.sensiblewrite(info_file, INFO_SERIALIAZER.dump({:status => :error, :messages => ["Info file lost"]}))
    raise $!
  end
end

#info_file ⇒ Object

{{{ INFO



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# File 'lib/rbbt/workflow/accessor.rb', line 63

def info_file
  @info_file ||= Step.info_file(path)
end

#info_lock ⇒ Object 



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# File 'lib/rbbt/workflow/accessor.rb', line 67

def info_lock
  @info_lock ||= begin
                   path = Persist.persistence_path(info_file + '.lock', {:dir => Step.lock_dir})
                   Lockfile.new path
                 end
end

#join ⇒ Object 



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# File 'lib/rbbt/workflow/step/run.rb', line 428

def join

  grace

  join_stream if status.to_s == "streaming"

  return self if not Open.exists? info_file

  return self if info[:joined]
  pid = @pid 

  Misc.insist [0.1, 0.2, 0.5, 1] do
    pid ||= info[:pid]
  end

  begin
    if pid.nil? or Process.pid == pid
      dependencies.each{|dep| dep.join }
    else
      begin
        Log.debug{"Waiting for pid: #{pid}"}
        Process.waitpid pid 
      rescue Errno::ECHILD
        Log.debug{"Process #{ pid } already finished: #{ path }"}
      end if Misc.pid_exists? pid
      pid = nil
      dependencies.each{|dep| dep.join }
    end
    sleep 1 until path.exists?
    self
  ensure
    set_info :joined, true
  end
end

#join_stream ⇒ Object 



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# File 'lib/rbbt/workflow/step/run.rb', line 407

def join_stream
  stream = get_stream if @result
  if stream
    begin
      Misc.consume_stream stream 
      stream.join if stream.respond_to? :join
    rescue Exception
      stream.abort
      self._abort
      raise $!
    end
  end
end

#kill_children ⇒ Object 



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# File 'lib/rbbt/workflow/step/run.rb', line 102

def kill_children
  begin
    children_pids = info[:children_pids]
    if children_pids and children_pids.any?
      Log.medium("Killing children: #{ children_pids * ", " }")
      children_pids.each do |pid|
        Log.medium("Killing child #{ pid }")
        begin
          Process.kill "INT", pid
        rescue Exception
          Log.medium("Exception killing child #{ pid }: #{$!.message}")
        end
      end
    end
  rescue
    Log.medium("Exception finding children")
  end
end

#load ⇒ Object 



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# File 'lib/rbbt/workflow/step.rb', line 151

def load
  return prepare_result @result, @task.result_description if @result and not @path == @result
  join if not done?
  return Persist.load_file(@path, @task.result_type) if @path.exists?
  exec
end

#load_file(name, type = nil, options = {}) ⇒ Object 



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# File 'lib/rbbt/workflow/accessor.rb', line 316

def load_file(name, type = nil, options = {})
  if type.nil? and name =~ /.*\.(\w+)$/
    extension = name.match(/.*\.(\w+)$/)[1]
    case extension
    when "tc"
      type = :tc
    when "tsv"
      type = :tsv
    when "list", "ary", "array"
      type = :array
    when "yaml"
      type = :yaml
    when "marshal"
      type = :marshal
    else
      type = :other
    end
  else
    type ||= :other
  end

  case type.to_sym
  when :tc
    Persist.open_tokyocabinet(file(name), false)
  when :tsv
    TSV.open Open.open(file(name)), options
  when :array
    #Open.read(file(name)).split /\n|,\s*/
    Open.read(file(name)).split "\n"
  when :yaml
    YAML.load(Open.open(file(name)))
  when :marshal
    Marshal.load(Open.open(file(name)))
  else
    Open.read(file(name))
  end
end

#log(status, message = nil, &block) ⇒ Object 



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# File 'lib/rbbt/workflow/accessor.rb', line 237

def log(status, message = nil, &block)
  self.status = status
  self.message Log.uncolor(message)
  Step.log(status, message, path, &block)
end

#merge_info(hash) ⇒ Object 



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# File 'lib/rbbt/workflow/accessor.rb', line 118

def merge_info(hash)
  return nil if @exec or info_file.nil?
  value = Annotated.purge value if defined? Annotated
  Open.lock(info_file, :lock => info_lock) do
    i = info(false)
    i.merge! hash
    @info_cache = i
    Misc.sensiblewrite(info_file, INFO_SERIALIAZER.dump(i), :force => true)
    @info_cache_time = Time.now
    value
  end
end

#message(message) ⇒ Object 



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# File 'lib/rbbt/workflow/accessor.rb', line 152

def message(message)
  set_info(:messages, (messages || []) << message)
end

#messages ⇒ Object 



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# File 'lib/rbbt/workflow/accessor.rb', line 144

def messages
  if messages = info[:messages]
    messages
  else
    set_info(:messages, []) if self.respond_to?(:set_info)
  end
end

#name ⇒ Object 



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# File 'lib/rbbt/workflow/accessor.rb', line 53

def name
  path.sub(/.*\/#{Regexp.quote task.name.to_s}\/(.*)/, '\1')
end

#prepare_result(value, description = nil, info = {}) ⇒ Object 



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# File 'lib/rbbt/workflow/step.rb', line 94

def prepare_result(value, description = nil, info = {})
  case 
  when IO === value
    begin
      res = case @task.result_type
            when :array
              array = []
              while line = value.gets
                array << line.strip
              end
              array
            when :tsv
              begin
                TSV.open(value)
              rescue IOError
                TSV.setup({})
              end
            else
              value.read
            end
      value.join if value.respond_to? :join
      res
    rescue Exception
      value.abort if value.respond_to? :abort
      self.abort
      raise $!
    end
  when (not defined? Entity or description.nil? or not Entity.formats.include? description)
    value
  when (Annotated === value and info.empty?)
    value
  when Annotated === value
    annotations = value.annotations
    info.each do |k,v|
      value.send("#{h}=", v) if annotations.include? k
    end
    value
  else
    Entity.formats[description].setup(value, info.merge(:format => description))
  end
end

#provenance ⇒ Object 



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# File 'lib/rbbt/workflow/accessor.rb', line 354

def provenance
  provenance = {}
  dependencies.each do |dep|
    next unless dep.path.exists?
    if File.exists? dep.info_file
      provenance[dep.path] = dep.provenance if File.exists? dep.path
    else
      provenance[dep.path] = nil
    end
  end
  {:inputs => info[:inputs], :provenance => provenance}
end

#provenance_paths ⇒ Object 



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# File 'lib/rbbt/workflow/accessor.rb', line 367

def provenance_paths
  provenance = {}
  dependencies.each do |dep|
    provenance[dep.path] = dep.provenance_paths if File.exists? dep.path
  end
  provenance
end

#rec_dependencies ⇒ Object 



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# File 'lib/rbbt/workflow/step.rb', line 185

def rec_dependencies

  # A step result with no info_file means that it was manually
  # placed. In that case, do not consider its dependencies
  return [] if Open.exists?(self.path.to_s) and not Open.exists? self.info_file

  return [] if dependencies.nil? or dependencies.empty?
  new_dependencies = dependencies.collect{|step| 
    step.rec_dependencies 
  }.flatten.uniq.compact

  dependencies = self.dependencies ? self.dependencies + new_dependencies : new_dependencies
  dependencies.flatten!
  dependencies.uniq!
  dependencies
end

#recursive_clean ⇒ Object 



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# File 'lib/rbbt/workflow/step.rb', line 202

def recursive_clean
  clean
  rec_dependencies.each do |step| 
    if Open.exists?(step.info_file) 
      step.clean 
    else
    end
  end
  self
end

#relay_log(step) ⇒ Object 



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# File 'lib/rbbt/workflow/step.rb', line 77

def relay_log(step)
  return self unless Task === self.task and not self.task.name.nil?
  if not self.respond_to? :original_log
    class << self
      attr_accessor :relay_step
      alias original_log log 
      def log(status, message = nil)
        self.status = status
        message Log.uncolor message
        relay_step.log([task.name.to_s, status.to_s] * ">", message.nil? ? nil : message ) unless (relay_step.done? or relay_step.error? or relay_step.aborted?)
      end
    end
  end
  @relay_step = step
  self
end

#run(no_load = false) ⇒ Object 



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# File 'lib/rbbt/workflow/step/run.rb', line 165

def run(no_load = false)
  result = nil

  begin
    @mutex.synchronize do
      no_load = no_load ? :stream : false
      result = Persist.persist "Job", @task.result_type, :file => path, :check => checks, :no_load => no_load do |lockfile|
        if Step === Step.log_relay_step and not self == Step.log_relay_step
          relay_log(Step.log_relay_step) unless self.respond_to? :relay_step and self.relay_step
        end
        @exec = false

        Open.rm info_file if Open.exists? info_file

        log :setup, "#{Log.color :cyan, "Setup"} #{Log.color :yellow, task.name.to_s || ""}"

        merge_info({
          :pid => Process.pid,
          :issued => Time.now,
          :name => name,
          :clean_name => clean_name,
          :dependencies => dependencies.collect{|dep| [dep.task_name, dep.name, dep.path]},
        })

        dup_inputs
        begin
          run_dependencies
        rescue Exception
          stop_dependencies
          raise $!
        end


        set_info :inputs, Misc.remove_long_items(Misc.zip2hash(task.inputs, @inputs)) unless task.inputs.nil?

        set_info :started, (start_time = Time.now)
        log :started, "#{Log.color :magenta, "Starting"} #{Log.color :yellow, task.name.to_s || ""}"

        begin
          result = _exec
        rescue Aborted
          stop_dependencies
          log(:aborted, "Aborted")
          raise $!
        rescue Exception
          backtrace = $!.backtrace

          # HACK: This fixes an strange behaviour in 1.9.3 where some
          # backtrace strings are coded in ASCII-8BIT
          set_info :backtrace, backtrace 
          log(:error, "#{$!.class}: #{$!.message}")
          backtrace.each{|l| l.force_encoding("UTF-8")} if String.instance_methods.include? :force_encoding
          stop_dependencies
          raise $!
        end

        if not no_load or ENV["RBBT_NO_STREAM"] == "true" 
          result = prepare_result result, @task.description, info if IO === result 
          result = prepare_result result.stream, @task.description, info if TSV::Dumper === result 
        end

        stream = case result
                 when IO
                   result
                 when TSV::Dumper
                   result.stream
                 end

        if stream
          log :streaming, "#{Log.color :magenta, "Streaming"} #{Log.color :yellow, task.name.to_s || ""}"
          ConcurrentStream.setup stream do
            begin
              if status != :done
                Misc.insist do
                  set_info :done, (done_time = Time.now)
                  set_info :time_elapsed, (time_elapsed = done_time - start_time)
                  log :done, "#{Log.color :magenta, "Completed"} #{Log.color :yellow, task.name.to_s || ""} in #{time_elapsed.to_i} sec."
                end
              end
            rescue
              Log.exception $!
            ensure
              join
            end
          end
          stream.abort_callback = Proc.new do
            begin
              log :aborted, "#{Log.color :red, "Aborted"} #{Log.color :yellow, task.name.to_s || ""}" if status == :streaming
            rescue
              Log.exception $!
            end
          end
        else
          set_info :done, (done_time = Time.now)
          set_info :time_elapsed, (time_elapsed = done_time - start_time)
          log :done, "#{Log.color :magenta, "Completed"} #{Log.color :yellow, task.name.to_s || ""} in #{time_elapsed.to_i} sec."
        end

        result
      end

      if no_load
        @result ||= result
        self
      else
        @result = prepare_result result, @task.result_description
      end
    end
  rescue Exception
    exception $!
    raise $!
  end
end

#run_dependencies ⇒ Object 



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# File 'lib/rbbt/workflow/step/run.rb', line 121

def run_dependencies
  @seen ||= []
  dependencies.uniq.each do |dependency| 
    next if seen.collect{|d| d.path}.include?(dependency.path)
    dependency.seen = seen
    @seen.concat dependency.rec_dependencies.collect{|d| d } 
    @seen << dependency
    @seen.uniq!
  end

  @seen.each do |dependency|
    next if dependency == self
    next unless dependencies.include? dependency
    dependency.dup_inputs
  end

  @seen.each do |dependency| 
    next if dependency == self
    next unless dependencies.include? dependency
    Log.info "#{Log.color :cyan, "dependency"} #{Log.color :yellow, task.name.to_s || ""} => #{Log.color :yellow, dependency.task_name.to_s || ""} -- #{Log.color :blue, dependency.path}"
    begin
      if dependency.streaming? 
        next if dependency.running?
        dependency.clean 
      else
        dependency.clean if (dependency.error? or dependency.aborted? or dependency.status.nil? or not (dependency.done? or dependency.running?))
      end

      unless dependency.started? 
        dependency.run(true)
      end
    rescue Aborted
      Log.error "Aborted dep. #{Log.color :red, dependency.task.name.to_s}"
      raise $!
    rescue Interrupt
      Log.error "Interrupted while in dep. #{Log.color :red, dependency.task.name.to_s}"
      raise $!
    rescue Exception
      Log.error "Exception in dep. #{ Log.color :red, dependency.task.name.to_s }"
      raise $!
    end
  end
end

#running? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rbbt/workflow/accessor.rb', line 267

def running?
  return nil if not Open.exists? info_file
  return nil if info[:pid].nil?

  pid = @pid || info[:pid]
  return Misc.pid_exists?(pid) 
end

#save_file(name, content) ⇒ Object 



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# File 'lib/rbbt/workflow/accessor.rb', line 300

def save_file(name, content)
  content = case
            when String === content
              content
            when Array === content
              content * "\n"
            when TSV === content
              content.to_s
            when Hash === content
              content.collect{|*p| p * "\t"} * "\n"
            else
              content.to_s
            end
  Open.write(file(name), content)
end

#set_info(key, value) ⇒ Object 



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# File 'lib/rbbt/workflow/accessor.rb', line 105

def set_info(key, value)
  return nil if @exec or info_file.nil?
  value = Annotated.purge value if defined? Annotated
  Open.lock(info_file, :lock => info_lock) do
    i = info(false)
    i[key] = value 
    @info_cache = i
    Misc.sensiblewrite(info_file, INFO_SERIALIAZER.dump(i), :force => true, :lock => false)
    @info_cache_time = Time.now
    value
  end
end

#started? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rbbt/workflow/accessor.rb', line 255

def started?
  Open.exists? info_file or Open.exists? path
end

#status ⇒ Object 



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# File 'lib/rbbt/workflow/accessor.rb', line 131

def status
  begin
    info[:status]
  rescue Exception
    Log.error "Exception reading status: #{$!.message}" 
    :error
  end
end

#status=(status) ⇒ Object 



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# File 'lib/rbbt/workflow/accessor.rb', line 140

def status=(status)
  set_info(:status, status)
end

#step(name) ⇒ Object 



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# File 'lib/rbbt/workflow/step.rb', line 213

def step(name)
  @steps ||= {}
  @steps[name] ||= begin
                     deps = rec_dependencies.select{|step| 
                       step.task_name.to_sym == name.to_sym
                     }
                     deps.first
                   end

end

#stop_dependencies ⇒ Object 



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# File 'lib/rbbt/workflow/step/run.rb', line 329

def stop_dependencies
  dependencies.each do |dep|
    dep.abort
  end
  kill_children
end

#streaming? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rbbt/workflow/accessor.rb', line 263

def streaming?
  IO === @result or status == :streaming
end

#task_name ⇒ Object 



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# File 'lib/rbbt/workflow/step.rb', line 64

def task_name
  @task.name
end