Class: Step

Inherits:
Object
  • Object
show all
Defined in:
lib/rbbt/util/python/step.rb,
lib/rbbt/workflow/refactor.rb,
lib/rbbt/workflow/refactor.rb,
lib/rbbt/workflow/step/info.rb,
lib/rbbt/workflow/step/status.rb,
lib/rbbt/workflow/step/produce.rb,
lib/rbbt/workflow/util/archive.rb,
lib/rbbt/workflow/step/accessor.rb,
lib/rbbt/workflow/refactor/inputs.rb,
lib/rbbt/workflow/util/provenance.rb,
lib/rbbt/workflow/step/dependencies.rb

Direct Known Subclasses

RemoteStep

Constant Summary collapse

MAIN_RSYNC_ARGS = 
"-avztAXHP --copy-links"
INFO_SERIALIZER = 
begin
  if ENV["RBBT_INFO_SERIALIZER"]
    Kernel.const_get ENV["RBBT_INFO_SERIALIZER"]
  else
    Marshal
  end
end
STREAM_CACHE = 
{}
STREAM_CACHE_MUTEX = 
Mutex.new

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Instance Attribute Details

#bindings ⇒ Object

Returns the value of attribute bindings.



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# File 'lib/rbbt/workflow/step/accessor.rb', line 2

def bindings
  @bindings
end

#clean_name ⇒ Object

Returns the value of attribute clean_name.



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# File 'lib/rbbt/workflow/step/accessor.rb', line 2

def clean_name
  @clean_name
end

#dependencies ⇒ Object

Returns the value of attribute dependencies.



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# File 'lib/rbbt/workflow/step/accessor.rb', line 2

def dependencies
  @dependencies
end

#exec(noload = false) ⇒ Object

Returns the value of attribute exec.



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

def exec(noload = false)
  old_exec
end

#inputs ⇒ Object

Returns the value of attribute inputs.



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# File 'lib/rbbt/workflow/step/accessor.rb', line 2

def inputs
  @inputs
end

#mutex ⇒ Object

Returns the value of attribute mutex.



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

def mutex
  @mutex
end

#original_task_name ⇒ Object

Returns the value of attribute original_task_name.



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

def original_task_name
  @original_task_name
end

#original_workflow ⇒ Object

Returns the value of attribute original_workflow.



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

def original_workflow
  @original_workflow
end

#overriden ⇒ Object

Returns the value of attribute overriden.



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

def overriden
  @overriden
end

#path ⇒ Object

Returns the value of attribute path.



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# File 'lib/rbbt/workflow/step/accessor.rb', line 2

def path
  @path
end

#pid ⇒ Object

Returns the value of attribute pid.



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# File 'lib/rbbt/workflow/step/accessor.rb', line 4

def pid
  @pid
end

#real_inputs=(value) ⇒ Object

Sets the attribute real_inputs

Parameters:

  • value —

    the value to set the attribute real_inputs to.



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

def real_inputs=(value)
  @real_inputs = value
end

#relocated ⇒ Object

Returns the value of attribute relocated.



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# File 'lib/rbbt/workflow/step/accessor.rb', line 6

def relocated
  @relocated
end

#result ⇒ Object

Returns the value of attribute result.



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

def result
  @result
end

#seen ⇒ Object

Returns the value of attribute seen.



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

def seen
  @seen
end

#task ⇒ Object

Returns the value of attribute task.



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# File 'lib/rbbt/workflow/step/accessor.rb', line 2

def task
  @task
end

#task_name ⇒ Object

Returns the value of attribute task_name.



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

def task_name
  @task_name
end

#workflow ⇒ Object

Returns the value of attribute workflow.



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# File 'lib/rbbt/workflow/step/accessor.rb', line 2

def workflow
  @workflow
end

Class Method Details

.archive(files, target = nil, recursive = true) ⇒ Object 



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# File 'lib/rbbt/workflow/util/archive.rb', line 109

def self.archive(files, target = nil, recursive = true)
  target = self.path + '.tar.gz' if target.nil?
  target = File.expand_path(target) if String === target

  job_files = job_files_for_archive files, recursive
  TmpFile.with_file do |tmpdir|
    job_files.each do |file|
      Step.link_job file, tmpdir
    end

    Misc.in_dir(tmpdir) do
      if File.directory?(target)
        CMD.cmd_log("rsync #{MAIN_RSYNC_ARGS} --copy-unsafe-links '#{ tmpdir }/' '#{ target }/'")
      else
        Misc.tarize('.', target)
        #CMD.cmd_log("tar cvhzf '#{target}'  ./*")
      end
    end
    Log.debug "Archive finished at: #{target}"
  end
end

.clean(path) ⇒ Object 



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# File 'lib/rbbt/workflow/step/status.rb', line 2

def self.clean(path)
  info_file = Step.info_file path
  pid_file = Step.pid_file path
  md5_file = Step.md5_file path
  files_dir = Step.files_dir path
  tmp_path = Step.tmp_path path

  if ! (Open.writable?(path) && Open.writable?(info_file))
    Log.warn "Could not clean #{path}: not writable"
    return 
  end

  if ENV["RBBT_DEBUG_CLEAN"] == 'true'
    raise "DO NOT CLEAN" 
  end

  if (Open.exists?(path) or Open.broken_link?(path)) or Open.exists?(pid_file) or Open.exists?(info_file) or Open.exists?(files_dir) or Open.broken_link?(files_dir) or Open.exists?(pid_file)

    @result = nil
    @pid = nil

    Misc.insist do
      Open.rm info_file if Open.exists?(info_file)
      Open.rm md5_file if Open.exists?(md5_file)
      Open.rm path if (Open.exists?(path) || Open.broken_link?(path))
      Open.rm_rf files_dir if Open.exists?(files_dir) || Open.broken_link?(files_dir)
      Open.rm pid_file if Open.exists?(pid_file)
      Open.rm tmp_path if Open.exists?(tmp_path)
    end
  end
end

.dup_stream(stream) ⇒ Object 



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# File 'lib/rbbt/workflow/step/dependencies.rb', line 12

def self.dup_stream(stream)
  case stream
  when IO, File, Step
    return stream if stream.respond_to?(:closed?) and stream.closed?
    return stream if stream.respond_to?(:done?) and stream.done?

    STREAM_CACHE_MUTEX.synchronize do
      stream_key = Misc.fingerprint(stream)
      current = STREAM_CACHE[stream_key]
      case current
      when nil, Step
        Log.medium "Not duplicating stream #{stream_key}"
        STREAM_CACHE[stream_key] = stream
      when File
        if Open.exists?(current.path)
          Log.medium "Reopening file #{stream_key}"
          Open.open(current.path)
        else
          new = Misc.dup_stream(current)
          Log.medium "Duplicating file #{stream_key} #{current.inspect} => #{Misc.fingerprint(new)}"
          new
        end
      else
        new = Misc.dup_stream(current)
        Log.medium "Duplicating stream #{stream_key} #{ Misc.fingerprint(stream) } => #{Misc.fingerprint(new)}"
        new
      end
    end
  when TSV::Dumper, TSV::Parser
    orig_stream = stream
    stream = stream.stream
    return stream if stream.closed?

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

.files_dir(path) ⇒ Object 



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# File 'lib/rbbt/workflow/step/accessor.rb', line 65

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

.info_file(path) ⇒ Object 



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# File 'lib/rbbt/workflow/step/accessor.rb', line 69

def self.info_file(path)
  return nil if path.nil?
  info_file = path + '.info'
  return info_file if Open.exist?(info_file)

  if path.end_with?('.gz')
    info_file_nogz = path.sub(/\.gz$/,'') + '.info'
    return info_file_nogz if Open.exists?(info_file_nogz)
  end

  info_file
end

.job_files_for_archive(files, recursive = false, skip_overriden = false) ⇒ Object 



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# File 'lib/rbbt/workflow/util/archive.rb', line 55

def self.job_files_for_archive(files, recursive = false, skip_overriden = false)
  job_files = Set.new

  jobs = files.collect do |file|  
    if Step === file
      file
    else
      file = file.sub(/\.info$/,'')
      Step.new(File.expand_path(file))
    end
  end.uniq

  jobs.each do |step|
    next unless File.exist?(step.path)
    next if skip_overriden && step.overriden

    job_files << step.path
    job_files << step.info_file if File.exist?(step.info_file)
    job_files << Step.md5_file(step.path) if File.exist?(Step.md5_file step.path)
    job_file_dir_content = Dir.glob(step.files_dir + '/**/*')
    job_files += job_file_dir_content
    job_files << step.files_dir if File.exist?(step.files_dir)
    rec_dependencies = Set.new

    next unless recursive

    deps = [step.path]
    seen = Set.new
    while deps.any?
      path = deps.shift

      dep = Step.load path
      seen << dep.path

      #dep.load_dependencies_from_info

      dep.dependencies.each do |dep|
        next if seen.include? dep.path
        deps << dep.path
        rec_dependencies << dep.path
      end if dep.info[:dependencies]
    end

    rec_dependencies.each do |path|
      dep = Workflow.load_step path.dup
      job_files << dep.path
      job_files << dep.files_dir if Dir.glob(dep.files_dir + '/*').any?
      job_files << dep.info_file if File.exist?(dep.info_file)
    end
  end

  job_files.to_a
end

.job_name_for_info_file(info_file, extension = nil) ⇒ Object 



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# File 'lib/rbbt/workflow/step/accessor.rb', line 109

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

.link_job(path, target_dir, task = nil, workflow = nil) ⇒ Object 



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# File 'lib/rbbt/workflow/util/archive.rb', line 6

def self.link_job(path, target_dir, task = nil, workflow = nil)
  Path.setup(target_dir)

  name = File.basename(path)
  task = File.basename(File.dirname(path)) if task.nil?
  workflow = File.basename(File.dirname(File.dirname(path))) if workflow.nil?

  return if target_dir[workflow][task][name].exists? || File.symlink?(target_dir[workflow][task][name].find)
  Log.debug "Linking #{ path }"
  FileUtils.mkdir_p target_dir[workflow][task] unless target_dir[workflow][task].exists?
  FileUtils.ln_s path, target_dir[workflow][task][name].find if File.exist?(path)
  FileUtils.ln_s path + '.files', target_dir[workflow][task][name].find + '.files' if File.exist?(path + '.files')
  FileUtils.ln_s path + '.info', target_dir[workflow][task][name].find + '.info' if File.exist?(path + '.info')
end

.load_serialized_info(io) ⇒ Object 



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# File 'lib/rbbt/workflow/step/accessor.rb', line 35

def self.load_serialized_info(io)
  IndiferentHash.setup(INFO_SERIALIZER.load(io))
end

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



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

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



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# File 'lib/rbbt/workflow/step/info.rb', line 162

def self.log_block(status, 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 and message != :result
    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, "%.2f" % (eend - start)}"
    str << ": #{ res }" if message == :result
    str << " -- #{Log.color :blue, path.to_s}" if path
    str << " #{Log.color :yellow, Process.pid}"
    str
  end
  res
end

.log_progress(status, options = {}, path = nil, &block) ⇒ Object 



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# File 'lib/rbbt/workflow/step/info.rb', line 204

def self.log_progress(status, options = {}, path = nil, &block)
  options = Misc.add_defaults options, :severity => Log::INFO, :file => (@exec ? nil : path)
  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 $!
      raise $!
    end
  end
end

.log_string(status, message, path) ⇒ Object 



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# File 'lib/rbbt/workflow/step/info.rb', line 189

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

.md5_file(path) ⇒ Object 



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# File 'lib/rbbt/workflow/refactor.rb', line 12

def self.md5_file(path)
  path.nil? ? nil : path + '.md5'
end

.migrate(paths, search_path, options = {}) ⇒ Object 



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# File 'lib/rbbt/workflow/util/archive.rb', line 164

def self.migrate(paths, search_path, options = {})
  subpath_files = {}
  target_paths = []
  resource = options[:resource] || Rbbt

  target = Rbbt.migrate_target_path('var/jobs', search_path, resource, options[:target])

  (Array === paths ? paths : [paths]).each do |path|
    if Step === path
      if options[:source]
        path = Rbbt.identify(path.path)
      else
        path = path.path
      end
    end
    search_path = 'user' if search_path.nil?


    path, real_paths, lpath = self.migrate_source_paths(path, resource, options[:source], options[:recursive])

    real_paths.sort.each do |path|
      parts = path.split("/")
      subpath = parts[0..-4] * "/" + "/"

      if subpath_files.keys.any? && subpath.start_with?(subpath_files.keys.last)
        subpath = subpath_files.keys.last
      end

      source = path.chars[subpath.length..-1] * ""

      subpath_files[subpath] ||= []
      subpath_files[subpath] << source
    end


    target_paths << File.join(target, *path.split("/")[-3..-1])
  end


  subpath_files.each do |subpath, files|
    Rbbt.migrate_files([subpath], target, options.merge(:files => files))
  end

  target_paths
end

.migrate_source_paths(path, resource = Rbbt, source = nil, recursive = true) ⇒ Object 



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

def self.migrate_source_paths(path, resource = Rbbt, source = nil, recursive = true)
  recursive = false if recursive.nil?
  if source
    lpath, *paths = Misc.ssh_run(source, <<-EOF).split("\n")
require 'rbbt-util'
require 'rbbt/workflow'

recursive = #{ recursive.to_s }
path = "#{path}"

if Open.exists?(path)
path = #{resource.to_s}.identify(path)
else
path = Path.setup(path)
end

files = path.glob_all.collect{|p| File.directory?(p) ? p + "/" : p }
files = Step.job_files_for_archive(files, recursive)

puts path
puts files * "\n"
    EOF

    [path, paths.collect{|p| [source, p] * ":"}, lpath]
  else
    path = Path.setup(path.dup)
    files = path.glob_all
    files = Step.job_files_for_archive(files, recursive)

    [path, files, path]
  end
end

.pid_file(path) ⇒ Object 



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

def self.pid_file(path)
  path.nil? ? nil : path + '.pid'
end

.prepare_for_execution(job) ⇒ Object 



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# File 'lib/rbbt/workflow/step/dependencies.rb', line 72

def self.prepare_for_execution(job)
  return if job.done? && ! job.dirty?

  status = job.status.to_s

  if defined?(WorkflowRemoteClient) && WorkflowRemoteClient::RemoteStep === job 
    return unless (status == 'done' or status == 'error' or status == 'aborted')
  else
    return if status == 'streaming' and job.running?
  end

  canfail = nil
  job.status_lock.synchronize do
    status = job.status.to_s

    if (status == 'error' && (job.recoverable_error? || job.dirty?)) ||
        (job.noinfo? && Open.exists?(job.pid_file)) ||
        job.aborted? ||
        (job.done? && ! job.updated?)  || (job.error? && ! job.updated?) ||
        (job.done? && job.dirty?)  || (job.error? && job.dirty?) ||
        (!(job.noinfo? || job.done? || job.error? || job.aborted? || job.running?))

      if ! (job.resumable? && (job.updated? && ! job.dirty?))
        Log.high "About to clean -- status: #{status}, present #{File.exist?(job.path)}, " +
          %w(done? error? recoverable_error? noinfo? updated? dirty? aborted? running? resumable?).
          collect{|v| [v, job.send(v)]*": "} * ", " if RBBT_DEBUG_CLEAN

        job.clean
      end
      job.set_info :status, :cleaned
    end

    job.dup_inputs unless status == 'done' or job.started?
    job.init_info(status == 'noinfo') unless status == 'waiting' || status == 'done' || job.started? || ! Workflow.job_path?(job.path)

    canfail = ComputeDependency === job && job.canfail?
  end

  Step.raise_dependency_error(job) if job.error? and not canfail
end

.produce_dependencies(jobs, tasks, cpus) ⇒ Object 



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# File 'lib/rbbt/workflow/step/produce.rb', line 2

def self.produce_dependencies(jobs, tasks, cpus)
  deps = []

  jobs = [jobs] unless Array === jobs
  tasks = [tasks] unless Array === tasks
  tasks = tasks.collect{|t| t.to_s}

  jobs.each do |job|
    job.rec_dependencies.each do |dep|
      next if dep.done?
      dep.clean if dep.error? && dep.recoverable_error?
      deps << dep if tasks.include?(dep.task_name.to_s) or tasks.include?([dep.workflow.to_s, dep.task_name] * "#")
    end
  end

  cpus = jobs.length if cpus.to_s == "max"
  cpus = cpus.to_i if String === cpus
  TSV.traverse deps.collect{|dep| dep.path}, :type => :array, :cpus => cpus, :bar => "Prepare dependencies #{Misc.fingerprint tasks} for #{Misc.fingerprint jobs}" do |path|
    dep = deps.select{|dep| dep.path == path}.first
    dep.produce
    nil
  end
end

.prov_report(step, offset = 0, task = nil, seen = [], expand_repeats = false, input = nil) ⇒ Object 



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# File 'lib/rbbt/workflow/util/provenance.rb', line 86

def self.prov_report(step, offset = 0, task = nil, seen = [], expand_repeats = false, input = nil)
  info = step.info  || {}
  info[:task_name] = task
  path  = step.path
  status = info[:status] || :missing
  status = "remote" if Open.remote?(path) || Open.ssh?(path)
  name = info[:name] || File.basename(path)
  status = :unsync if status == :done and not Open.exist?(path)
  status = :notfound if status == :noinfo and not Open.exist?(path)


  this_step_msg = prov_report_msg(status, name, path, info, input)

  input_dependencies = {}
  step.dependencies.each do |dep|
    if dep.input_dependencies.any?
      dep.input_dependencies.each do |id|
        input_name, _dep = dep.recursive_inputs.fields.zip(dep.recursive_inputs).select{|f,d| 
          d == id || (String === d && d.start_with?(id.files_dir)) || (Array === d && d.include?(id))
        }.last
        if input_name
          input_dependencies[id] ||= []
          input_dependencies[id] << [dep, input_name]
        end
      end
    end
  end if step.dependencies

  str = ""
  str = " " * offset + this_step_msg if ENV["RBBT_ORIGINAL_STACK"] == 'true'

  step.dependencies.dup.tap{|l| 
    l.reverse! if ENV["RBBT_ORIGINAL_STACK"] == 'true'
  }.each do |dep|
    path = dep.path
    new = ! seen.include?(path)
    if new
      seen << path
      str << prov_report(dep, offset + 1, task, seen, expand_repeats, input_dependencies[dep])
    else
      if expand_repeats
        str << Log.color(Step.status_color(dep.status), Log.uncolor(prov_report(dep, offset+1, task)))
      else
        info = dep.info  || {}
        status = info[:status] || :missing
        status = "remote" if Open.remote?(path) || Open.ssh?(path)
        name = info[:name] || File.basename(path)
        status = :unsync if status == :done and not Open.exist?(path)
        status = :notfound if status == :noinfo and not Open.exist?(path)

        str << Log.color(Step.status_color(status), " " * (offset + 1) + Log.uncolor(prov_report_msg(status, name, path, info, input_dependencies[dep])))
      end
    end
  end if step.dependencies

  str += (" " * offset) + this_step_msg unless ENV["RBBT_ORIGINAL_STACK"] == 'true'

  str
end

.prov_report_msg(status, name, path, info, input = nil) ⇒ Object 



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# File 'lib/rbbt/workflow/util/provenance.rb', line 29

def self.prov_report_msg(status, name, path, info, input = nil)
  parts = path.sub(/\{.*/,'').split "/"

  parts.pop

  task = Log.color(:yellow, parts.pop)
  workflow = Log.color(:magenta, parts.pop)
  #if status.to_s == 'noinfo' && parts.last != 'jobs'
  if ! Workflow.job_path?(path)
    task, status, workflow = Log.color(:yellow, info[:task_name]), Log.color(:green, "file"), Log.color(:magenta, "-")
  end

  path_mtime = begin
                 Open.mtime(path)
               rescue Exception
                 nil
               end

  if input.nil? || input.empty?
    input_str = nil
  else
    input = input.reject{|dep,name| (input & dep.dependencies.collect{|d| [d,name]}).any? }
    input = input.reject{|dep,name| (input & dep.input_dependencies.collect{|d| [d,name]}).any? }
    input_str = Log.color(:magenta, "-> ") + input.collect{|dep,name| Log.color(:yellow, dep.task_name.to_s) + ":" + Log.color(:yellow, name) }.uniq * " "
  end

  str = if ! (Open.remote?(path) || Open.ssh?(path)) && (Open.exists?(path) && $main_mtime && path_mtime && ($main_mtime - path_mtime) < -2)
          prov_status_msg(status.to_s) << " " << [workflow, task, path, input_str].compact * " " << " (#{Log.color(:red, "Mtime out of sync") })"
        else
          prov_status_msg(status.to_s) << " " << [workflow, task, path, input_str].compact * " " 
        end

  if $inputs and $inputs.any? 
    job_inputs = Workflow.load_step(path).recursive_inputs.to_hash
    IndiferentHash.setup(job_inputs)

    $inputs.each do |input|
      value = job_inputs[input]
      next if  value.nil?
      value_str = Misc.fingerprint(value)
      str << "\t#{Log.color :magenta, input}=#{value_str}"
    end
  end

  if $info_fields and $info_fields.any?
    $info_fields.each do |field|
      IndiferentHash.setup(info)
      value = info[field]
      next if value.nil?
      value_str = Misc.fingerprint(value)
      str << "\t#{Log.color :magenta, field}=#{value_str}"
    end
  end

  str << "\n"
end

.prov_status_msg(status) ⇒ Object 



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# File 'lib/rbbt/workflow/util/provenance.rb', line 24

def self.prov_status_msg(status)
  color = status_color(status)
  Log.color(color, status.to_s)
end

.purge(path, recursive = false, skip_overriden = true) ⇒ Object 



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# File 'lib/rbbt/workflow/util/archive.rb', line 210

def self.purge(path, recursive = false, skip_overriden = true)
  path = [path] if String === path
  job_files = job_files_for_archive path, recursive, skip_overriden

  job_files.each do |file|
    begin
      Log.debug "Purging #{file}"
      Open.rm_rf file if Open.exists?(file)
    rescue
      Log.warn "Could not erase '#{file}': #{$!.message}"
    end
  end
end

.purge_stream_cache ⇒ Object 



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# File 'lib/rbbt/workflow/step/dependencies.rb', line 5

def self.purge_stream_cache
  # Log.debug "Purging dup. stream cache"
  STREAM_CACHE_MUTEX.synchronize do
    STREAM_CACHE.clear
  end
end

.raise_dependency_error(job) ⇒ Object 



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# File 'lib/rbbt/workflow/step/dependencies.rb', line 113

def self.raise_dependency_error(job)
  begin
    if job.get_exception
      klass = job.get_exception.class
    else
      klass = Kernel.const_get(info[:exception][:class])
    end
  rescue
    Log.exception $!
    raise DependencyError, job 
  end

  if (klass <= RbbtException)
    raise DependencyRbbtException, job 
  else
    raise DependencyError, job 
  end
end

.save_inputs(inputs, input_types, dir) ⇒ Object 



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# File 'lib/rbbt/workflow/refactor/inputs.rb', line 2

def self.save_inputs(inputs, input_types, dir)
  inputs.collect do |name,value|
    next if value.nil?
    type = input_types[name]
    type = type.to_s if type

    Task.save_input(dir, name, type, value)
    name
  end.compact.any?
end

.serialize_info(info) ⇒ Object 



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

def self.serialize_info(info)
  info = info.clean_version if IndiferentHash === info
  INFO_SERIALIZER.dump(info)
end

.status_color(status) ⇒ Object 



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# File 'lib/rbbt/workflow/step/info.rb', line 148

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/step/accessor.rb', line 98

def self.step_info(path)
  begin
    Open.open(info_file(path), :mode => 'rb') do |f|
      self.load_serialized_info(f)
    end
  rescue Exception
    Log.exception $!
    {}
  end
end

.tmp_path(path) ⇒ Object 



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# File 'lib/rbbt/workflow/step/accessor.rb', line 82

def self.tmp_path(path)
  path = path.find if Path === path
  path = File.expand_path(path)
  dir = File.dirname(path)
  filename = File.basename(path)
  File.join(dir, '.' << filename)
end

.wait_for_jobs(jobs) ⇒ Object 



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# File 'lib/rbbt/workflow/step/accessor.rb', line 40

def self.wait_for_jobs(jobs)
  jobs = [jobs] if Step === jobs
  begin
    threads = []

    threads = jobs.collect do |j| 
      Thread.new do
        begin
          j.soft_grace
          j.join unless j.done?
        rescue Exception
          Log.error "Exception waiting for job: #{Log.color :blue, j.path}"
          raise $!
        end
      end
    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

#aborted? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rbbt/workflow/step/status.rb', line 142

def aborted?
  status = self.status
  status == :aborted || ((status != :ending && status != :dependencies && status != :cleaned && status != :noinfo && status != :setup && status != :noinfo && status != :waiting) && nopid?)
end

#access ⇒ Object 



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# File 'lib/rbbt/workflow/step/accessor.rb', line 361

def access
  CMD.cmd("touch -c -h -a #{self.path} #{self.info_file}")
end

#archive(target = nil) ⇒ Object 



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

def archive(target = nil)
  target = self.path + '.tar.gz' if target.nil?
  target = File.expand_path(target)
  TmpFile.with_file do |tmpdir|
    Step.link_job self.path, tmpdir
    rec_dependencies = Set.new
    deps = [self.path]
    seen = Set.new
    while deps.any?
      path = deps.shift
      dep = Step.load path
      seen << dep.path
      dep.dependencies.each do |dep|
        next if seen.include? dep.path
        deps << dep.path
        rec_dependencies << dep.path
      end if dep.dependencies
    end

    rec_dependencies.each do |path|
      Step.link_job path, tmpdir
    end

    Misc.in_dir(tmpdir) do
      if File.directory?(target)
        CMD.cmd_log("rsync #{MAIN_RSYNC_ARGS} --copy-unsafe-links '#{ tmpdir }/' '#{ target }/'")
      else
        CMD.cmd_log("tar cvhzf '#{target}'  ./*")
      end
    end
    Log.debug "Archive finished at: #{target}"
  end
end

#archive_deps ⇒ Object 



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# File 'lib/rbbt/workflow/step/info.rb', line 79

def archive_deps
  self.set_info :archived_info, archived_info
  self.set_info :archived_dependencies, info[:dependencies]
end

#archived_info ⇒ Object 



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# File 'lib/rbbt/workflow/step/info.rb', line 84

def archived_info
  return info[:archived_info] if info[:archived_info]

  archived_info = {}
  dependencies.each do |dep|
    if Symbol === dep.overriden && ! Open.exists?(dep.info_file)
      archived_info[dep.path] = dep.overriden
    else
      archived_info[dep.path] = dep.info
    end
    archived_info.merge!(dep.archived_info)
  end if dependencies

  archived_info
end

#archived_inputs ⇒ Object 



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# File 'lib/rbbt/workflow/step/info.rb', line 100

def archived_inputs
  return {} unless info[:archived_dependencies]
  archived_info = self.archived_info

  all_inputs = IndiferentHash.setup({})
  deps = info[:archived_dependencies].collect{|p| p.last}
  seen = []
  while path = deps.pop
    dep_info = archived_info[path]
    if Hash === dep_info
      dep_info[:inputs].each do |k,v|
        all_inputs[k] = v unless all_inputs.include?(k)
      end if dep_info[:inputs]
      deps.concat(dep_info[:dependencies].collect{|p| p.last } - seen) if dep_info[:dependencies]
      deps.concat(dep_info[:archived_dependencies].collect{|p| p.last } - seen) if dep_info[:archived_dependencies]
    end
    seen << path
  end

  all_inputs
end

#canfail_paths ⇒ Object 



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# File 'lib/rbbt/workflow/step/dependencies.rb', line 355

def canfail_paths
  return Set.new if done? && ! Open.exists?(info_file)

  @canfail_paths ||= begin 
                       if info[:canfail] 
                         paths = info[:canfail].uniq
                         paths = Workflow.relocate_array self.path, paths if relocated
                         Set.new(paths)
                       else
                         canfail_paths = Set.new
                         all_deps = dependencies || []
                         all_deps.each do |dep|
                           next if canfail_paths.include? dep.path
                           canfail_paths += dep.canfail_paths
                           next unless ComputeDependency === dep && dep.canfail?
                           canfail_paths << dep.path
                           canfail_paths += dep.rec_dependencies.collect{|d| d.path }
                         end
                         canfail_paths
                         begin
                           set_info :canfail, canfail_paths.to_a
                         rescue Errno::EROFS
                         end
                         canfail_paths
                       end
                     end
end

#clean ⇒ Object 



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

def clean
  if ! Open.exists?(info_file)
    Log.high "Refusing to clean step with no .info file: #{path}"
    return self
  end
  status = []
  status << "dirty" if done? && dirty?
  status << "not running" if ! done? && ! running? 
  status.unshift " " if status.any?
  Log.high "Cleaning step: #{path}#{status * " "}"
  Log.stack caller if RBBT_DEBUG_CLEAN
  abort if ! done? && running?
  Step.clean(path)
  @done = false
  self
end

#config(key, *tokens) ⇒ Object 



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# File 'lib/rbbt/workflow/step/accessor.rb', line 346

def config(key, *tokens)
  options = tokens.pop if Hash === tokens.last
  options ||= {}

  new_tokens = []
  if workflow
    workflow_name = workflow.to_s
    new_tokens << ("workflow:" << workflow_name)
    new_tokens << ("task:" << workflow_name << "#" << task_name.to_s)
  end
  new_tokens << ("task:" << task_name.to_s)

  Rbbt::Config.get(key, tokens + new_tokens, options)
end

#dirty? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rbbt/workflow/step/status.rb', line 76

def dirty?
  return true if Open.exists?(pid_file) && ! ( Open.exists?(info_file) || done? )
  return true if done? && ! (status == :done || status == :noinfo)
  return false unless done? || status == :done
  return false unless ENV["RBBT_UPDATE"] == "true"

  status = self.status

  if done? and not (status == :done or status == :ending or status == :producing) and not status == :noinfo
    return true 
  end

  if status == :done and not done?
    return true 
  end

  if dirty_files.any?
    Log.low "Some dirty files found for #{self.path}: #{Misc.fingerprint dirty_files}"
    true
  else
    ! self.updated?
  end
end

#dirty_files ⇒ Object 



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

def dirty_files
  rec_dependencies = self.rec_dependencies(true)
  return [] if rec_dependencies.empty?
  canfail_paths = self.canfail_paths

  dirty_files = rec_dependencies.reject{|dep|
    (defined?(WorkflowRemoteClient) && WorkflowRemoteClient::RemoteStep === dep) || 
      ! Open.exists?(dep.info_file) ||
      (dep.path && (Open.exists?(dep.path) || Open.remote?(dep.path))) || 
      ((dep.error? || dep.aborted?) && (! dep.recoverable_error? || canfail_paths.include?(dep.path)))
  }
end

#done? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rbbt/workflow/step/status.rb', line 100

def done?
  @done ||= path and Open.exists?(path)
end

#dup_inputs ⇒ Object 



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# File 'lib/rbbt/workflow/step/dependencies.rb', line 60

def dup_inputs
  return if @inputs.nil?
  return if @dupped or ENV["RBBT_NO_STREAM"] == 'true'
  return if ComputeDependency === self and self.compute == :produce
  Log.low "Dupping inputs for #{path}"
  dupped_inputs = @inputs.collect do |input|
    Step.dup_stream input
  end
  @inputs.replace dupped_inputs
  @dupped = true
end

#error? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rbbt/workflow/step/status.rb', line 134

def error?
  status == :error
end

#exception(ex, msg = nil) ⇒ Object 



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

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

#execute_and_dup(step, dep_step, log = true) ⇒ Object 



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# File 'lib/rbbt/workflow/step/dependencies.rb', line 227

def execute_and_dup(step, dep_step, log = true)
  dup = step.result.nil?
  execute_dependency(step, log)
  if dup and step.streaming? and not step.result.nil?
    if dep_step[step.path] and dep_step[step.path].length > 1
      stream = step.result
      other_steps = dep_step[step.path].uniq.reject{|d| d.overriden }

      other_steps = other_steps.collect{|d|
        deps_using_step_input = d.rec_dependencies.select{|d| d.inputs.include? step  }
        deps_using_step_input.any? ? deps_using_step_input : d
      }.flatten.uniq

      return unless other_steps.length > 1

      log_dependency_exec(step, "duplicating #{other_steps.length}") 
      copies = Misc.tee_stream_thread_multiple(stream, other_steps.length)
      copies.extend StreamArray
      step.instance_variable_set("@result", copies)
    end
  end
end

#execute_dependency(dependency, log = true) ⇒ Object 



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

def execute_dependency(dependency, log = true)
  task_name = self.task_name
  canfail_paths = self.canfail_paths
  already_failed = []
  begin

    dependency.resolve_input_steps

    if dependency.done?
      dependency.inputs.each do |v|
        Misc.consume_stream(v) if IO === v
        Misc.consume_stream(TSV.get_stream v) if Step === v and not v.done?  and  v.streaming?
      end
      log_dependency_exec(dependency, :done) if log
      return
    end

    dependency.status_lock.synchronize do
      if dependency.aborted? || (dependency.error? && dependency.recoverable_error? && ! canfail_paths.include?(dependency.path) && ! already_failed.include?(dependency.path)) || (!Open.remote?(dependency.path) && dependency.missing?)
        if dependency.resumable?
          dependency.status = :resume
        else
          Log.warn "Cleaning dep. on exec #{Log.color :blue, dependency.path} (missing: #{dependency.missing?}; error #{dependency.error?})"
          dependency.clean
          already_failed << dependency.path
          raise TryAgain
        end
      end
    end

    if dependency.status == :resume || ! (dependency.started? || dependency.error?)
      log_dependency_exec(dependency, :starting)
      dependency.run(true)
      raise TryAgain
    end

    dependency.grace

    if dependency.error?
      log_dependency_exec(dependency, :error)
      Step.raise_dependency_error dependency 
    end

    if dependency.streaming?
      log_dependency_exec(dependency, :streaming) if log
      return
    end

    begin
      log_dependency_exec(dependency, :joining)
      dependency.join
      raise TryAgain unless dependency.done?
    rescue Aborted
      raise TryAgain
    end

  rescue TryAgain
    #Log.low "Retrying dep. #{Log.color :yellow, dependency.task_name.to_s} -- [#{dependency.status}] #{(dependency.messages || ["No message"]).last}"
    retry
  rescue Aborted, Interrupt
    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 $!
  rescue Exception
    Log.error "Exception in dep. #{ Log.color :red, dependency.task_name.to_s } -- #{$!.message}"
    raise $! unless canfail_paths.include? dependency.path
  end
end

#file(name = nil) ⇒ Object 



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

def file(name=nil)
  Path.setup(File.join(files_dir, name.to_s), workflow, self)
end

#files ⇒ Object 



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# File 'lib/rbbt/workflow/step/accessor.rb', line 260

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/step/accessor.rb', line 252

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

#get_exception ⇒ Object 



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# File 'lib/rbbt/workflow/step/info.rb', line 277

def get_exception
  if info[:exception].nil?
    return Aborted if aborted?
    return Exception.new(messages.last) if error?
    Exception.new "" 
  else
    ex_class, ex_message, ex_backtrace = info[:exception].values_at :class, :message, :backtrace
    begin
      klass = Kernel.const_get(ex_class)
      ex = klass.new ex_message
      ex.set_backtrace ex_backtrace unless ex_backtrace.nil? or ex_backtrace.empty?
      ex
    rescue
      Log.exception $!
      Exception.new ex_message
    end
  end
end

#info(check_lock = true) ⇒ Object 



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# File 'lib/rbbt/workflow/step/info.rb', line 2

def info(check_lock = true)
  return {:status => :noinfo} if info_file.nil? || ! Open.exists?(info_file)

  begin
    Misc.insist do

      begin
        return @info_cache if @info_cache and @info_cache_time and Open.ctime(info_file) < @info_cache_time 
      rescue Exception
        raise $!
      end


      begin
        @info_cache = Misc.insist(3, 1.6, 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?
              info_lock.lock if check_lock and false
              begin
                Open.open(info_file, :mode => 'rb') do |file|
                  Step.load_serialized_info(file)
                end
              ensure
                info_lock.unlock if check_lock and false
              end
            end
          end
        end
        @info_cache_time = Time.now
        @info_cache
      end
    end
  rescue Exception
    Log.debug{"Error loading info file: " + info_file}
    Log.exception $!
    #Open.rm info_file
    #Misc.sensiblewrite(info_file, Step.serialize_info({:status => :error, :messages => ["Info file lost"]}))
    raise $!
  end
end

#info_file ⇒ Object

{{{ INFO



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# File 'lib/rbbt/workflow/step/accessor.rb', line 175

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

#info_lock ⇒ Object 



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# File 'lib/rbbt/workflow/step/accessor.rb', line 183

def info_lock
  @info_lock = begin
                 path = Persist.persistence_path(info_file + '.lock', {:dir => Step.lock_dir})
                 #Lockfile.new path, :refresh => false, :dont_use_lock_id => true
                 Lockfile.new path
               end if @info_lock.nil?
               @info_lock
end

#init_info(force = false) ⇒ Object 



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# File 'lib/rbbt/workflow/step/accessor.rb', line 201

def init_info(force = false)
  return nil if @exec || info_file.nil? || (Open.exists?(info_file) && ! force)
  batch_job = info[:batch_job] if Open.exists?(info_file)
  batch_system = info[:batch_system] if Open.exists?(info_file)
  Open.lock(info_file, :lock => info_lock) do
    i = {:status => :waiting, :pid => Process.pid, :path => path, :real_inputs => real_inputs, :overriden => overriden}
    i[:batch_job] = batch_job if batch_job
    i[:batch_system] = batch_system if batch_system
    i[:dependencies] = dependencies.collect{|dep| [dep.task_name, dep.name, dep.path]} if dependencies
    Misc.sensiblewrite(info_file, Step.serialize_info(i), :force => true, :lock => false)
    @info_cache = IndiferentHash.setup(i)
    @info_cache_time = Time.now
  end
end

#input_dependencies ⇒ Object 



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# File 'lib/rbbt/workflow/step/dependencies.rb', line 147

def input_dependencies
  @input_dependencies ||= recursive_inputs(true).flatten.
    select{|i| Step === i || (defined?(RemoteStep) && RemoteStep === i) } + 
    recursive_inputs(true).flatten.
    select{|dep| Path === dep && Step === dep.resource }.
    #select{|dep| ! dep.resource.started? }. # Ignore input_deps already started
    collect{|dep| dep.resource }
end

#inspect ⇒ Object 



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# File 'lib/rbbt/workflow/step/accessor.rb', line 431

def inspect
  Misc.fingerprint(self)
end

#knowledge_base(organism = nil) ⇒ Object 



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# File 'lib/rbbt/workflow/step/accessor.rb', line 424

def knowledge_base(organism = nil)
  @_kb ||= begin
             kb_dir = self.file('knowledge_base')
             KnowledgeBase.new kb_dir, organism
           end
end

#load_dependencies_from_info ⇒ Object 



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

def load_dependencies_from_info
  relocated = nil
  @dependencies = (self.info[:dependencies] || []).collect do |task,name,dep_path|
    dep_path = task if dep_path.nil?
    if Open.exists?(dep_path) || Open.exists?(dep_path + '.info')
      Workflow._load_step dep_path
    else
      next if FalseClass === relocated
      new_path = Workflow.relocate(path, dep_path)
      relocated = true if Open.exists?(new_path) || Open.exists?(new_path + '.info')
      Workflow._load_step new_path
    end
  end.compact
  @relocated = relocated
end

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



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# File 'lib/rbbt/workflow/step/accessor.rb', line 287

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
    Misc.load_yaml(file(name))
  when :marshal
    Marshal.load(Open.open(file(name)))
  else
    Open.read(file(name))
  end
end

#load_inputs_from_info ⇒ Object 



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# File 'lib/rbbt/workflow/step/info.rb', line 44

def load_inputs_from_info
  if info[:inputs]
    info_inputs = info[:inputs]
    if task && task.respond_to?(:inputs) && task.inputs
      IndiferentHash.setup info_inputs
      @inputs = NamedArray.setup info_inputs.values_at(*task.inputs.collect{|name| name.to_s}), task.inputs
    else
      if Hash === info_inputs
        @inputs = NamedArray.setup info_inputs.values, info_inputs.keys
      else
        @inputs = info_inputs
      end
    end
  else
    nil
  end
end

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



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

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

#log_dependency_exec(dependency, action) ⇒ Object 



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# File 'lib/rbbt/workflow/step/dependencies.rb', line 132

def log_dependency_exec(dependency, action)
  task_name = self.task_name

  str = Log.color(:reset, "")
  str << Log.color(:yellow, task_name.to_s || "") 
  str << " "
  str << Log.color(:magenta, action.to_s)
  str << " "
  str << Log.color(:yellow, dependency.task_name.to_s || "")
  str << " -- "
  str << "#{Log.color :blue, dependency.path}"

  Log.info str
end

#log_progress(status, options = {}, &block) ⇒ Object 



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# File 'lib/rbbt/workflow/step/info.rb', line 219

def log_progress(status, options = {}, &block)
  Step.log_progress(status, options, file(:progress), &block)
end

#md5_file ⇒ Object 



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# File 'lib/rbbt/workflow/refactor.rb', line 16

def md5_file
  Step.md5_file(path)
end

#merge_info(hash) ⇒ Object 



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# File 'lib/rbbt/workflow/step/accessor.rb', line 235

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

#message(message) ⇒ Object 



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# File 'lib/rbbt/workflow/step/info.rb', line 143

def message(message)
  message = Log.uncolor(message)
  set_info(:messages, (messages || []) << message)
end

#messages ⇒ Object 



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# File 'lib/rbbt/workflow/step/info.rb', line 135

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

#missing? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rbbt/workflow/step/status.rb', line 130

def missing?
  status == :done && ! Open.exists?(path)
end

#monitor_stream(stream, options = {}, &block) ⇒ Object 



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# File 'lib/rbbt/workflow/step/accessor.rb', line 372

def monitor_stream(stream, options = {}, &block)
  case options[:bar] 
  when TrueClass
    bar = progress_bar 
  when Hash
    bar = progress_bar options[:bar]
  when Numeric
    bar = progress_bar :max => options[:bar]
  else
    bar = options[:bar]
  end

  out = if bar.nil?
          Misc.line_monitor_stream stream, &block
        elsif (block.nil? || block.arity == 0)
          Misc.line_monitor_stream stream do
            bar.tick
          end
        elsif block.arity == 1
          Misc.line_monitor_stream stream do |line|
            bar.tick
            block.call line
          end
        elsif block.arity == 2
          Misc.line_monitor_stream stream do |line|
            block.call line, bar
          end
        end

  ConcurrentStream.setup(out, :abort_callback => Proc.new{
    Log::ProgressBar.remove_bar(bar, true) if bar
  }, :callback => Proc.new{
    Log::ProgressBar.remove_bar(bar) if bar
  })

  bgzip = (options[:compress] || options[:gzip]).to_s == 'bgzip'
  bgzip = true if options[:bgzip]

  gzip = true if options[:compress] || options[:gzip]
  if bgzip
    Open.bgzip(out)
  elsif gzip
    Open.gzip(out)
  else
    out
  end
end

#name ⇒ Object 



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

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

#noinfo? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rbbt/workflow/step/status.rb', line 108

def noinfo?
  status == :noinfo
end

#nopid? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rbbt/workflow/step/status.rb', line 138

def nopid?
  ! Open.exists?(pid_file) && ! (status.nil? || status == :aborted || status == :done || status == :error || status == :cleaned)
end

#old_exec ⇒ Object 



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# File 'lib/rbbt/workflow/refactor.rb', line 6

alias old_exec exec

#overriden? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rbbt/workflow/step/dependencies.rb', line 538

def overriden?
  return @overriden
  return true if @overriden
  return true if dependencies && dependencies.select{|dep| TrueClass === dep.overriden }.any?
  info[:archived_info].each do |f,i|
    next if Symbol === i
    return true if i[:overriden] || i["overriden"]
  end if info[:archived_info]
  return false
end

#overriden_deps ⇒ Object 



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# File 'lib/rbbt/workflow/step/dependencies.rb', line 559

def overriden_deps
  ord = []
  deps = dependencies.dup
  while dep = deps.shift
    case dep.overriden
    when FalseClass
      next
    when Symbol
      ord << dep
    else
      deps += dep.dependencies
    end
  end
  ord
end

#pid_file ⇒ Object 



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# File 'lib/rbbt/workflow/step/accessor.rb', line 179

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

#progress_bar(msg = "Progress", options = nil, &block) ⇒ Object 



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# File 'lib/rbbt/workflow/step/info.rb', line 223

def progress_bar(msg = "Progress", options = nil, &block)
  if Hash === msg and options.nil?
    options = msg
    msg = nil
  end
  options = {} if options.nil?

  max = options[:max]
  bar = Log::ProgressBar.new_bar(max, {:desc => msg, :file => (@exec ? nil : file(:progress))}.merge(options))

  if block_given?
    bar.init
    res = yield bar
    bar.remove
    res
  else
    bar
  end
end

#provenance ⇒ Object 



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# File 'lib/rbbt/workflow/step/accessor.rb', line 325

def provenance
  provenance = {}
  dependencies.each do |dep|
    next unless dep.path.exists?
    if Open.exists? dep.info_file
      provenance[dep.path] = dep.provenance if Open.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/step/accessor.rb', line 338

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

#python(python = nil, options = {}, &block) ⇒ Object 



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# File 'lib/rbbt/util/python/step.rb', line 12

def python(python = nil, options = {}, &block)
  begin
    RbbtPython.add_path self.workflow.libdir.python.find
  rescue
    Log.warn "Error loading libdir python for workflow '#{Misc.fingerprint self.workflow}'"
  end
  case python
  when Path
    python_file python.find, options
  when String
    if Open.exists?(python)
      python_file python
    else
      TmpFile.with_file do |dir|
        pkg = "pkg#{rand(100)}"
        Open.write File.join(dir, "#{pkg}/__init__.py"), code

        RbbtPython.add_path dir

        Misc.in_dir dir do
          yield pkg
        end
      end
    end
  else
    python_block(python, &block)
  end
end

#python_block(options = {}, &block) ⇒ Object 



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

def python_block(options = {}, &block)
  RbbtPython.run options, &block
end

#python_file(file, options = {}) ⇒ Object 



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# File 'lib/rbbt/util/python/step.rb', line 4

def python_file(file, options = {})
  CMD.cmd_log(:python, file, options)
end

#rec_access ⇒ Object 



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# File 'lib/rbbt/workflow/step/accessor.rb', line 365

def rec_access
  access
  rec_dependencies.each do |dep|
    dep.access
  end
end

#rec_dependencies(connected = false, seen = []) ⇒ Object

connected = true means that dependency searching ends when a result is done but dependencies are absent, meanining that the file could have been dropped in



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# File 'lib/rbbt/workflow/step/dependencies.rb', line 583

def rec_dependencies(connected = false, seen = [])
  # A step result with no info_file means that it was manually
  # placed. In that case, do not consider its dependencies
  return [] if ! (defined? WorkflowRemoteClient && WorkflowRemoteClient::RemoteStep === self) && ! Open.exists?(self.info_file) && Open.exists?(self.path.to_s) 

  return [] if dependencies.nil? or dependencies.empty?

  if self.overriden?
    archived_deps = []
  else
    archived_deps = self.info[:archived_info] ? self.info[:archived_info].keys : []
  end

  new_dependencies = []
  dependencies.each{|step| 
    #next if self.done? && Open.exists?(info_file) && info[:dependencies] && info[:dependencies].select{|task,name,path| path == step.path }.empty?
    next if archived_deps.include? step.path
    next if seen.include? step
    next if step.done? && connected && ! step.updatable?

    r = step.rec_dependencies(connected, new_dependencies)
    new_dependencies.concat r
    new_dependencies << step
  }

  new_dependencies.uniq
end

#recoverable_error? ⇒ Boolean

Returns:

  • (Boolean) 


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

def recoverable_error?
  return true if aborted?
  return false unless error?
  begin
    return true unless info[:exception]
    klass = Kernel.const_get(info[:exception][:class])
    ! (klass <= RbbtException )
  rescue Exception
    true
  end
end

#relocated? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rbbt/workflow/step/accessor.rb', line 420

def relocated?
  done? && info[:path] && info[:path] != path
end

#reset_info(info = {}) ⇒ Object 



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# File 'lib/rbbt/workflow/refactor.rb', line 22

def reset_info(info = {})
  if ENV["BATCH_SYSTEM"]
    info = info.dup
    info[:batch_system] = ENV["BATCH_SYSTEM"]
    info[:batch_job] = ENV["BATCH_JOB_ID"]
  end
  save_info(info)
end

#result_description ⇒ Object 



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

def result_description
  @result_description ||= if @task.respond_to?(:result_description)
                            @task.result_description
                          else
                            nil
                          end
end

#result_description=(description) ⇒ Object 



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# File 'lib/rbbt/workflow/step/accessor.rb', line 148

def result_description=(description)
  @result_description = description
end

#result_type ⇒ Object 



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# File 'lib/rbbt/workflow/step/accessor.rb', line 128

def result_type
  @result_type ||= if @task.respond_to?(:result_type)
                     @task.result_type || info[:result_type]
                   else
                     info[:result_type]
                   end
end

#result_type=(type) ⇒ Object 



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# File 'lib/rbbt/workflow/step/accessor.rb', line 136

def result_type=(type)
  @result_type = type
end

#resumable? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rbbt/workflow/step/status.rb', line 51

def resumable?
  (task && task.resumable) || status == :waiting || status == :cleaned
end

#run_compute_dependencies(type, list, dep_step = {}) ⇒ Object 



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# File 'lib/rbbt/workflow/step/dependencies.rb', line 250

def run_compute_dependencies(type, list, dep_step = {})
  if Array === type
    type, *rest = type
  end

  canfail = (rest && rest.include?(:canfail)) || type == :canfail

  case type
  when :canfail
    list.each do |dep|
      begin
        dep.produce
      rescue RbbtException
        Log.warn "Allowing failing of #{dep.path}: #{dep.messages.last if dep.messages}"
      rescue Exception
        Log.warn "Not Allowing failing of #{dep.path} because #{$!.class} not RbbtException"
        raise $!
      end
      nil
    end
  when :produce, :no_dup
    list.each do |step|
      Misc.insist do
        begin
          step.produce
        rescue RbbtException
          raise $! unless canfail || step.canfail?
        rescue Exception
          step.exception $!
          if step.recoverable_error?
            raise $!
          else
            raise StopInsist.new($!)
          end
        end
      end
    end
    nil
  when :bootstrap
    cpus = rest.nil? ? nil : rest.first 

    if cpus.nil? 
      keys = ['bootstrap'] + list.collect{|d| [d.task_name, d.task_signature] }.flatten.uniq
      cpus = config('dep_cpus', *keys, :default => [5, list.length / 2].min)
    elsif Symbol === cpus
      cpus = config('dep_cpus', cpus, :default => [5, list.length / 2].min)
    end

    respawn = rest && rest.include?(:respawn)
    respawn = false if rest && rest.include?(:norespawn)
    respawn = rest && rest.include?(:always_respawn)
    respawn = :always if respawn.nil?

    Misc.bootstrap(list, cpus, :bar => "Bootstrapping dependencies for #{self.short_path} [#{cpus}]", :respawn => respawn) do |dep|
      begin
        Signal.trap(:INT) do
          dep.abort
          raise Aborted
        end

        Misc.insist do
          begin
            dep.produce 
            Log.warn "Error in bootstrap dependency #{dep.path}: #{dep.messages.last}" if dep.error? or dep.aborted?

          rescue Aborted
            ex = $!
            begin
              dep.abort
              Log.warn "Aborted bootstrap dependency #{dep.path}: #{dep.messages.last}" if dep.error? or dep.aborted?
            rescue
            end
            raise StopInsist.new(ex)

          rescue RbbtException
            if canfail || dep.canfail?
              Log.warn "Allowing failing of #{dep.path}: #{dep.messages.last}"
            else
              Log.warn "NOT Allowing failing of #{dep.path}: #{dep.messages.last}"
              dep.exception $!
              if dep.recoverable_error?
                begin
                  dep.abort
                rescue
                end
                raise $!
              else
                raise StopInsist.new($!)
              end
            end
          end
        end
      rescue
        dep.abort
        raise $!
      end
      nil
    end
  else
    list.each do |step|
      execute_and_dup(step, dep_step, false)
    end
  end
end

#run_dependencies ⇒ Object 



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# File 'lib/rbbt/workflow/step/dependencies.rb', line 383

def run_dependencies

  rec_dependencies = self.rec_dependencies(true) + input_dependencies.reject{|d| d.started? }

  return if rec_dependencies.empty?

  all_deps = rec_dependencies + [self]

  compute_deps = rec_dependencies.collect do |dep|
    next unless ComputeDependency === dep
    dep.rec_dependencies + dep.inputs.flatten.select{|i| Step === i}
  end.compact.flatten.uniq

  canfail_paths = self.canfail_paths

  dep_step = {}
  seen_paths = Set.new
  all_deps.uniq.each do |step|
    next if seen_paths.include? step.path
    seen_paths << step.path

    begin
      Step.prepare_for_execution(step) unless step == self 
    rescue DependencyError, DependencyRbbtException
      raise $! unless canfail_paths.include? step.path
    end

    next unless step.dependencies and step.dependencies.any?

    # ToDo is this really necessary
    #(step.dependencies + step.input_dependencies).each do |step_dep|
    step.dependencies.each do |step_dep|
      next unless step.dependencies.include?(step_dep)
      next if step_dep.done? or step_dep.running? or 
        (ComputeDependency === step_dep and (step_dep.compute == :nodup or step_dep.compute == :ignore))
      dep_step[step_dep.path] ||= []
      dep_step[step_dep.path] << step
    end

  end

  produced = []
  (dependencies + input_dependencies).each do |dep|
    next if dep.started?
    next unless ComputeDependency === dep
    if dep.compute == :produce
      dep.produce 
      produced << dep.path
    end
  end

  self.dup_inputs

  required_dep_paths = []
  dep_step.each do |path,list|
    required_dep_paths << path if (list & dependencies).any?
  end

  required_dep_paths.concat dependencies.collect{|dep| dep.path}

  required_dep_paths.concat input_dependencies.collect{|dep| dep.path}

  required_dep_paths.concat(dependencies.collect do |dep| 
    [dep.path] + dep.input_dependencies
  end.flatten)


  pre_deps = []
  simple_dependencies = []
  compute_simple_dependencies = {}
  compute_last_deps = {}
  seen_paths = Set.new
  rec_dependencies.uniq.reverse.each do |step| 
    next if seen_paths.include? step.path
    seen_paths << step.path
    next unless required_dep_paths.include? step.path
    required_seen_paths = seen_paths & required_dep_paths

    inputs = step.inputs
    inputs = inputs.values if Hash === inputs
    internal = inputs.select{|i| i.respond_to?(:path) && required_seen_paths.include?(i.path) }.any?

    if ComputeDependency === step 
      next if produced.include? step.path
      if internal
        compute_last_deps[step.compute] ||= []
        compute_last_deps[step.compute] << step
      else
        compute_simple_dependencies[step.compute] ||= []
        compute_simple_dependencies[step.compute] << step
      end
    else
      if internal
        simple_dependencies << step
      else
        simple_dependencies.prepend(step)
      end
    end
  end

  log :dependencies, "Processing dependencies for #{Log.color :yellow, task_name.to_s || ""}" if compute_simple_dependencies.any? || simple_dependencies.any? || compute_last_deps.any?

  Log.debug "compute_simple_dependencies: #{Misc.fingerprint(compute_simple_dependencies)} - #{Log.color :blue, self.path}" if compute_simple_dependencies.any?
  compute_simple_dependencies.each do |type,list|
    run_compute_dependencies(type, list, dep_step)
  end

  Log.low "pre_deps: #{Misc.fingerprint(pre_deps)} - #{Log.color :blue, self.path}" if pre_deps.any?
  pre_deps.each do |step|
    next if compute_deps.include? step
    begin
      execute_and_dup(step, dep_step, false)
    rescue Exception
      raise $! unless canfail_paths.include?(step.path)
    end
  end

  Log.debug "simple_dependencies: #{Misc.fingerprint(simple_dependencies)} - #{Log.color :blue, self.path}" if simple_dependencies.any?
  simple_dependencies.each do |step|
    next if compute_deps.include? step
    begin Exception
      execute_and_dup(step, dep_step) 
    rescue 
      raise $! unless canfail_paths.include?(step.path)
    end
  end

  Log.low "compute_last_deps: #{Misc.fingerprint(compute_simple_dependencies)} - #{Log.color :blue, self.path}" if compute_simple_dependencies.any?
  compute_simple_dependencies.each do |type,list|
    run_compute_dependencies(type, list, dep_step)
  end

  dangling_deps = all_deps.reject{|dep| dep.done? || canfail_paths.include?(dep.path) }.
    select{|dep| dep.waiting? }

  Log.medium "Aborting (actually not) waiting dangling dependencies #{Misc.fingerprint dangling_deps}" if dangling_deps.any?
  #dangling_deps.each{|dep| dep.abort }

end

#running? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rbbt/workflow/step/status.rb', line 112

def running? 
  return false if ! (started? || status == :ending)
  return nil unless Open.exist?(self.pid_file)
  pid = Open.read(self.pid_file).to_i

  return false if done? or error? or aborted? 

  if Misc.pid_exists?(pid) 
    pid
  else
    done? or error? or aborted? 
  end
end

#save_file(name, content) ⇒ Object 



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# File 'lib/rbbt/workflow/step/accessor.rb', line 271

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/step/accessor.rb', line 216

def set_info(key, value)
  return nil if @exec or info_file.nil?
  return nil if ! writable?
  value = Annotated.purge value if defined? Annotated
  Open.lock(info_file, :lock => info_lock) do
    i = info(false).dup
    value = Annotated.purge(value)

    i[key] = value 

    dump = Step.serialize_info(i)

    @info_cache = IndiferentHash.setup(i)
    Misc.sensiblewrite(info_file, dump, :force => true, :lock => false) if Open.exists?(info_file)
    @info_cache_time = Time.now
    value
  end
end

#short_path ⇒ Object 



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

def short_path
  [task_name, name] * "/"
end

#short_path_real ⇒ Object 



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# File 'lib/rbbt/workflow/step/accessor.rb', line 160

def short_path_real
  [(Symbol === overriden ? overriden : task_name).to_s, name] * "/"
end

#soft_grace ⇒ Object 



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# File 'lib/rbbt/workflow/refactor.rb', line 57

def soft_grace
  sleep 1 until Open.exists?(info_file)
end

#stalled? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rbbt/workflow/step/status.rb', line 126

def stalled?
  started? && ! (done? || running? || done? || error? || aborted?)
end

#started? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rbbt/workflow/step/status.rb', line 55

def started?
  Open.exists?(path) or (Open.exists?(pid_file) && Open.exists?(info_file))
end

#status ⇒ Object 



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# File 'lib/rbbt/workflow/step/info.rb', line 122

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/step/info.rb', line 131

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

#status_lock ⇒ Object 



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# File 'lib/rbbt/workflow/step/accessor.rb', line 192

def status_lock
  return @mutex
  #@status_lock = begin
  #               path = Persist.persistence_path(info_file + '.status.lock', {:dir => Step.lock_dir})
  #               Lockfile.new path, :refresh => false, :dont_use_lock_id => true
  #             end if @status_lock.nil?
  #@status_lock
end

#stop_dependencies ⇒ Object 



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# File 'lib/rbbt/workflow/step/dependencies.rb', line 523

def stop_dependencies
  return if dependencies.nil?
  dependencies.each do |dep|
    if dep.nil?
      Log.warn "Dependency is nil #{Misc.fingerprint step} -- #{Misc.fingerprint dependencies}"
      next
    end

    next if dep.done? or dep.aborted?

    dep.abort if dep.running?
  end
  kill_children
end

#streaming? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rbbt/workflow/step/status.rb', line 104

def streaming?
  (IO === @result) or (not @saved_stream.nil?) or status == :streaming
end

#task_signature ⇒ Object 



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# File 'lib/rbbt/workflow/step/accessor.rb', line 169

def task_signature
  [workflow.to_s, task_name] * "#"
end

#tmp_path ⇒ Object 



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# File 'lib/rbbt/workflow/step/accessor.rb', line 256

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

#waiting? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rbbt/workflow/step/status.rb', line 59

def waiting?
  Open.exists?(info_file) and not started?
end

#workflow_short_path ⇒ Object 



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# File 'lib/rbbt/workflow/step/accessor.rb', line 164

def workflow_short_path
  return short_path unless workflow
  workflow.to_s + "#" + short_path
end