Class: Step

Inherits:
Object
  • Object
show all
Defined in:
lib/rbbt/workflow/step.rb,
lib/rbbt/workflow/step/run.rb,
lib/rbbt/workflow/step/prepare.rb,
lib/rbbt/workflow/util/archive.rb,
lib/rbbt/workflow/step/accessor.rb,
lib/rbbt/workflow/util/provenance.rb,
lib/rbbt/workflow/step/dependencies.rb

Direct Known Subclasses

RemoteStep

Constant Summary collapse

RBBT_DEBUG_CLEAN = 
ENV["RBBT_DEBUG_CLEAN"] == 'true'
MAIN_RSYNC_ARGS = 
"-avztAXHP"
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

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 46

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
  if Open.exists?(info_file) and (info[:path] != path)
    @relocated = true
  end
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 20

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 232

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 9

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 9

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 9

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 9

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 12

def exec
  @exec
end

#inputs ⇒ Object

Returns the value of attribute inputs.



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

def inputs
  @inputs
end

#mutex ⇒ Object

Returns the value of attribute mutex.



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

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.rb', line 15

def original_task_name
  @original_task_name
end

#overriden ⇒ Object

Returns the value of attribute overriden.



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

def overriden
  @overriden
end

#path ⇒ Object

Returns the value of attribute path.



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

def path
  @path
end

#pid ⇒ Object

Returns the value of attribute pid.



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

def pid
  @pid
end

#real_inputs ⇒ Object

Returns the value of attribute real_inputs.



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# File 'lib/rbbt/workflow/step.rb', line 15

def real_inputs
  @real_inputs
end

#relocated ⇒ Object

Returns the value of attribute relocated.



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

def relocated
  @relocated
end

#result ⇒ Object

Returns the value of attribute result.



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

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 9

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 14

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 9

def stream
  @stream
end

#task ⇒ Object

Returns the value of attribute task.



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

def task
  @task
end

#task_name ⇒ Object

Returns the value of attribute task_name.



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

def task_name
  @task_name
end

#workflow ⇒ Object

Returns the value of attribute workflow.



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

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 108

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
        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.rb', line 425

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 (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)

    @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 13

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 45

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

.info_file(path) ⇒ Object 



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# File 'lib/rbbt/workflow/step/accessor.rb', line 49

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

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



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# File 'lib/rbbt/workflow/util/archive.rb', line 54

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.exists?(step.path)
    next if skip_overriden && step.overriden

    job_files << step.path
    job_files << step.info_file if File.exists?(step.info_file)
    job_files << Step.md5_file(step.path) if File.exists?(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.exists?(step.files_dir)
    rec_dependencies = Set.new

    next unless recursive

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

      dep = Workflow.load_step 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
      job_files << dep.path
      job_files << dep.files_dir if Dir.glob(dep.files_dir + '/*').any?
      job_files << dep.info_file if File.exists?(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 80

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 5

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.exists?(path)
  FileUtils.ln_s path + '.files', target_dir[workflow][task][name].find + '.files' if File.exists?(path + '.files')
  FileUtils.ln_s path + '.info', target_dir[workflow][task][name].find + '.info' if File.exists?(path + '.info')
end

.load_serialized_info(io) ⇒ Object 



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

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/accessor.rb', line 395

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/accessor.rb', line 323

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/accessor.rb', line 365

def self.log_progress(status, options = {}, path = nil, &block)
  options = Misc.add_defaults options, :severity => Log::INFO, :file => 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/accessor.rb', line 350

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/step/accessor.rb', line 61

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

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



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# File 'lib/rbbt/workflow/util/archive.rb', line 129

def self.migrate(path, search_path, options = {})
  resource=Rbbt

  orig_path = path
  other_rsync_args = options[:rsync]

  recursive = options[:recursive]
  recursive = false if recursive.nil?

  paths = if options[:source]
            Misc.ssh_run(options[:source], <<-EOF).split("\n")
require 'rbbt-util'
require 'rbbt/workflow'

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

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

files = path.glob_all

files = Step.job_files_for_archive(files, recursive)

puts files * "\n"
            EOF

          else
            if File.exists?(path)
              path = resource.identify(path)
              raise "Resource #{resource} could not identify #{orig_path}" if path.nil?
            else
              path = Path.setup(path)
            end
            files = path.glob_all
            files = Step.job_files_for_archive(files, recursive)
            files
          end


  target = if options[:target] 
             target = Misc.ssh_run(options[:target], <<-EOF).split("\n").first
require 'rbbt-util'
path = "var/jobs"
resource = #{resource.to_s}
search_path = "#{search_path}"
puts resource[path].find(search_path)
             EOF
           else
             resource['var/jobs'].find(search_path)
           end

  subpath_files = {}
  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[subpath.length..-1]

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

  synced_files = []
  subpath_files.each do |subpath, files|
    if options[:target]
      CMD.cmd("ssh #{options[:target]} mkdir -p '#{File.dirname(target)}'")
    else
      Open.mkdir File.dirname(target)
    end

    if options[:source]
      source = [options[:source], subpath] * ":"
    else
      source = subpath
    end
    target = [options[:target], target] * ":" if options[:target]

    next if File.exists?(source) && File.exists?(target) && File.expand_path(source) == File.expand_path(target)

    files_and_dirs = Set.new( files )
    files.each do |file|
      synced_files << File.join(subpath, file)

      parts = file.split("/")[0..-2].reject{|p| p.empty?}
      while parts.any?
        files_and_dirs <<  parts * "/"
        parts.pop
      end
    end

    TmpFile.with_file(files_and_dirs.sort_by{|l| l.length}.to_a * "\n") do |tmp_include_file|
      test_str = options[:test] ? '-nv' : ''

      cmd = "rsync #{MAIN_RSYNC_ARGS} --progress #{test_str} --files-from='#{tmp_include_file}' #{source}/ #{target}/ #{other_rsync_args}"

      #cmd << " && rm -Rf #{source}" if options[:delete]
      if options[:print]
        ppp Open.read(tmp_include_file)
        puts cmd 
      else
        CMD.cmd_log(cmd, :log => Log::INFO)
      end
    end
  end

  if options[:delete] && synced_files.any?
    puts Log.color :magenta, "About to erase these files:"
    synced_files.each do |p|
      puts Log.color :red, p
    end 

    if options[:non_interactive]
      response = 'yes'
    else
      puts Log.color :magenta, "Type 'yes' if you are sure:"
      response = STDIN.gets.chomp
    end

    if response == 'yes'
      synced_files.each do |p|
        Open.rm p
      end
    end
  end
end

.pid_file(path) ⇒ Object 



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

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

.prepare_dependencies(jobs, tasks, cpus) ⇒ Object 



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

def self.prepare_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

.prepare_for_execution(job) ⇒ Object

Raises:



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# File 'lib/rbbt/workflow/step/dependencies.rb', line 73

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.exists?(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

  raise DependencyError, job if job.error? and not canfail
end

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



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# File 'lib/rbbt/workflow/util/provenance.rb', line 72

def self.prov_report(step, offset = 0, task = nil, seen = [], expand_repeats = false)
  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)

  str = " " * offset
  str << prov_report_msg(status, name, path, info)
  step.dependencies.reverse.each do |dep|
    path = dep.path
    new = ! seen.include?(path)
    if new
      seen << path
      str << prov_report(dep, offset + 1, task, seen, expand_repeats)
    else
      if expand_repeats
        str << Log.color(:green, 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(status == :notfound ? :blue : :green, " " * (offset + 1) + Log.uncolor(prov_report_msg(status, name, path, info)))
      end
    end
  end if step.dependencies
  str
end

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



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

def self.prov_report_msg(status, name, path, info = 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
  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].compact * " " << " (#{Log.color(:red, "Mtime out of sync") })"
        else
          prov_status_msg(status.to_s) << " " << [workflow, task, path].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 2

def self.prov_status_msg(status)
  color = case status.to_sym
          when :error, :aborted, :missing, :dead, :unsync
            :red
          when :streaming, :started
            :cyan
          when :done, :noinfo
            :green
          when :dependencies, :waiting, :setup
            :yellow
          when :notfound, :cleaned
            :blue
          else
            if status.to_s.index ">"
              :cyan
            else
              :cyan
            end
          end
  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 263

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 6

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

.save_inputs(inputs, input_types, dir) ⇒ Object 



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# File 'lib/rbbt/workflow/step/accessor.rb', line 88

def self.save_inputs(inputs, input_types, dir)
  inputs.each do |name,value|
    type = input_types[name]
    type = type.to_s if type
    path = File.join(dir, name.to_s)

    Log.debug "Saving job input #{name} (#{type}) into #{path}"
    case
    when Step === value
      Open.ln_s(value.path, path)
    when type.to_s == "file"
      if String === value && File.exists?(value)
        Open.ln_s(value, path)
      else
        Open.write(path + '.yaml', value.to_yaml)
      end
    when Array === value
      Open.write(path, value.collect{|v| Step === v ? v.path : v.to_s} * "\n")
    when IO === value
      if value.filename && String === value.filename && File.exists?(value.filename)
        Open.ln_s(value.filename, path)
      else
        Open.write(path, value)
      end
    else
      Open.write(path, value.to_s)
    end
  end.any?
end

.save_job_inputs(job, dir, options = nil) ⇒ Object 



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

def self.save_job_inputs(job, dir, options = nil)
  options = IndiferentHash.setup options.dup if options

  task_name = Symbol === job.overriden ? job.overriden : job.task_name
  workflow = job.workflow
  workflow = Kernel.const_get workflow if String === workflow
  if workflow
    task_info = workflow.task_info(task_name)
    input_types = task_info[:input_types]
    task_inputs = task_info[:inputs]
    input_defaults = task_info[:input_defaults]
  else
    task_info = input_types = task_inputs = input_defaults = {}
  end

  inputs = {}
  real_inputs = job.real_inputs || job.info[:real_inputs]
  job.recursive_inputs.zip(job.recursive_inputs.fields).each do |value,name|
    next unless task_inputs.include? name.to_sym
    next unless real_inputs.include? name.to_sym
    next if options && ! options.include?(name)
    next if value.nil?
    next if input_defaults[name] == value
    inputs[name] = value
  end

  if options && options.include?('override_dependencies')
    inputs.merge!(:override_dependencies => open[:override_dependencies])
    input_types = IndiferentHash.setup(input_types.merge(:override_dependencies => :array))
  end
  save_inputs(inputs, input_types, dir)

  inputs.keys
end

.serialize_info(info) ⇒ Object 



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

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/accessor.rb', line 309

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 69

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 53

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 21

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

    threads = jobs.collect do |j| 
      Thread.new do
        begin
          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

#_abort ⇒ Object 



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# File 'lib/rbbt/workflow/step/run.rb', line 628

def _abort
  return if @aborted
  @aborted = true
  Log.medium{"#{Log.color :red, "Aborting"} #{Log.color :blue, path}"}
  doretry = true
  begin
    return if done?
    abort_pid if running?
    kill_children
    abort_stream
    stop_dependencies
  rescue Aborted, Interrupt
    Log.medium{"#{Log.color :red, "Aborting ABORTED RETRY"} #{Log.color :blue, path}"}
    if doretry
      doretry = false
      retry
    end
    raise $!
  rescue Exception
    if doretry
      doretry = false
      retry
    end
  ensure
    _clean_finished
  end
end

#_clean_finished ⇒ Object 



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# File 'lib/rbbt/workflow/step/run.rb', line 617

def _clean_finished
  if Open.exists?(path) && status != :done
    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

#_exec ⇒ Object 



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# File 'lib/rbbt/workflow/step/run.rb', line 93

def _exec
  resolve_input_steps
  rewind_inputs
  @exec = true if @exec.nil?
  begin
    old = Signal.trap("INT"){ Thread.current.raise Aborted }
    @task.exec_in((bindings ? bindings : self), *@inputs)
  ensure
    Signal.trap("INT", old)
  end
end

#abort ⇒ Object 



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# File 'lib/rbbt/workflow/step/run.rb', line 656

def abort
  return if done? and (status == :done or status == :noinfo)
  _abort
  log(:aborted, "Job aborted") unless aborted? or error?
  self
end

#abort_pid ⇒ Object 



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# File 'lib/rbbt/workflow/step/run.rb', line 576

def abort_pid
  @pid ||= info[:pid] || Open.read(pid_file)

  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 pid #{path}: #{ @pid } #{Process.pid}"
    begin
      Process.kill("TERM", @pid.to_i)
      s = Process.waitpid2 @pid.to_i
      Log.medium "Aborted pid #{path} #{s}"
    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 599

def abort_stream
  stream = @result if IO === @result
  @saved_stream = nil
  if stream and stream.respond_to? :abort and not stream.aborted?
    doretry = true
    begin
      Log.medium "Aborting job stream #{stream.inspect} -- #{Log.color :blue, path}"
      stream.abort 
    rescue Aborted, Interrupt
      Log.medium "Aborting job stream #{stream.inspect} ABORTED RETRY -- #{Log.color :blue, path}"
      if doretry
        doretry = false
        retry
      end
    end
  end
end

#aborted? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rbbt/workflow/step/accessor.rb', line 546

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

#access ⇒ Object 



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# File 'lib/rbbt/workflow/step/accessor.rb', line 666

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 20

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 = Workflow.load_step 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.rb', line 127

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.rb', line 132

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

  archived_info = {}
  dependencies.each do |dep|
    archived_info[dep.path] = dep.info
    archived_info.merge!(dep.archived_info)
  end if dependencies

  archived_info
end

#archived_inputs ⇒ Object 



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

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 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 317

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

#checks ⇒ Object 



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

def checks
  (dependency_checks + input_checks).uniq
end

#child(&block) ⇒ Object 



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# File 'lib/rbbt/workflow/step.rb', line 342

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
  set_info :children_pids, children_pids
  child_pid
end

#clean ⇒ Object 



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# File 'lib/rbbt/workflow/step.rb', line 460

def clean
  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)
  self
end

#cmd(*args) ⇒ Object 



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

def cmd(*args)
  all_args = *args

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

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

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

  io = CMD.cmd(*all_args)
  child_pid = io.pids.first

  children_pids = info[:children_pids]
  if children_pids.nil?
    children_pids = [child_pid]
  else
    children_pids << child_pid
  end
  set_info :children_pids, children_pids

  while c = io.getc
    STDERR << c if Log.severity <= level
    if c == "\n"
      if pid
        Log.logn "STDOUT [#{pid}]: ", level
      else
        Log.logn "STDOUT: ", level
      end
    end
  end 

  io.join

  nil
end

#config(key, *tokens) ⇒ Object 



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# File 'lib/rbbt/workflow/step/accessor.rb', line 651

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

#copy_files_dir ⇒ Object 



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# File 'lib/rbbt/workflow/step.rb', line 115

def copy_files_dir
  if File.symlink?(self.files_dir)
    begin
      realpath = Open.realpath(self.files_dir)
      Open.rm self.files_dir
      Open.cp realpath, self.files_dir
    rescue
      Log.warn "Copy files_dir for #{self.workflow_short_path}: " + $!.message
    end
  end
end

#dependency_checks ⇒ Object 



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

def dependency_checks
  return [] if ENV["RBBT_UPDATE"] != "true"

  rec_dependencies(true).
    reject{|dependency| (defined?(WorkflowRemoteClient) && WorkflowRemoteClient::RemoteStep === dependency) || Open.remote?(dependency.path) }.
    reject{|dependency| dependency.error? }.
    #select{|dependency| Open.exists?(dependency.path) || ((Open.exists?(dependency.info_file) && (dependency.status == :cleaned) || dependency.status == :waiting)) }.
    #select{|dependency| dependency.updatable? }.
    collect{|dependency| Workflow.relocate_dependency(self, dependency)}
end

#dirty? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rbbt/workflow/step/accessor.rb', line 481

def dirty?
  return true if Open.exists?(pid_file) && ! ( Open.exists?(info_file) || done? )
  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/accessor.rb', line 468

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/accessor.rb', line 504

def done?
  path and Open.exists? path
end

#dup_inputs ⇒ Object 



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# File 'lib/rbbt/workflow/step/dependencies.rb', line 61

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/accessor.rb', line 538

def error?
  status == :error
end

#exception(ex, msg = nil) ⇒ Object 



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# File 'lib/rbbt/workflow/step/accessor.rb', line 415

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 204

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]
      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 133

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)
      raise DependencyError, [dependency.path, dependency.messages.last] * ": " if dependency.error?
    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) ⇒ Object 



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# File 'lib/rbbt/workflow/step/accessor.rb', line 568

def file(name)
  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 561

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 553

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

#fork(no_load = false, semaphore = nil) ⇒ Object 



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# File 'lib/rbbt/workflow/step/run.rb', line 497

def fork(no_load = false, 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]
  sout, sin = Misc.pipe if no_load == :stream
  @pid = Process.fork do
    Signal.trap(:TERM) do
      raise Aborted, "Recieved TERM Signal on forked process #{Process.pid}"
    end
    sout.close if sout
    Misc.pre_fork
    Open.mkdir File.dirname(path) unless Open.exist?(File.dirname(path))
    Open.write(pid_file, Process.pid.to_s) unless Open.exists?(path) or Open.exists?(pid_file)

    if semaphore
      init_info
      log :queue, "Queued over semaphore: #{semaphore}"
      ret = RbbtSemaphore.wait_semaphore(semaphore)
      raise SemaphoreInterrupted if ret == -1
    end

    begin
      begin
        @forked = true
        res = run no_load
        set_info :forked, true
        if sin
          io = TSV.get_stream res
          if io.respond_to? :setup
            io.setup(sin) 
            sin.pair = io
            io.pair = sin
          end
          begin
            Misc.consume_stream(io, false, sin)
          rescue 
            Log.warn "Could not consume stream (#{io.closed? ? 'closed' : 'open'}) into pipe for forked job: #{self.path}"
            Misc.consume_stream(io) unless io.closed?
          end
        end
      rescue Aborted, Interrupt
        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
    end
  end
  sin.close if sin
  @result = sout if sout 
  Process.detach(@pid)
  self
end

#get_exception ⇒ Object 



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# File 'lib/rbbt/workflow/step/accessor.rb', line 429

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

#get_stream ⇒ Object 



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

def get_stream
  @mutex.synchronize do
    Log.low "Getting stream from #{path} #{!@saved_stream} [#{object_id}-#{Misc.fingerprint(@result)}]"
    begin
      if IO === @result 
        return nil if @saved_stream
        @saved_stream = @result 
      elsif StreamArray === @result and @result.any?
        @saved_stream = @result.pop 
      else
        nil
      end
    end
  end
end

#grace ⇒ Object 



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# File 'lib/rbbt/workflow/step/run.rb', line 684

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

#info(check_lock = true) ⇒ Object 



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# File 'lib/rbbt/workflow/step/accessor.rb', line 203

def info(check_lock = true)
  return {:status => :noinfo} if info_file.nil? or not 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 177

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 185

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 242

def init_info(force = false)
  return nil if @exec || info_file.nil? || (Open.exists?(info_file) && ! force)
  Open.lock(info_file, :lock => info_lock) do
    i = {:status => :waiting, :pid => Process.pid, :path => path, :real_inputs => real_inputs}
    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_checks ⇒ Object 



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# File 'lib/rbbt/workflow/step/run.rb', line 133

def input_checks
  (inputs.select{|i| Step === i } + inputs.select{|i| Path === i && Step === i.resource}.collect{|i| i.resource})
    #select{|dependency| dependency.updatable? }
end

#input_dependencies ⇒ Object 



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# File 'lib/rbbt/workflow/step/dependencies.rb', line 129

def input_dependencies
  (inputs.flatten.select{|i| Step === i} + inputs.flatten.select{|dep| Path === dep && Step === dep.resource}.collect{|dep| dep.resource})
end

#join ⇒ Object 



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# File 'lib/rbbt/workflow/step/run.rb', line 691

def join

  grace if Open.exists?(info_file) 

  if streaming?
    join_stream 
  end

  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
        pid = pid.to_i if String === pid
        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

    until (Open.exists?(path) && (status == :done || status == :noinfo)) or error? or aborted? or waiting?
      sleep 1
      join_stream if streaming?
    end

    self
  ensure
    begin
      set_info :joined, true 
    rescue
    end if Open.exists?(info_file) && writable?
    @result = nil
  end
end

#join_stream ⇒ Object 



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# File 'lib/rbbt/workflow/step/run.rb', line 663

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

#kill_children ⇒ Object 



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# File 'lib/rbbt/workflow/step/run.rb', line 197

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 "TERM", pid.to_i
        rescue Exception
          Log.medium("Exception killing child #{ pid }: #{$!.message}")
        end
      end
    end
  rescue
    Log.medium("Exception finding children")
  end
end

#knowledge_base(organism = nil) ⇒ Object 



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# File 'lib/rbbt/workflow/step/accessor.rb', line 729

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

#load ⇒ Object 



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# File 'lib/rbbt/workflow/step.rb', line 395

def load
  res = begin
          @result = nil if IO === @result && @result.closed?
          if @result && @path != @result
            res = @result
          else
            join if not done?
            res = @path.exists? ? Persist.load_file(@path, result_type) : exec
          end

          if result_description
            entity_info = info.dup
            entity_info.merge! info[:inputs] if info[:inputs]
            res = prepare_result res, result_description, entity_info 
          end

          res
        rescue IOError
          if @result
            @result = nil
            retry
          end
          raise $!
        ensure
          @result = nil if IO === @result
        end

  res
end

#load_dependencies_from_info ⇒ Object 



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# File 'lib/rbbt/workflow/step.rb', line 89

def load_dependencies_from_info
  relocated = nil
  @dependencies = (self.info[:dependencies] || []).collect do |task,name,dep_path|
    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 588

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

#load_inputs_from_info ⇒ Object 



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

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
      @inputs = NamedArray.setup info_inputs.values, info_inputs.keys
    end
  else
    nil
  end
end

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



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

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 114

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/accessor.rb', line 380

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

#merge_info(hash) ⇒ Object 



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# File 'lib/rbbt/workflow/step/accessor.rb', line 268

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/accessor.rb', line 304

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

#messages ⇒ Object 



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

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/accessor.rb', line 534

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 677

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 153

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/accessor.rb', line 512

def noinfo?
  status == :noinfo
end

#nopid? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rbbt/workflow/step/accessor.rb', line 542

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

#out_of_date ⇒ Object 



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

def out_of_date

  checks = self.checks
  return [] if checks.empty?
  outdated_time  = []
  outdated_dep  = []
  canfail_paths = self.canfail_paths
  this_mtime = Open.mtime(self.path) if Open.exists?(self.path)

  #outdated_time = checks.select{|dep| dep.updatable? && dep.done? && Persist.newer?(path, dep.path) }
  outdated_time = checks.select{|dep| dep.done? && Persist.newer?(path, dep.path) }
  outdated_dep = checks.reject{|dep| dep.done? || (dep.error? && ! dep.recoverable_error? && canfail_paths.include?(dep.path)) }

  #checks.each do |dep| 
  #  next unless dep.updatable?
  #  dep_done = dep.done?

  #  begin
  #    if this_mtime && dep_done && Open.exists?(dep.path) && (Open.mtime(dep.path) > this_mtime + 1)
  #      outdated_time << dep
  #    end
  #  rescue
  #  end

  #  # Is this pointless? this would mean some dep got updated after a later
  #  # dep but but before this one.
  #  #if (! dep.done? && ! canfail_paths.include?(dep.path)) || ! dep.updated?

  #  if (! dep_done && ! canfail_paths.include?(dep.path))
  #    outdated_dep << dep
  #  end
  #end

  Log.high "Some newer files found: #{Misc.fingerprint outdated_time}" if outdated_time.any?
  Log.high "Some outdated files found: #{Misc.fingerprint outdated_dep}" if outdated_dep.any?

  outdated_time + outdated_dep
end

#persist_checks ⇒ Object 



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

def persist_checks
  canfail_paths = self.canfail_paths
  checks.collect do |dep| 
    path = dep.path
    next if ! dep.done? && canfail_paths.include?(path)
    path 
  end.compact
end

#pid_file ⇒ Object 



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# File 'lib/rbbt/workflow/step/accessor.rb', line 181

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

#prepare_result(value, description = nil, entity_info = nil) ⇒ Object 



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# File 'lib/rbbt/workflow/step.rb', line 268

def prepare_result(value, description = nil, entity_info = nil)
  res = case 
  when IO === value
    begin
      res = case result_type
            when :array
              array = []
              while line = value.gets
                array << line.chomp
              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
    entity_info ||= begin 
                      entity_info = info.dup
                      entity_info.merge! info[:inputs] if info[:inputs]
                      entity_info
                    end
    entity_info.each do |k,v|
      value.send("#{h}=", v) if annotations.include? k
    end
                      
    value
  else
    entity_info ||= begin 
                      entity_info = info.dup
                      entity_info.merge! info[:inputs] if info[:inputs]
                      entity_info
                    end
    Entity.formats[description].setup(value, entity_info.merge(:format => description))
  end

  if Annotated === res
    dep_hash = nil
    res.annotations.each do |a|
      a = a.to_s
      varname = "@" + a
      next unless res.instance_variable_get(varname).nil? 

      dep_hash ||= begin
                     h = {}
                     rec_dependencies.each{|dep| h[dep.task_name.to_s] ||= dep }
                     h
                   end
      dep = dep_hash[a]
      next if dep.nil?
      res.send(a.to_s+"=", dep.load)
    end 
  end

  res
end

#produce(force = false, dofork = false) ⇒ Object 



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# File 'lib/rbbt/workflow/step/run.rb', line 459

def produce(force=false, dofork=false)
  return self if done? and not dirty?

  self.status_lock.synchronize do
    if error? || aborted? || stalled?
      if stalled?
        Log.warn "Aborting stalled job #{self.path}"
        abort
      end
      if force or aborted? or recoverable_error?
        clean
      else
        e = get_exception
        if e
          Log.error "Raising exception in produced job #{self.path}: #{e.message}" 
          raise e
        else
          raise "Error in job: #{self.path}"
        end
      end
    end
  end

  update if done?

  if dofork
    fork(true) unless started?

    join unless done?
  else
    run(true) unless started?

    join unless done?
  end

  self
end

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



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# File 'lib/rbbt/workflow/step/accessor.rb', line 384

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

  max = options[:max]
  Log::ProgressBar.new_bar(max, {:desc => msg, :file => file(:progress)}.merge(options))
end

#provenance ⇒ Object 



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# File 'lib/rbbt/workflow/step/accessor.rb', line 626

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 639

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

#rec_access ⇒ Object 



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# File 'lib/rbbt/workflow/step/accessor.rb', line 670

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.rb', line 475

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?

  new_dependencies = []
  archived_deps = self.info[:archived_info] ? self.info[:archived_info].keys : []

  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.path
    next if self.done? && connected && ! updatable?

    r = step.rec_dependencies(connected, new_dependencies.collect{|d| d.path})
    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/accessor.rb', line 448

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

#recursive_clean ⇒ Object 



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# File 'lib/rbbt/workflow/step.rb', line 503

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

#recursive_inputs ⇒ Object 



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# File 'lib/rbbt/workflow/step.rb', line 171

def recursive_inputs
  if NamedArray === inputs
    i = {}
    inputs.zip(inputs.fields).each do |v,f|
      i[f] = v
    end
  else
    i = {}
  end
  rec_dependencies.each do |dep|
    next unless NamedArray === dep.inputs

    dep.inputs.zip(dep.inputs.fields).each do |v,f|
      if i.include?(f) && i[f] != v
        Log.debug "Conflict in #{ f }: #{[Misc.fingerprint(i[f]), Misc.fingerprint(v)] * " <-> "}"
      else 
        i[f] = v
      end
    end

    dep.archived_inputs.each do |k,v|
      i[k] = v unless i.include? k
    end
  end

  self.archived_inputs.each do |k,v|
    i[k] = v unless i.include? k
  end

  #dependencies.each do |dep|
  #  di = dep.recursive_inputs
  #  next unless NamedArray === di
  #  di.fields.zip(di).each do |k,v|
  #    i[k] = v unless i.include? k
  #  end
  #end
  
  v = i.values
  NamedArray.setup v, i.keys 
  v
end

#relay_log(step) ⇒ Object 



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

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

#relocated? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rbbt/workflow/step/accessor.rb', line 725

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

#resolve_input_steps ⇒ Object 



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# File 'lib/rbbt/workflow/step/run.rb', line 27

def resolve_input_steps
  step = false
  pos = 0

  input_options = Workflow === workflow ? workflow.task_info(task_name)[:input_options] : {}
  new_inputs = inputs.collect do |i| 
    begin
      if Step === i
        if i.error?
          e = i.get_exception
          if e
            raise e
          else
            raise DependencyError, "Error in dep. #{Log.blue e.path}"
          end
        end
        step = true
        i.produce unless i.done? || i.error? || i.started?
        if i.done?
          if (task.input_options[task.inputs[pos]] || {})[:stream]
            TSV.get_stream i
          else
            if (task.input_options[task.inputs[pos]] || {})[:nofile]
              i.path
            else
              i.load
            end
          end
        elsif i.streaming? and (task.input_options[task.inputs[pos]] || {})[:stream]
          TSV.get_stream i
        else
          i.join
          if (task.input_options[task.inputs[pos]] || {})[:stream]
            TSV.get_stream i
          else
            if (task.input_options[task.inputs[pos]] || {})[:nofile]
              i.path
            else
              i.load
            end
          end
        end
      else
        i
      end
    ensure
      pos += 1
    end
  end
  @inputs.replace new_inputs if step
end

#result_description ⇒ Object 



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

def result_description
  @result_description ||= if @task.nil?
                     info[:result_description]
                   else
                     @task.result_description
                   end
end

#result_type ⇒ Object 



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# File 'lib/rbbt/workflow/step.rb', line 252

def result_type
  @result_type ||= if @task.nil?
                     info[:result_type] || :binary
                   else
                     @task.result_type || info[:result_type] || :string
                   end
end

#resumable? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rbbt/workflow/step/accessor.rb', line 647

def resumable?
  task && task.resumable
end

#rewind_inputs ⇒ Object 



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

def rewind_inputs
  return if @inputs.nil?
  Log.debug "Rewinding inputs for #{path}"
  @inputs.each do |input|
    next unless input.respond_to? :rewind
    begin
      input.rewind
      input.first_line = nil if TSV::Parser === input
      Log.debug "Rewinded #{Misc.fingerprint input}"
    rescue
    end
  end
end

#run(no_load = false) ⇒ Object 



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# File 'lib/rbbt/workflow/step/run.rb', line 216

def run(no_load = false)
  result = nil

  begin
    time_elapsed = total_time_elapsed = nil
    res = @mutex.synchronize do
      no_load = :stream if no_load

      Open.write(pid_file, Process.pid.to_s) unless Open.exists?(path) or Open.exists?(pid_file)
      result_type = @task.result_type if @task
      result_type = info[:result_type] if result_type.nil?
      result = Persist.persist "Job", result_type, :file => path, :check => persist_checks, :no_load => no_load do 
        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

        Open.write(pid_file, Process.pid.to_s) unless Open.exists? pid_file

        @exec = false
        init_info(true)

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

        merge_info({
          :issued => (issue_time = Time.now),
          :name => name,
          :pid => Process.pid.to_s,
          :pid_hostname => Socket.gethostname,
          :clean_name => clean_name,
          :workflow => (@workflow || @task.workflow).to_s,
          :task_name => @task.name,
          :result_type => @task.result_type,
          :result_description => @task.result_description,
          :dependencies => dependencies.collect{|dep| [dep.task_name, dep.name, dep.path]},
          :versions => Rbbt.versions
        })

        new_inputs = []
        @inputs.each_with_index do |input,i|
          name = @task.inputs[i]
          type = @task.input_types[name]

          if type == :directory
            directory_inputs = file('directory_inputs')
            input_source = directory_inputs['.source'][name].find
            input_dir = directory_inputs[name].find

            case input
            when Path
              if input.directory?
                new_inputs << input
              else
                input.open do |io|
                  begin
                    Misc.untar(io, input_source)
                  rescue
                    raise ParameterException, "Error unpackaging tar directory input '#{name}':\n\n#{$!.message}"
                  end
                end
                tar_1 = input_source.glob("*")
                raise ParameterException, "When using tar.gz files for directories, the directory must be the single first level entry" if tar_1.length != 1
                FileUtils.ln_s Misc.path_relative_to(directory_inputs, tar_1.first), input_dir
                new_inputs << input_dir
              end
            when File, IO, Tempfile
              begin
                Misc.untar(Open.gunzip(input), input_source)
              rescue
                raise ParameterException, "Error unpackaging tar directory input '#{name}':\n\n#{$!.message}"
              end
              tar_1 = input_source.glob("*")
              raise ParameterException, "When using tar.gz files for directories, the directory must be the single first level entry" if tar_1.length != 1
              FileUtils.ln_s Misc.path_relative_to(directory_inputs, tar_1.first), input_dir
              new_inputs << input_dir
            else
              raise ParameterException, "Format of directory input '#{name}' not understood: #{Misc.fingerprint input}"
            end
          else
            new_inputs << input
          end
        end if @inputs

        @inputs = new_inputs if @inputs

        if @inputs && ! task.inputs.nil?
          info_inputs = @inputs.collect do |i| 
            if Path === i 
              i.to_s
            else 
              i 
            end
          end
          set_info :inputs, Misc.remove_long_items(Misc.zip2hash(task.inputs, info_inputs)) 
        end

        begin
          run_dependencies
        rescue Exception
          Open.rm pid_file if Open.exists?(pid_file)
          stop_dependencies
          raise $!
        end

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

        config_keys_pre = Rbbt::Config::GOT_KEYS.dup
        begin

          result = _exec
        rescue Aborted, Interrupt
          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
          backtrace = backtrace.collect{|l| l.dup.force_encoding("UTF-8")} if String.instance_methods.include? :force_encoding
          set_info :backtrace, backtrace 
          log(:error, "#{$!.class}: #{$!.message}")
          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, "Streaming step #{Log.color :yellow, task.name.to_s || ""}"

          callback = Proc.new do
            if AbortedStream === stream
              if stream.exception
                raise stream.exception 
              else
                raise Aborted
              end
            end
            begin
              status = self.status
              if status != :done and status != :error and status != :aborted
                Misc.insist do
                  merge_info({
                    :done => (done_time = Time.now),
                    :total_time_elapsed => (total_time_elapsed = done_time - issue_time),
                    :time_elapsed => (time_elapsed = done_time - start_time),
                    :versions => Rbbt.versions
                  })
                  log :done, "Completed step #{Log.color :yellow, task.name.to_s || ""} in #{time_elapsed.to_i}+#{(total_time_elapsed - time_elapsed).to_i} sec."
                end
              end
            rescue
              Log.exception $!
            ensure
              Step.purge_stream_cache
              Open.rm pid_file if Open.exist?(pid_file)
            end
          end

          abort_callback = Proc.new do |exception|
            begin
              if exception
                self.exception exception
              else
                log :aborted, "#{Log.color :red, "Aborted"} step #{Log.color :yellow, task.name.to_s || ""}" if status == :streaming
              end
              _clean_finished
            rescue
              stop_dependencies
              Open.rm pid_file if Open.exist?(pid_file)
            end
          end

          ConcurrentStream.setup stream, :callback => callback, :abort_callback => abort_callback

          if AbortedStream === stream 
            exception = stream.exception || Aborted.new("Aborted stream: #{Misc.fingerprint stream}")
            self.exception exception
            _clean_finished
            raise exception
          end
        else
          merge_info({
            :done => (done_time = Time.now),
            :total_time_elapsed => (total_time_elapsed = done_time - issue_time),
            :time_elapsed => (time_elapsed = done_time - start_time),
            :versions => Rbbt.versions
          })
          log :ending
          Step.purge_stream_cache
          Open.rm pid_file if Open.exist?(pid_file)
        end

        set_info :dependencies, dependencies.collect{|dep| [dep.task_name, dep.name, dep.path]}

        config_keys = Rbbt::Config::GOT_KEYS[config_keys_pre.length..-1]
        set_info :config_keys, config_keys

        if result.nil? && File.exists?(self.tmp_path) && ! File.exists?(self.path)
          Open.mv self.tmp_path, self.path
        end
        result
      end # END PERSIST
      log :done, "Completed step #{Log.color :yellow, task.name.to_s || ""} in #{time_elapsed.to_i}+#{(total_time_elapsed - time_elapsed).to_i} sec." unless stream or time_elapsed.nil?

      if no_load
        @result ||= result
        self
      else
        Step.purge_stream_cache
        @result = prepare_result result, @task.result_description
      end
    end # END SYNC
    res
  rescue DependencyError
    exception $!
  rescue LockInterrupted
    raise $!
  rescue Aborted, Interrupt
    abort
    stop_dependencies
    raise $!
  rescue Exception
    exception $!
    stop_dependencies
    raise $!
  ensure 
    no_load = false unless IO === result
    Open.rm pid_file if Open.exist?(pid_file) unless no_load
    #set_info :pid, nil unless no_load
  end
end

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



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# File 'lib/rbbt/workflow/step/dependencies.rb', line 220

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}"
      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 

    cpus = config('dep_cpus', 'bootstrap', :default => [5, list.length / 2].min) if cpus.nil? || cpus.to_i == 0

    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 345

def run_dependencies
  dep_step = {}

  rec_dependencies = self.rec_dependencies(true)

  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

  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
      raise $! unless canfail_paths.include? step.path
    end
    next unless step.dependencies and step.dependencies.any?
    (step.dependencies + step.input_dependencies).each do |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 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.length > 1
    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)

  log :dependencies, "Dependencies for step #{Log.color :yellow, task.name.to_s || ""}"

  pre_deps = []
  compute_pre_deps = {}
  last_deps = []
  compute_last_deps = {}
  seen_paths = Set.new
  rec_dependencies.uniq.each do |step| 
    next if seen_paths.include? step.path
    seen_paths << step.path
    next unless required_dep_paths.include? step.path
    if step.inputs.flatten.select{|i| Step === i}.any?
      if ComputeDependency === step
        next if produced.include? step.path 
        compute_last_deps[step.compute] ||= []
        compute_last_deps[step.compute] << step
      else
        last_deps << step
      end
    else
      if ComputeDependency === step
        next if produced.include? step.path 
        compute_pre_deps[step.compute] ||= []
        compute_pre_deps[step.compute] << step
      else
        pre_deps << step #if dependencies.include?(step)
      end
    end
  end

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

  Log.medium "Processing pre dependencies: #{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.medium "Processing last dependencies: #{Misc.fingerprint(last_deps)} - #{Log.color :blue, self.path}" if last_deps.any?
  last_deps.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.medium "Computing last dependencies: #{Misc.fingerprint(compute_last_deps)} - #{Log.color :blue, self.path}" if compute_last_deps.any?
  compute_last_deps.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/accessor.rb', line 516

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 572

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 253

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
    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 158

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

#soft_grace ⇒ Object 



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# File 'lib/rbbt/workflow/step/run.rb', line 677

def soft_grace
  until done? or (Open.exist?(info_file) && info[:status] != :noinfo)
    sleep 1 
  end
  self
end

#stalled? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rbbt/workflow/step/accessor.rb', line 530

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

#started? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rbbt/workflow/step/accessor.rb', line 460

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/accessor.rb', line 283

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/accessor.rb', line 292

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

#status_lock ⇒ Object 



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# File 'lib/rbbt/workflow/step/accessor.rb', line 194

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

#step(name) ⇒ Object 



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# File 'lib/rbbt/workflow/step.rb', line 511

def step(name)
  @steps ||= {}
  @steps[name] ||= begin
                     deps = rec_dependencies.select{|step| 
                       step.task_name.to_sym == name.to_sym
                     }
                     raise "Dependency step not found: #{ name }" if deps.empty?
                     if (deps & self.dependencies).any?
                       (deps & self.dependencies).first
                     else
                       deps.first
                     end
                   end
end

#stop_dependencies ⇒ Object 



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# File 'lib/rbbt/workflow/step/dependencies.rb', line 471

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/accessor.rb', line 508

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 171

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

#tmp_path ⇒ Object 



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# File 'lib/rbbt/workflow/step/accessor.rb', line 557

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

#updatable? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rbbt/workflow/step/run.rb', line 114

def updatable?
  return true if ENV["RBBT_UPDATE_ALL_JOBS"] == 'true'
  return false unless ENV["RBBT_UPDATE"] == "true"
  return false unless Open.exists?(info_file)
  return true if status != :noinfo && ! (relocated? && done?)
  false
end

#update ⇒ Object 



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# File 'lib/rbbt/workflow/step.rb', line 453

def update
  if dirty?
    dependencies.collect{|d| d.update } if dependencies
    clean
  end
end

#updated? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rbbt/workflow/step/run.rb', line 190

def updated?
  return true if ENV["RBBT_UPDATE"] != "true"
  return true unless (done? || error? || ! writable?)

  @updated ||= out_of_date.empty?
end

#waiting? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rbbt/workflow/step/accessor.rb', line 464

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 162

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

#writable? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rbbt/workflow/step.rb', line 499

def writable?
  Open.writable?(self.path) && Open.writable?(self.info_file)
end