Class: RemoteStep

Inherits:
Step
  • Object
show all
Defined in:
lib/rbbt/workflow/remote_workflow/remote_step.rb,
lib/rbbt/workflow/remote_workflow/remote_step/ssh.rb,
lib/rbbt/workflow/remote_workflow/remote_step/rest.rb

Defined Under Namespace

Modules: REST, SSH

Constant Summary

Constants inherited from Step

Step::INFO_SERIALIZER, Step::MAIN_RSYNC_ARGS, Step::RBBT_DEBUG_CLEAN, Step::STREAM_CACHE, Step::STREAM_CACHE_MUTEX

Instance Attribute Summary collapse

Attributes inherited from Step

#bindings, #dependencies, #dupped, #mutex, #original_task_name, #original_workflow, #overriden, #pid, #real_inputs, #relocated, #result, #saved_stream, #seen, #stream, #workflow

Class Method Summary collapse

Instance Method Summary collapse

Methods inherited from Step

#_abort, #_clean_finished, #_exec, #abort, #abort_pid, #abort_stream, #aborted?, #access, #archive, archive, #archive_deps, #archived_info, #archived_inputs, #canfail_paths, #checks, #child, clean, #clean, #cmd, #config, #copy_files_dir, #dependency_checks, #dirty?, #dirty_files, dup_stream, #error?, #exception, #execute_and_dup, #execute_dependency, files_dir, #files_dir, #get_exception, info_file, #info_file, #info_lock, #input_dependencies, job_files_for_archive, job_name_for_info_file, #join_stream, #kill_children, #knowledge_base, link_job, #load, #load_dependencies_from_info, #load_file, #load_inputs_from_info, load_serialized_info, #log, log, log_block, #log_dependency_exec, #log_progress, log_progress, log_string, md5_file, #merge_info, #message, #messages, migrate, migrate_source_paths, #missing?, #monitor_stream, #noinfo?, #out_of_date, #overriden?, #overriden_deps, #persist_checks, #pid_file, pid_file, prepare_for_execution, #prepare_result, #produce, produce_dependencies, #progress_bar, prov_report, prov_report_msg, prov_status_msg, #provenance, #provenance_paths, purge, purge_stream_cache, #python, #python_block, #python_file, raise_dependency_error, #rec_access, #rec_dependencies, #recoverable_error?, #recursive_clean, #recursive_inputs, #relay_log, #relocated?, #resolve_input_steps, #resumable?, #rewind_inputs, #run_compute_dependencies, #run_dependencies, #save_file, save_input, save_inputs, save_job_inputs, serialize_info, #set_info, #short_path_real, #soft_grace, #stalled?, #status=, status_color, #status_lock, #step, step_info, #stop_dependencies, #streaming?, #task_signature, #tmp_path, tmp_path, #updatable?, #update, #updated?, wait_for_jobs, #waiting?, #writable?

Constructor Details

#initialize(base_url, task = nil, base_name = nil, inputs = nil, input_types = nil, result_type = nil, result_description = nil, is_exec = false, is_stream = false, stream_input = nil) ⇒ RemoteStep

Returns a new instance of RemoteStep.



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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 7

def initialize(base_url, task = nil, base_name = nil, inputs = nil, input_types = nil, result_type = nil, result_description = nil, is_exec = false, is_stream = false, stream_input = nil)
  @base_url, @task, @base_name, @inputs, @input_types, @result_type, @result_description, @is_exec, @is_stream, @stream_input = base_url, task, base_name, inputs, input_types, result_type, result_description, is_exec, is_stream, stream_input
  @base_url = "http://" << @base_url unless @base_url =~ /^[a-z]+:\/\//
  @mutex = Mutex.new
  rest = base_url.include?('ssh:') ? false : true

  if rest
    @adaptor = RemoteWorkflow::REST
    self.extend RemoteStep::REST
  else
    @adaptor = RemoteWorkflow::SSH
    self.extend RemoteStep::SSH
  end

end

Instance Attribute Details

#base_name ⇒ Object

Returns the value of attribute base_name.



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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 5

def base_name
  @base_name
end

#base_url ⇒ Object

Returns the value of attribute base_url.



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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 5

def base_url
  @base_url
end

#input_types ⇒ Object

Returns the value of attribute input_types.



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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 5

def input_types
  @input_types
end

#inputs ⇒ Object

Returns the value of attribute inputs.



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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 5

def inputs
  @inputs
end

#is_exec ⇒ Object

Returns the value of attribute is_exec.



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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 5

def is_exec
  @is_exec
end

#is_stream ⇒ Object

Returns the value of attribute is_stream.



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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 5

def is_stream
  @is_stream
end

#result_description ⇒ Object

Returns the value of attribute result_description.



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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 5

def result_description
  @result_description
end

#result_type ⇒ Object

Returns the value of attribute result_type.



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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 5

def result_type
  @result_type
end

#started ⇒ Object

Returns the value of attribute started.



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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 5

def started
  @started
end

#stream_input ⇒ Object

Returns the value of attribute stream_input.



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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 5

def stream_input
  @stream_input
end

#task ⇒ Object

Returns the value of attribute task.



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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 5

def task
  @task
end

#url ⇒ Object

Returns the value of attribute url.



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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 5

def url
  @url
end

Class Method Details

.get_streams(inputs, stream_input = nil) ⇒ Object 



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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 70

def self.get_streams(inputs, stream_input = nil)
  new_inputs = {}
  inputs.each do |k,v|
    stream = stream_input.to_s == k.to_s
    if Step === v 
      unless (v.done? or v.streaming?) # or RestClient::Step === v)
        v.run(true) and v.grace 
      end

      begin
        if stream
          new_inputs[k] = TSV.get_stream(v)
        else
          new_inputs[k] = v.load
        end
      rescue Exception
        raise $!
      end
    else
      new_inputs[k] = v
    end
  end
  new_inputs
end

Instance Method Details

#_restart ⇒ Object 



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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 336

def _restart
  @done = nil
  @name = nil
  @started = nil
  @aborted = nil
  new_inputs = {}
  inputs.each do |k,i| 
    if File === i 
      new_inputs[k] = File.open(i.path)
    else
      new_inputs[k] = i
    end
  end
  @inputs = new_inputs
  @info = nil
end

#cache_file ⇒ Object 



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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 27

def cache_file
  begin
    digest = Misc.obj2digest([base_url, task.to_s, base_name, inputs])
    Rbbt.var.cache.REST[task.to_s][[clean_name, digest].compact * "."].find
  rescue
    Log.exception $!
    raise $!
  end
end

#cache_files ⇒ Object 



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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 37

def cache_files
  Dir.glob(cache_file + '.*')
end

#clean_name ⇒ Object 



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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 23

def clean_name
  @base_name
end

#done? ⇒ Boolean

Returns:

  • (Boolean) 


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

def done?
  return true if cache_files.any?
  self.init_job unless @url
  @done || status.to_s == 'done' || status.to_s == 'noinfo'
end

#dup_inputs ⇒ Object 



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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 102

def dup_inputs
  return if @dupped or ENV["RBBT_NO_STREAM"] == 'true'
  Log.low "Dupping inputs for #{path}"
  dupped_inputs = {}
  @inputs.collect do |k,input|
    dupped_inputs[k] = Step.dup_stream input
  end
  @inputs = dupped_inputs
  @dupped = true
end

#exec(noload = false) ⇒ Object 



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

def exec(noload = false)
  @result ||= begin
                if noload == :stream
                  _run_job(:exec)
                else
                  exec_job 
                end
              ensure
                @started = true
              end
end

#file(file) ⇒ Object 



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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 190

def file(file)
  init_job
  @adaptor.get_raw(File.join(url, 'file', file.to_s))
end

#files ⇒ Object 



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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 186

def files
  @adaptor.get_json(File.join(url, 'files'))
end

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



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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 229

def fork(noload=false, semaphore=nil)
  init_job(:asynchronous)
end

#get_stream ⇒ Object 



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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 195

def get_stream
  case @result
  when IO 
    @result
  when String
    StringIO.new @result
  else
    nil
  end
end

#get_streams ⇒ Object 



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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 95

def get_streams
  return if @inputs_done
  @inputs = RemoteStep.get_streams @inputs, @stream_input
  @inputs_done = true
  @inputs
end

#grace ⇒ Object 



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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 206

def grace
  produce unless @started
  sleep 0.1 unless started?
  sleep 0.5 unless started?
  sleep 1 unless started?
  while not (done? or started?)
    sleep 1 
  end
end

#info(check_lock = false) ⇒ Object 



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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 133

def info(check_lock=false)
  return {:status => :waiting } unless started?
  @done = @info && @info[:status] && (@info[:status].to_sym == :done || @info[:status].to_sym == :error)

  if !@done && (@last_info_time.nil? || (Time.now - @last_info_time) > 0.5)
    update = true 
  else
    update = false
  end

  @info = Persist.memory("RemoteSteps Info", :url => @url, :persist => true, :update => update) do
    @last_info_time = Time.now
    init_job unless @url
    info = begin
             @adaptor.get_json(File.join(@url, 'info'))
           rescue
             {:status => :noinfo}
           end
    info = RemoteWorkflow.fix_hash(info)
    info[:status] = info[:status].to_sym if String === info[:status]
    info
  end

  @info
end

#init_info(*args) ⇒ Object 



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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 353

def init_info(*args)
  i = {:status => :waiting, :pid => Process.pid, :path => path}
  i[:dependencies] = dependencies.collect{|dep| [dep.task_name, dep.name, dep.path]} if dependencies
end

#input_checks ⇒ Object 



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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 332

def input_checks
  []
end

#inspect ⇒ Object 



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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 358

def inspect
  "RemoteWorkflow #{self.path}"
end

#join ⇒ Object 



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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 249

def join
  return true if cache_files.any?
  init_job unless @url
  produce unless @started
  Log.debug{ "Joining RemoteStep: #{path}" }

  if IO === @result
    res = @result
    @result = nil
    Misc.consume_stream(res, true) 
  end

  if not (self.done? || self.aborted? || self.error?)
    self.info 
    return self if self.done? || self.aborted? || self.error?
    sleep 0.2 unless self.done? || self.aborted? || self.error?
    sleep 1 unless self.done? || self.aborted? || self.error?
    while not (self.done? || self.aborted? || self.error?)
      sleep 3
    end
  end

  raise "Error in remote step" if self.error?

  self
end

#load_res(res, result_type = nil) ⇒ Object 



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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 276

def load_res(res, result_type = nil)

  stream = true if res.respond_to? :read
  join unless stream
  result_type ||= self.result_type

  case result_type.to_sym
  when :string
    stream ? res.read : res
  when :boolean
    (stream ? res.read : res) == 'true'
  when :tsv
    if stream
      TSV.open(res, :monitor => true)
    else
      TSV.open(StringIO.new(res))
    end
  when :annotations
    if stream
      Annotated.load_tsv(TSV.open(res))
    else
      Annotated.load_tsv(TSV.open(StringIO.new(res)))
    end
  when :array
    (stream ? res.read : res).split("\n")
  else
    json_text = if IO === res
                  res.read
                else
                  res
                end
    begin
      JSON.parse json_text
    rescue
      case
      when json_text =~ /^\d+$/
        json_text.to_i
      when json_text =~ /^\d+\.\d/
        json_text.to_f
      else
        raise $!
      end
    end
  end
end

#name ⇒ Object 



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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 113

def name
  return nil if @is_exec
  return @path if @url.nil?
  (Array === @url ? @url.first : @url).split("/").last
end

#name=(name) ⇒ Object 



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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 119

def name=(name)
  @url = [base_url,task, name] * "/"
end

#nopid? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 129

def nopid?
  false
end

#path ⇒ Object 



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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 219

def path
  if @url
    Misc.add_GET_param(@url, "_format", "raw")
  elsif @base_name
    [base_url, task, @base_name + '-' +  Misc.fingerprint(inputs)] * "/"
  else
    nil
  end
end

#run(no_load = false) ⇒ Object 



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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 41

def run(no_load = false)
  no_load = @is_stream ? :stream : true if no_load

  @result ||= @mutex.synchronize do
    begin
      if @is_exec
        exec(no_load)
      elsif no_load == :stream
        _run_job(:stream)
      elsif no_load
        init_job 
        nil
      else
        if ! done?
          init_job 
          produce
          join
        end
        self.load
      end
    ensure
      @started = true
    end
  end

  return @result if no_load == :stream
  no_load ? Misc.add_GET_param(path, "_format", "raw") : @result
end

#running? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 233

def running?
  ! %w(done error aborted noinfo).include? status.to_s
end

#short_path ⇒ Object 



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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 327

def short_path
  init_job unless @url
  [@task, @name] * "/"
end

#started? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 176

def started?
  @result != nil || @started || @streaming
end

#status ⇒ Object 



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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 159

def status
  return :done if @done
  return nil unless url or started?
  #return :streaming if @streaming 
  begin
    status = info[:status]
    @done = true if status and status.to_sym == :done
    Log.low "RemoteStep status '#{status}' #{self.url}"
    status
  rescue
    Log.exception $!
    nil
  ensure
    @info = nil
  end
end

#task_name ⇒ Object 



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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 123

def task_name
  return task if task
  init_job
  (Array === @url ? @url.first : @url).split("/")[-2]
end

#workflow_short_path ⇒ Object 



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# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 322

def workflow_short_path
  init_job unless @url
  [@base_url, @task, @name] * "/"
end