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_dependencies, prepare_for_execution, #prepare_result, #produce, #progress_bar, prov_report, prov_report_msg, prov_status_msg, #provenance, #provenance_paths, purge, purge_stream_cache, 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.



7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
# 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_nameObject

Returns the value of attribute base_name.



5
6
7
# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 5

def base_name
  @base_name
end

#base_urlObject

Returns the value of attribute base_url.



5
6
7
# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 5

def base_url
  @base_url
end

#input_typesObject

Returns the value of attribute input_types.



5
6
7
# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 5

def input_types
  @input_types
end

#inputsObject

Returns the value of attribute inputs.



5
6
7
# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 5

def inputs
  @inputs
end

#is_execObject

Returns the value of attribute is_exec.



5
6
7
# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 5

def is_exec
  @is_exec
end

#is_streamObject

Returns the value of attribute is_stream.



5
6
7
# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 5

def is_stream
  @is_stream
end

#result_descriptionObject

Returns the value of attribute result_description.



5
6
7
# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 5

def result_description
  @result_description
end

#result_typeObject

Returns the value of attribute result_type.



5
6
7
# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 5

def result_type
  @result_type
end

#startedObject

Returns the value of attribute started.



5
6
7
# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 5

def started
  @started
end

#stream_inputObject

Returns the value of attribute stream_input.



5
6
7
# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 5

def stream_input
  @stream_input
end

#taskObject

Returns the value of attribute task.



5
6
7
# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 5

def task
  @task
end

#urlObject

Returns the value of attribute url.



5
6
7
# 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



70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
# 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

#_restartObject



332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 332

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_fileObject



27
28
29
30
31
32
33
34
35
# 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_filesObject



37
38
39
# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 37

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

#clean_nameObject



23
24
25
# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 23

def clean_name
  @base_name
end

#done?Boolean

Returns:

  • (Boolean)


179
180
181
182
183
# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 179

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

#dup_inputsObject



102
103
104
105
106
107
108
109
110
111
# 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



235
236
237
238
239
240
241
242
243
244
245
# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 235

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

#file(file) ⇒ Object



189
190
191
# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 189

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

#filesObject



185
186
187
# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 185

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

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



227
228
229
# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 227

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

#get_streamObject



193
194
195
196
197
198
199
200
201
202
# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 193

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

#get_streamsObject



95
96
97
98
99
100
# 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

#graceObject



204
205
206
207
208
209
210
211
212
# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 204

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



133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
# 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



349
350
351
352
# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 349

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_checksObject



328
329
330
# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 328

def input_checks
  []
end

#joinObject



247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 247

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

  self
end

#load_res(res, result_type = nil) ⇒ Object



272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 272

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

#nameObject



113
114
115
116
117
# 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



119
120
121
# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 119

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

#nopid?Boolean

Returns:

  • (Boolean)


129
130
131
# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 129

def nopid?
  false
end

#pathObject



217
218
219
220
221
222
223
224
225
# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 217

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



41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
# 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)


231
232
233
# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 231

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

#short_pathObject



323
324
325
326
# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 323

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

#started?Boolean

Returns:

  • (Boolean)


175
176
177
# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 175

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

#statusObject



159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
# 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
    status
  rescue
    Log.exception $!
    nil
  ensure
    @info = nil
  end
end

#task_nameObject



123
124
125
126
127
# 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_pathObject



318
319
320
321
# File 'lib/rbbt/workflow/remote_workflow/remote_step.rb', line 318

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