Class: WorkflowManager::Server

Inherits:
Object
  • Object
show all
Defined in:
lib/workflow_manager/server.rb

Defined Under Namespace

Classes: Config, KyotoDB, PStoreDB

Constant Summary collapse

@@config = 
nil

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize ⇒ Server

Returns a new instance of Server.



83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
 
# File 'lib/workflow_manager/server.rb', line 83

def initialize
  @interval = config.interval
  @resubmit = config.resubmit
  extension = NO_KYOTO ? '.pstore' : '.kch'
  db_mode = NO_KYOTO ? 'PStore' : 'KyotoCabinet'
  @db_stat = File.join(config.db_dir, 'statuses'+extension)
  @db_logs  = File.join(config.db_dir, 'logs'+extension)

  @log_dir = File.expand_path(config.log_dir)
  @db_dir  = File.expand_path(config.db_dir)
  FileUtils.mkdir_p @log_dir unless File.exist?(@log_dir)
  FileUtils.mkdir_p @db_dir unless File.exist?(@db_dir)
  #@statuses = KyotoCabinet::DB.new
  @statuses = NO_KYOTO ? PStoreDB.new(@db_stat) : KyotoDB.new(@db_stat)
  #@logs = KyotoCabinet::DB.new 
  @logs = NO_KYOTO ? PStoreDB.new(@db_logs) : KyotoDB.new(@db_logs)
  @system_log = File.join(@log_dir, "system.log")
  @mutex = Mutex.new
  @cluster = config.cluster
  puts("DB = #{db_mode}")
  puts("Cluster = #{@cluster.name}")
  log_puts("DB = #{db_mode}")
  log_puts("Cluster = #{@cluster.name}")
  log_puts("Server starts")
end

Class Method Details

.config ⇒ Object 



41
42
43
 
# File 'lib/workflow_manager/server.rb', line 41

def self.config
  @@config
end

.config=(config) ⇒ Object 



38
39
40
 
# File 'lib/workflow_manager/server.rb', line 38

def self.config=(config)
  @@config = config
end

.configure {|@@config| ... } ⇒ Object

Yields:



47
48
49
50
51
52
53
54
55
56
57
58
59
 
# File 'lib/workflow_manager/server.rb', line 47

def self.configure
  @@config = Config.new
  # default values
  @@config.log_dir  = LOG_DIR
  @@config.db_dir   = DB_DIR
  @@config.interval = INTERVAL  # interval to check jobs, [s]
  @@config.resubmit = RESUBMIT  # how many times at maximum to resubmit when job fails
  yield(@@config)
  if @@config.cluster
    @@config.cluster.log_dir = File.expand_path(@@config.log_dir)
  end
  @@config
end

Instance Method Details

#cluster_nodes ⇒ Object 



121
122
123
 
# File 'lib/workflow_manager/server.rb', line 121

def cluster_nodes
  @cluster.cluster_nodes
end

#config ⇒ Object 



44
45
46
 
# File 'lib/workflow_manager/server.rb', line 44

def config
  @@config ||= WorkflowManager.configure{}
end

#copy_commands(org_dir, dest_parent_dir, now = nil) ⇒ Object 



111
112
113
 
# File 'lib/workflow_manager/server.rb', line 111

def copy_commands(org_dir, dest_parent_dir, now=nil)
  @cluster.copy_commands(org_dir, dest_parent_dir, now)
end

#default_node ⇒ Object 



124
125
126
 
# File 'lib/workflow_manager/server.rb', line 124

def default_node
  @cluster.default_node.to_s
end

#delete_command(target) ⇒ Object 



118
119
120
 
# File 'lib/workflow_manager/server.rb', line 118

def delete_command(target)
  @cluster.delete_command(target)
end

#finalize_monitoring(current_status, log_file, log_dir) ⇒ Object 



191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
 
# File 'lib/workflow_manager/server.rb', line 191

def finalize_monitoring(current_status, log_file, log_dir)
  if current_status == 'success' or current_status == 'fail'
    unless log_dir.empty?
      copy_commands(log_file, log_dir).each do |command|
        log_puts(command)
        system command
      end
      err_file = log_file.gsub('_o.log','_e.log')
      copy_commands(err_file, log_dir).each do |command|
        log_puts(command)
        system command
      end
    end
    Thread.current.kill
  end
end

#get_log(job_id, with_err = false) ⇒ Object 



389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
 
# File 'lib/workflow_manager/server.rb', line 389

def get_log(job_id, with_err=false)
  log_file = nil
  @logs.transaction do |logs|
    log_file = logs[job_id.to_s]
  end
  log_data = if log_file and File.exist?(log_file)
               "__STDOUT LOG__\n\n" + File.read(log_file)
             else
               'no log file'
             end
  if with_err
    err_file = log_file.gsub(/_o\.log/,'_e.log')
    if err_file and File.exist?(err_file)
      log_data << "\n\n__STDERR LOG__\n\n"
      log_data << File.read(err_file)
    end
  end
  log_data
end

#get_script(job_id) ⇒ Object 



408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
 
# File 'lib/workflow_manager/server.rb', line 408

def get_script(job_id)
  script_file = nil
  @logs.transaction do |logs|
    script_file = logs[job_id.to_s]
  end
  if script_file
    script_file = script_file.gsub(/_o\.log/,'')
  end
  script = if script_file and File.exist?(script_file)
             File.read(script_file)
           else
             'no script file'
           end
  script
end

#get_script_path(job_id) ⇒ Object 



423
424
425
426
427
428
429
430
431
 
# File 'lib/workflow_manager/server.rb', line 423

def get_script_path(job_id)
  script_file = nil
  @logs.transaction do |logs|
    script_file = logs[job_id.to_s]
  end
  script_path = if script_file and File.exist?(script_file)
                  script_file.gsub(/_o\.log/,'')
                end
end

#hello ⇒ Object 



108
109
110
 
# File 'lib/workflow_manager/server.rb', line 108

def hello
  'hello test hoge, '+ @cluster.name
end

#input_dataset_exist?(file_list) ⇒ Boolean

Returns:

  • (Boolean) 


159
160
161
162
163
164
165
166
167
168
 
# File 'lib/workflow_manager/server.rb', line 159

def input_dataset_exist?(file_list)
  flag = true
  file_list.each do |file|
    unless File.exist?(file)
      flag = false
      break
    end
  end
  flag
end

#input_dataset_file_list(dataset_tsv_path) ⇒ Object 



148
149
150
151
152
153
154
155
156
157
158
 
# File 'lib/workflow_manager/server.rb', line 148

def input_dataset_file_list(dataset_tsv_path)
  file_list = []
  CSV.foreach(dataset_tsv_path, :headers=>true, :col_sep=>"\t") do |row|
    row.each do |header, value|
      if header =~ /\[File\]/
        file_list << value
      end
    end
  end
  file_list
end

#input_dataset_tsv_path(script_content) ⇒ Object 



135
136
137
138
139
140
141
142
143
144
145
146
147
 
# File 'lib/workflow_manager/server.rb', line 135

def input_dataset_tsv_path(script_content)
  gstore_dir = nil
  input_dataset_path = nil
  script_content.split(/\n/).each do |line|
    if line =~ /GSTORE_DIR=(.+)/
      gstore_dir = $1.chomp
    elsif line =~ /INPUT_DATASET=(.+)/
      input_dataset_path = $1.chomp
      break
    end
  end
  [gstore_dir, input_dataset_path]
end

#job_list(with_results = false, project_number = nil, job_ids: nil) ⇒ Object 



368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
 
# File 'lib/workflow_manager/server.rb', line 368

def job_list(with_results=false, project_number=nil, job_ids:nil)
  s = []
  job_idsh = if job_ids
               Hash[*(job_ids.split(',')).map{|job_id| [job_id, true]}.flatten]
             end
  @statuses.transaction do |statuses|
    statuses.each do |key, value|
      if project_number 
        if x = value.split(/,/)[4].to_i==project_number.to_i
          s << [key, value]
        end
      else
        s << [key, value]
      end
    end
  end
  if job_ids
    s = s.select{|job_id, stat| job_idsh[job_id]}
  end
  s.sort_by{|key, value| value.split(',')[2]}.reverse.map{|v| v.join(',')}.join("\n")
end

#kill_job(job_id) ⇒ Object 



114
115
116
117
 
# File 'lib/workflow_manager/server.rb', line 114

def kill_job(job_id)
  status(job_id, 'fail')
  status = `#{@cluster.kill_command(job_id)}`
end

#log_puts(str) ⇒ Object 



127
128
129
130
131
132
133
134
 
# File 'lib/workflow_manager/server.rb', line 127

def log_puts(str)
  time = Time.now.strftime("[%Y.%m.%d %H:%M:%S]")
  @mutex.synchronize do
     open(@system_log, "a") do |out|
       out.print time + " " + str + "\n"
     end
  end
end

#start_monitoring(submit_command, user = 'sushi lover', resubmit = 0, script = '', project_number = 0, sge_options = '', log_dir = '') ⇒ Object 



257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
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
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
 
# File 'lib/workflow_manager/server.rb', line 257

def start_monitoring(submit_command, user = 'sushi lover', resubmit = 0, script = '', project_number = 0, sge_options='', log_dir = '')
  log_puts("monitoring: script=" + submit_command + " user=" + user + " resubmit=" + resubmit.to_s + " project=" + project_number.to_s + " sge option=" + sge_options + " log dir=" + log_dir.to_s)

  #warn submit_command
  #
  # TODO: analyze arguments
  #
  job_id, log_file, command = @cluster.submit_job(submit_command, script, sge_options)
  log_puts("submit: " + job_id + " " + command)

  #
  # monitor worker
  #
  if job_id and log_file
    monitor_worker = Thread.new(job_id, log_file, submit_command, user, resubmit, script, project_number, sge_options, log_dir) do |t_job_id, t_log_file, t_submit_command, t_user, t_resubmit, t_script, t_project_number, t_sge_options, t_log_dir|
      loop do
        status = success_or_fail(t_job_id, t_log_file) 
        script_name = File.basename(submit_command).split(/-/).first
        #@statuses.open(@db_stat)
        @statuses.transaction do |statuses|
        #start_time = if stat = @statuses[t_job_id] and stat = stat.split(/,/) and time = stat[2]
          start_time = if stat = statuses[t_job_id] and stat = stat.split(/,/) and time = stat[2]
                         time
                       end
          time = if start_time 
                   if status == 'success' or status == 'fail'
                     start_time + '/' + Time.now.strftime("%Y-%m-%d %H:%M:%S")
                   else
                     start_time
                   end
                 else
                   Time.now.strftime("%Y-%m-%d %H:%M:%S")
                 end
        #@statuses[t_job_id] = [status, script_name, time, user, project_number].join(',')
          statuses[t_job_id] = [status, script_name, time, user, project_number].join(',')
        #@statuses.close
        end
        @logs.transaction do |logs|
          logs[t_job_id] = t_log_file
        end
        #warn t_job_id + " " + status
        if status == 'success'
          log_puts(status + ": " + t_job_id)
          unless t_log_dir.empty?
            copy_commands(t_log_file, t_log_dir).each do |command|
              log_puts(command)
              system command
            end
            err_file = t_log_file.gsub('_o.log','_e.log')
            copy_commands(err_file, t_log_dir).each do |command|
              log_puts(command)
              system command
            end
          end
          Thread.current.kill
        elsif status == 'fail'
          log_puts(status + ": " + t_job_id)
          #
          # TODO: re-submit
          #
          if t_resubmit < RESUBMIT
            log_puts("resubmit: " + t_job_id)
            resubmit_job_id = start_monitoring(t_submit_command, t_user, t_resubmit + 1, t_script, t_project_number, t_sge_options)
            script_name = File.basename(submit_command).split(/-/).first
            #@statuses.open(@db_stat)
            @statuses.transaction do |statuses|
              statuses[t_job_id] = ["resubmit: " + resubmit_job_id.to_s, script_name, Time.now.strftime("%Y-%m-%d %H:%M:%S"), t_user, t_project_number].join(',')
            #@statuses.close
            end
          else
            log_puts("fail: " + t_job_id)
          end
          unless t_log_dir.empty?
            copy_commands(t_log_file, t_log_dir).each do |command|
              log_puts(command)
              system command
            end
            err_file = t_log_file.gsub('_o.log','_e.log')
            copy_commands(err_file, t_log_dir).each do |command|
              log_puts(command)
              system command
            end
          end
          Thread.current.kill
        end
        sleep @interval
      end	
    end
    job_id.to_i
  end
end

#start_monitoring2(script_path, script_content, user = 'sushi_lover', project_number = 0, sge_options = '', log_dir = '') ⇒ Object 



207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
 
# File 'lib/workflow_manager/server.rb', line 207

def start_monitoring2(script_path, script_content, user='sushi_lover', project_number=0, sge_options='', log_dir='')
  # script_path is only used to generate a log file name
  # It is not used to read the script contents
  go_submit = false
  waiting_time = 0
  gstore_dir, input_dataset_path = input_dataset_tsv_path(script_content)
  if gstore_dir and input_dataset_path
    waiting_max = 60*60*8 # 8h
    # wait until the files come
    until waiting_time > waiting_max or 
      File.exist?(input_dataset_path) and
      file_list = input_dataset_file_list(input_dataset_path) and
      file_list.map!{|file| File.join(gstore_dir, file)} and
      go_submit = input_dataset_exist?(file_list)
      sleep @interval
      waiting_time += @interval
    end
  end 

  job_id, log_file, command = if go_submit 
                                @cluster.submit_job(script_path, script_content, sge_options)
                              else
                                raise "stop submitting #{File.basename(script_path)}, since waiting_time #{waiting_time} > #{waiting_max}"
                              end

  if job_id and log_file 
    # save log_file in logs
    @logs.transaction do |logs|
      logs[job_id] = log_file
    end

    # job status check until it finishes with success or fail 
    worker = Thread.new(log_dir, script_path, script_content, sge_options) do |log_dir, script_path, script_content, sge_options|
      loop do
        # check status
        current_status = check_status(job_id, log_file)

        # save time and status
        update_time_status(job_id, current_status, script_path, user, project_number)

        # finalize (kill current thred) in case of success or fail 
        finalize_monitoring(current_status, log_file, log_dir)

        # wait
        sleep @interval
      end # loop
    end
    job_id
  end
end

#status(job_id, new_status = nil) ⇒ Object 



348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
 
# File 'lib/workflow_manager/server.rb', line 348

def status(job_id, new_status=nil)
  stat = nil
  #@statuses.open(@db_stat)
  @statuses.transaction do |statuses|
    if new_status and stat = statuses[job_id.to_s]
      status_list = ['success', 'running', 'pending', 'fail']
      if status_list.include?(new_status)
        items = stat.split(/,/)
        items.shift
        items.unshift(new_status)
        stat = items.join(',')
        statuses[job_id.to_s] = stat
      end
    else
      stat = statuses[job_id.to_s]
    end
  end
  #@statuses.close
  stat
end

#success_or_fail(job_id, log_file) ⇒ Object Also known as: check_status 



432
433
434
435
436
437
438
439
440
441
442
 
# File 'lib/workflow_manager/server.rb', line 432

def success_or_fail(job_id, log_file)
  msg = if @cluster.job_running?(job_id)
          'running'
        elsif @cluster.job_ends?(log_file)
          'success'
        elsif @cluster.job_pending?(job_id)
          'pending'
        else
          'fail'
        end
end

#update_time_status(job_id, current_status, script_name, user, project_number) ⇒ Object 



169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
 
# File 'lib/workflow_manager/server.rb', line 169

def update_time_status(job_id, current_status, script_name, user, project_number)
  # if the current status changed from last time, then save, otherwise do nothing
  # once status changes into success or fail, then the thread is expected to be killed in later process
  @statuses.transaction do |statuses|
    start_time = nil
    if stat = statuses[job_id] 
      last_status, script_name, start_time, user, project_number = stat.split(/,/)
    end
    time = if start_time 
             if current_status == 'success' or current_status == 'fail'
               start_time + '/' + Time.now.strftime("%Y-%m-%d %H:%M:%S")
             elsif current_status != last_status
               Time.now.strftime("%Y-%m-%d %H:%M:%S")
             end
           else
             Time.now.strftime("%Y-%m-%d %H:%M:%S")
           end
    if time
      statuses[job_id] = [current_status, script_name, time, user, project_number].join(',')
    end
  end
end