rbbt-util 5.44.1 → 6.0.3
Sign up to get free protection for your applications and to get access to all the features.
- checksums.yaml +4 -4
- data/bin/rbbt +67 -90
- data/etc/app.d/base.rb +2 -2
- data/etc/app.d/semaphores.rb +3 -3
- data/lib/rbbt/annotations/annotated_array.rb +207 -207
- data/lib/rbbt/annotations/refactor.rb +27 -0
- data/lib/rbbt/annotations/util.rb +282 -282
- data/lib/rbbt/annotations.rb +343 -320
- data/lib/rbbt/association/database.rb +200 -225
- data/lib/rbbt/association/index.rb +294 -291
- data/lib/rbbt/association/item.rb +227 -227
- data/lib/rbbt/association/open.rb +35 -34
- data/lib/rbbt/association/util.rb +0 -169
- data/lib/rbbt/association.rb +2 -4
- data/lib/rbbt/entity/identifiers.rb +119 -118
- data/lib/rbbt/entity/refactor.rb +12 -0
- data/lib/rbbt/entity.rb +319 -315
- data/lib/rbbt/hpc/batch.rb +72 -53
- data/lib/rbbt/hpc/lsf.rb +2 -2
- data/lib/rbbt/hpc/orchestrate/batches.rb +2 -2
- data/lib/rbbt/hpc/orchestrate/chains.rb +25 -5
- data/lib/rbbt/hpc/orchestrate/rules.rb +2 -2
- data/lib/rbbt/hpc/orchestrate.rb +19 -13
- data/lib/rbbt/hpc/slurm.rb +18 -18
- data/lib/rbbt/knowledge_base/entity.rb +13 -5
- data/lib/rbbt/knowledge_base/query.rb +2 -2
- data/lib/rbbt/knowledge_base/registry.rb +32 -31
- data/lib/rbbt/knowledge_base/traverse.rb +1 -1
- data/lib/rbbt/knowledge_base.rb +1 -1
- data/lib/rbbt/monitor.rb +36 -25
- data/lib/rbbt/persist/refactor.rb +166 -0
- data/lib/rbbt/persist/tsv/tokyocabinet.rb +105 -105
- data/lib/rbbt/persist/tsv.rb +187 -185
- data/lib/rbbt/persist.rb +556 -551
- data/lib/rbbt/refactor.rb +20 -0
- data/lib/rbbt/resource/path/refactor.rb +178 -0
- data/lib/rbbt/resource/path.rb +317 -497
- data/lib/rbbt/resource/util.rb +0 -48
- data/lib/rbbt/resource.rb +3 -390
- data/lib/rbbt/tsv/accessor.rb +2 -838
- data/lib/rbbt/tsv/attach.rb +303 -299
- data/lib/rbbt/tsv/change_id.rb +244 -245
- data/lib/rbbt/tsv/csv.rb +87 -85
- data/lib/rbbt/tsv/dumper.rb +2 -100
- data/lib/rbbt/tsv/excel.rb +26 -24
- data/lib/rbbt/tsv/field_index.rb +4 -1
- data/lib/rbbt/tsv/filter.rb +3 -2
- data/lib/rbbt/tsv/index.rb +2 -284
- data/lib/rbbt/tsv/manipulate.rb +750 -747
- data/lib/rbbt/tsv/marshal.rb +3 -3
- data/lib/rbbt/tsv/matrix.rb +2 -2
- data/lib/rbbt/tsv/parallel/through.rb +2 -1
- data/lib/rbbt/tsv/parallel/traverse.rb +783 -781
- data/lib/rbbt/tsv/parser.rb +678 -678
- data/lib/rbbt/tsv/refactor.rb +195 -0
- data/lib/rbbt/tsv/stream.rb +253 -251
- data/lib/rbbt/tsv/util.rb +420 -420
- data/lib/rbbt/tsv.rb +210 -208
- data/lib/rbbt/util/R/eval.rb +4 -4
- data/lib/rbbt/util/R/plot.rb +62 -166
- data/lib/rbbt/util/R.rb +21 -18
- data/lib/rbbt/util/cmd.rb +2 -318
- data/lib/rbbt/util/color.rb +269 -269
- data/lib/rbbt/util/colorize.rb +89 -89
- data/lib/rbbt/util/concurrency/processes/refactor.rb +22 -0
- data/lib/rbbt/util/concurrency/processes/worker.rb +2 -2
- data/lib/rbbt/util/concurrency/processes.rb +389 -386
- data/lib/rbbt/util/config.rb +169 -167
- data/lib/rbbt/util/iruby.rb +20 -0
- data/lib/rbbt/util/log/progress/report.rb +241 -241
- data/lib/rbbt/util/log/progress/util.rb +99 -99
- data/lib/rbbt/util/log/progress.rb +102 -102
- data/lib/rbbt/util/log/refactor.rb +49 -0
- data/lib/rbbt/util/log.rb +486 -532
- data/lib/rbbt/util/migrate.rb +1 -1
- data/lib/rbbt/util/misc/concurrent_stream.rb +248 -246
- data/lib/rbbt/util/misc/development.rb +12 -11
- data/lib/rbbt/util/misc/exceptions.rb +117 -112
- data/lib/rbbt/util/misc/format.rb +2 -230
- data/lib/rbbt/util/misc/indiferent_hash.rb +2 -107
- data/lib/rbbt/util/misc/inspect.rb +2 -476
- data/lib/rbbt/util/misc/lock.rb +109 -106
- data/lib/rbbt/util/misc/omics.rb +9 -1
- data/lib/rbbt/util/misc/pipes.rb +765 -793
- data/lib/rbbt/util/misc/refactor.rb +20 -0
- data/lib/rbbt/util/misc/ssw.rb +27 -17
- data/lib/rbbt/util/misc/system.rb +0 -15
- data/lib/rbbt/util/misc.rb +39 -20
- data/lib/rbbt/util/named_array/refactor.rb +4 -0
- data/lib/rbbt/util/named_array.rb +3 -220
- data/lib/rbbt/util/open/refactor.rb +7 -0
- data/lib/rbbt/util/open.rb +3 -857
- data/lib/rbbt/util/procpath.rb +6 -6
- data/lib/rbbt/util/python/paths.rb +27 -0
- data/lib/rbbt/util/python/run.rb +115 -0
- data/lib/rbbt/util/python/script.rb +110 -0
- data/lib/rbbt/util/python/util.rb +3 -3
- data/lib/rbbt/util/python.rb +22 -81
- data/lib/rbbt/util/semaphore.rb +152 -148
- data/lib/rbbt/util/simpleopt.rb +9 -8
- data/lib/rbbt/util/ssh/refactor.rb +19 -0
- data/lib/rbbt/util/ssh.rb +122 -118
- data/lib/rbbt/util/tar.rb +117 -115
- data/lib/rbbt/util/tmpfile.rb +69 -67
- data/lib/rbbt/util/version.rb +2 -0
- data/lib/rbbt/workflow/refactor/entity.rb +11 -0
- data/lib/rbbt/workflow/refactor/export.rb +66 -0
- data/lib/rbbt/workflow/refactor/inputs.rb +24 -0
- data/lib/rbbt/workflow/refactor/recursive.rb +64 -0
- data/lib/rbbt/workflow/refactor/task_info.rb +65 -0
- data/lib/rbbt/workflow/refactor.rb +153 -0
- data/lib/rbbt/workflow/remote_workflow/driver/ssh.rb +55 -32
- data/lib/rbbt/workflow/remote_workflow/remote_step/rest.rb +3 -1
- data/lib/rbbt/workflow/remote_workflow/remote_step/ssh.rb +14 -5
- data/lib/rbbt/workflow/remote_workflow/remote_step.rb +19 -7
- data/lib/rbbt/workflow/remote_workflow.rb +6 -1
- data/lib/rbbt/workflow/step/run.rb +766 -766
- data/lib/rbbt/workflow/step/save_load_inputs.rb +254 -254
- data/lib/rbbt/workflow/step.rb +2 -362
- data/lib/rbbt/workflow/task.rb +118 -118
- data/lib/rbbt/workflow/usage.rb +289 -287
- data/lib/rbbt/workflow/util/archive.rb +6 -5
- data/lib/rbbt/workflow/util/data.rb +1 -1
- data/lib/rbbt/workflow/util/orchestrator.rb +249 -246
- data/lib/rbbt/workflow/util/trace.rb +79 -44
- data/lib/rbbt/workflow.rb +4 -882
- data/lib/rbbt-util.rb +21 -13
- data/lib/rbbt.rb +16 -3
- data/python/rbbt/__init__.py +19 -1
- data/share/Rlib/plot.R +37 -37
- data/share/Rlib/svg.R +22 -5
- data/share/install/software/lib/install_helpers +1 -1
- data/share/rbbt_commands/hpc/list +2 -3
- data/share/rbbt_commands/hpc/orchestrate +4 -4
- data/share/rbbt_commands/hpc/tail +2 -0
- data/share/rbbt_commands/hpc/task +10 -7
- data/share/rbbt_commands/lsf/list +2 -3
- data/share/rbbt_commands/lsf/orchestrate +4 -4
- data/share/rbbt_commands/lsf/tail +2 -0
- data/share/rbbt_commands/lsf/task +10 -7
- data/share/rbbt_commands/migrate +1 -1
- data/share/rbbt_commands/pbs/list +2 -3
- data/share/rbbt_commands/pbs/orchestrate +4 -4
- data/share/rbbt_commands/pbs/tail +2 -0
- data/share/rbbt_commands/pbs/task +10 -7
- data/share/rbbt_commands/resource/produce +8 -1
- data/share/rbbt_commands/slurm/list +2 -3
- data/share/rbbt_commands/slurm/orchestrate +4 -4
- data/share/rbbt_commands/slurm/tail +2 -0
- data/share/rbbt_commands/slurm/task +10 -7
- data/share/rbbt_commands/system/clean +5 -5
- data/share/rbbt_commands/system/status +5 -5
- data/share/rbbt_commands/tsv/get +2 -3
- data/share/rbbt_commands/tsv/info +10 -13
- data/share/rbbt_commands/tsv/keys +18 -14
- data/share/rbbt_commands/tsv/slice +2 -2
- data/share/rbbt_commands/tsv/transpose +6 -2
- data/share/rbbt_commands/workflow/info +20 -24
- data/share/rbbt_commands/workflow/list +1 -1
- data/share/rbbt_commands/workflow/prov +20 -13
- data/share/rbbt_commands/workflow/server +11 -1
- data/share/rbbt_commands/workflow/task +76 -71
- data/share/rbbt_commands/workflow/write_info +26 -9
- data/share/software/opt/ssw/ssw.c +861 -0
- data/share/software/opt/ssw/ssw.h +130 -0
- data/share/workflow_config.ru +3 -3
- metadata +40 -2
data/lib/rbbt/util/log.rb
CHANGED
@@ -1,532 +1,486 @@
|
|
1
|
-
require '
|
2
|
-
|
3
|
-
|
4
|
-
|
5
|
-
|
6
|
-
|
7
|
-
|
8
|
-
|
9
|
-
|
10
|
-
|
11
|
-
|
12
|
-
|
13
|
-
|
14
|
-
|
15
|
-
|
16
|
-
|
17
|
-
|
18
|
-
|
19
|
-
|
20
|
-
|
21
|
-
|
22
|
-
|
23
|
-
|
24
|
-
|
25
|
-
|
26
|
-
|
27
|
-
|
28
|
-
|
29
|
-
|
30
|
-
|
31
|
-
|
32
|
-
|
33
|
-
|
34
|
-
|
35
|
-
|
36
|
-
|
37
|
-
|
38
|
-
|
39
|
-
|
40
|
-
|
41
|
-
|
42
|
-
|
43
|
-
line
|
44
|
-
|
45
|
-
|
46
|
-
|
47
|
-
|
48
|
-
|
49
|
-
|
50
|
-
|
51
|
-
|
52
|
-
|
53
|
-
|
54
|
-
|
55
|
-
|
56
|
-
|
57
|
-
|
58
|
-
|
59
|
-
|
60
|
-
|
61
|
-
|
62
|
-
|
63
|
-
while line =
|
64
|
-
Log.logn "#{
|
65
|
-
end
|
66
|
-
end
|
67
|
-
|
68
|
-
|
69
|
-
|
70
|
-
|
71
|
-
|
72
|
-
|
73
|
-
|
74
|
-
|
75
|
-
sin
|
76
|
-
sine
|
77
|
-
|
78
|
-
|
79
|
-
|
80
|
-
|
81
|
-
|
82
|
-
|
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
|
-
|
108
|
-
|
109
|
-
|
110
|
-
|
111
|
-
|
112
|
-
|
113
|
-
|
114
|
-
|
115
|
-
|
116
|
-
|
117
|
-
|
118
|
-
|
119
|
-
|
120
|
-
|
121
|
-
|
122
|
-
|
123
|
-
|
124
|
-
|
125
|
-
|
126
|
-
|
127
|
-
|
128
|
-
|
129
|
-
|
130
|
-
|
131
|
-
|
132
|
-
|
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
|
-
|
158
|
-
|
159
|
-
|
160
|
-
|
161
|
-
|
162
|
-
|
163
|
-
|
164
|
-
|
165
|
-
|
166
|
-
|
167
|
-
end
|
168
|
-
|
169
|
-
|
170
|
-
|
171
|
-
|
172
|
-
|
173
|
-
|
174
|
-
|
175
|
-
|
176
|
-
|
177
|
-
|
178
|
-
|
179
|
-
|
180
|
-
|
181
|
-
|
182
|
-
|
183
|
-
|
184
|
-
|
185
|
-
|
186
|
-
|
187
|
-
|
188
|
-
|
189
|
-
|
190
|
-
|
191
|
-
|
192
|
-
|
193
|
-
|
194
|
-
|
195
|
-
|
196
|
-
|
197
|
-
|
198
|
-
|
199
|
-
|
200
|
-
|
201
|
-
|
202
|
-
|
203
|
-
|
204
|
-
|
205
|
-
|
206
|
-
|
207
|
-
|
208
|
-
|
209
|
-
|
210
|
-
|
211
|
-
|
212
|
-
|
213
|
-
|
214
|
-
|
215
|
-
|
216
|
-
|
217
|
-
|
218
|
-
|
219
|
-
|
220
|
-
end
|
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
|
-
|
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
|
-
end
|
288
|
-
|
289
|
-
def self.
|
290
|
-
|
291
|
-
|
292
|
-
|
293
|
-
|
294
|
-
|
295
|
-
end
|
296
|
-
|
297
|
-
def self.
|
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
|
-
end
|
334
|
-
|
335
|
-
def self.
|
336
|
-
|
337
|
-
|
338
|
-
|
339
|
-
|
340
|
-
|
341
|
-
|
342
|
-
|
343
|
-
|
344
|
-
|
345
|
-
|
346
|
-
|
347
|
-
|
348
|
-
|
349
|
-
|
350
|
-
|
351
|
-
|
352
|
-
|
353
|
-
|
354
|
-
|
355
|
-
|
356
|
-
|
357
|
-
|
358
|
-
|
359
|
-
end
|
360
|
-
end
|
361
|
-
|
362
|
-
def self.
|
363
|
-
|
364
|
-
|
365
|
-
|
366
|
-
|
367
|
-
|
368
|
-
|
369
|
-
|
370
|
-
|
371
|
-
|
372
|
-
|
373
|
-
|
374
|
-
|
375
|
-
|
376
|
-
|
377
|
-
|
378
|
-
|
379
|
-
|
380
|
-
|
381
|
-
|
382
|
-
|
383
|
-
|
384
|
-
|
385
|
-
|
386
|
-
|
387
|
-
|
388
|
-
|
389
|
-
|
390
|
-
|
391
|
-
|
392
|
-
|
393
|
-
|
394
|
-
|
395
|
-
|
396
|
-
|
397
|
-
|
398
|
-
|
399
|
-
|
400
|
-
|
401
|
-
|
402
|
-
|
403
|
-
|
404
|
-
|
405
|
-
|
406
|
-
|
407
|
-
|
408
|
-
|
409
|
-
|
410
|
-
|
411
|
-
|
412
|
-
|
413
|
-
|
414
|
-
|
415
|
-
|
416
|
-
|
417
|
-
|
418
|
-
|
419
|
-
|
420
|
-
|
421
|
-
|
422
|
-
|
423
|
-
|
424
|
-
|
425
|
-
|
426
|
-
|
427
|
-
|
428
|
-
|
429
|
-
|
430
|
-
|
431
|
-
|
432
|
-
|
433
|
-
|
434
|
-
|
435
|
-
|
436
|
-
|
437
|
-
|
438
|
-
|
439
|
-
|
440
|
-
|
441
|
-
|
442
|
-
|
443
|
-
|
444
|
-
|
445
|
-
|
446
|
-
|
447
|
-
|
448
|
-
|
449
|
-
|
450
|
-
|
451
|
-
|
452
|
-
|
453
|
-
|
454
|
-
|
455
|
-
|
456
|
-
|
457
|
-
|
458
|
-
|
459
|
-
|
460
|
-
|
461
|
-
|
462
|
-
|
463
|
-
|
464
|
-
|
465
|
-
|
466
|
-
|
467
|
-
|
468
|
-
|
469
|
-
|
470
|
-
|
471
|
-
|
472
|
-
|
473
|
-
|
474
|
-
|
475
|
-
|
476
|
-
|
477
|
-
|
478
|
-
|
479
|
-
|
480
|
-
Log.
|
481
|
-
|
482
|
-
|
483
|
-
|
484
|
-
|
485
|
-
|
486
|
-
|
487
|
-
end
|
488
|
-
|
489
|
-
def lll(obj, file = $stdout)
|
490
|
-
Log.log_obj_inspect(obj, :low, file)
|
491
|
-
end
|
492
|
-
|
493
|
-
def mmm(obj, file = $stdout)
|
494
|
-
Log.log_obj_inspect(obj, :medium, file)
|
495
|
-
end
|
496
|
-
|
497
|
-
def iii(obj=nil, file = $stdout)
|
498
|
-
Log.log_obj_inspect(obj, :info, file)
|
499
|
-
end
|
500
|
-
|
501
|
-
def wwww(obj=nil, file = $stdout)
|
502
|
-
Log.log_obj_inspect(obj, :warn, file)
|
503
|
-
end
|
504
|
-
|
505
|
-
def eee(obj=nil, file = $stdout)
|
506
|
-
Log.log_obj_inspect(obj, :error, file)
|
507
|
-
end
|
508
|
-
|
509
|
-
def ddf(obj=nil, file = $stdout)
|
510
|
-
Log.log_obj_fingerprint(obj, :debug, file)
|
511
|
-
end
|
512
|
-
|
513
|
-
def llf(obj=nil, file = $stdout)
|
514
|
-
Log.log_obj_fingerprint(obj, :low, file)
|
515
|
-
end
|
516
|
-
|
517
|
-
def mmf(obj=nil, file = $stdout)
|
518
|
-
Log.log_obj_fingerprint(obj, :medium, file)
|
519
|
-
end
|
520
|
-
|
521
|
-
def iif(obj=nil, file = $stdout)
|
522
|
-
Log.log_obj_fingerprint(obj, :info, file)
|
523
|
-
end
|
524
|
-
|
525
|
-
def wwwf(obj=nil, file = $stdout)
|
526
|
-
Log.log_obj_fingerprint(obj, :warn, file)
|
527
|
-
end
|
528
|
-
|
529
|
-
def eef(obj=nil, file = $stdout)
|
530
|
-
Log.log_obj_fingerprint(obj, :error, file)
|
531
|
-
end
|
532
|
-
|
1
|
+
require 'rbbt/refactor'
|
2
|
+
Rbbt.require_instead 'scout/log'
|
3
|
+
require_relative 'log/refactor'
|
4
|
+
|
5
|
+
|
6
|
+
|
7
|
+
#require 'term/ansicolor'
|
8
|
+
#require 'rbbt/util/color'
|
9
|
+
#require 'rbbt/util/log/progress'
|
10
|
+
#
|
11
|
+
#class MockMutex
|
12
|
+
# def synchronize
|
13
|
+
# yield
|
14
|
+
# end
|
15
|
+
#end
|
16
|
+
#
|
17
|
+
#module Log
|
18
|
+
# extend Term::ANSIColor
|
19
|
+
#
|
20
|
+
#
|
21
|
+
# #ToDo: I'm not sure if using a Mutex here really gives troubles in CPU concurrency
|
22
|
+
# LOG_MUTEX = MockMutex.new
|
23
|
+
# #LOG_MUTEX = Mutex.new
|
24
|
+
#
|
25
|
+
# SEVERITY_NAMES ||= begin
|
26
|
+
# names = %w(DEBUG LOW MEDIUM HIGH INFO WARN ERROR NONE )
|
27
|
+
# names.each_with_index do |name,i|
|
28
|
+
# eval "#{ name } = #{ i }"
|
29
|
+
# end
|
30
|
+
# names
|
31
|
+
# end
|
32
|
+
#
|
33
|
+
# def self.terminal_width
|
34
|
+
# 80
|
35
|
+
# end
|
36
|
+
#
|
37
|
+
# def self.compact
|
38
|
+
# true
|
39
|
+
# end
|
40
|
+
#
|
41
|
+
#
|
42
|
+
# def self.last_caller(stack)
|
43
|
+
# line = nil
|
44
|
+
# pos ||= 0
|
45
|
+
# while line.nil? or line =~ /util\/log\.rb/ and stack.any?
|
46
|
+
# line = stack.shift
|
47
|
+
# end
|
48
|
+
# line ||= caller.first
|
49
|
+
# line.gsub('`', "'")
|
50
|
+
# end
|
51
|
+
#
|
52
|
+
#
|
53
|
+
# def self.trap_std(msg = "STDOUT", msge = "STDERR", severity = 0, severity_err = nil)
|
54
|
+
# sout, sin = Misc.pipe
|
55
|
+
# soute, sine = Misc.pipe
|
56
|
+
# backup_stderr = STDERR.dup
|
57
|
+
# backup_stdout = STDOUT.dup
|
58
|
+
# old_logfile = Log.logfile
|
59
|
+
# Log.logfile(backup_stderr)
|
60
|
+
#
|
61
|
+
# severity_err ||= severity
|
62
|
+
# th_log = Thread.new do
|
63
|
+
# while line = sout.gets
|
64
|
+
# Log.logn "#{msg}: " + line, severity
|
65
|
+
# end
|
66
|
+
# end
|
67
|
+
#
|
68
|
+
# th_loge = Thread.new do
|
69
|
+
# while line = soute.gets
|
70
|
+
# Log.logn "#{msge}: " + line, severity_err
|
71
|
+
# end
|
72
|
+
# end
|
73
|
+
#
|
74
|
+
# begin
|
75
|
+
# STDOUT.reopen(sin)
|
76
|
+
# STDERR.reopen(sine)
|
77
|
+
# yield
|
78
|
+
# ensure
|
79
|
+
# STDERR.reopen backup_stderr
|
80
|
+
# STDOUT.reopen backup_stdout
|
81
|
+
# sin.close
|
82
|
+
# sine.close
|
83
|
+
# th_log.join
|
84
|
+
# th_loge.join
|
85
|
+
# backup_stdout.close
|
86
|
+
# backup_stderr.close
|
87
|
+
# Log.logfile = old_logfile
|
88
|
+
# end
|
89
|
+
# end
|
90
|
+
#
|
91
|
+
# def self.trap_stderr(msg = "STDERR", severity = 0)
|
92
|
+
# sout, sin = Misc.pipe
|
93
|
+
# backup_stderr = STDERR.dup
|
94
|
+
# old_logfile = Log.logfile
|
95
|
+
# Log.logfile(backup_stderr)
|
96
|
+
#
|
97
|
+
# th_log = Thread.new do
|
98
|
+
# while line = sout.gets
|
99
|
+
# Log.logn "#{msg}: " + line, severity
|
100
|
+
# end
|
101
|
+
# end
|
102
|
+
#
|
103
|
+
# begin
|
104
|
+
# STDERR.reopen(sin)
|
105
|
+
# yield
|
106
|
+
# sin.close
|
107
|
+
# ensure
|
108
|
+
# STDERR.reopen backup_stderr
|
109
|
+
# th_log.join
|
110
|
+
# backup_stderr.close
|
111
|
+
# Log.logfile = old_logfile
|
112
|
+
# end
|
113
|
+
# end
|
114
|
+
#
|
115
|
+
#
|
116
|
+
# def self.get_level(level)
|
117
|
+
# case level
|
118
|
+
# when Numeric
|
119
|
+
# level.to_i
|
120
|
+
# when String
|
121
|
+
# begin
|
122
|
+
# Log.const_get(level.upcase)
|
123
|
+
# rescue
|
124
|
+
# Log.exception $!
|
125
|
+
# end
|
126
|
+
# when Symbol
|
127
|
+
# get_level(level.to_s)
|
128
|
+
# end || 0
|
129
|
+
# end
|
130
|
+
#
|
131
|
+
# class << self
|
132
|
+
# attr_accessor :logfile, :severity, :nocolor, :tty_size
|
133
|
+
# end
|
134
|
+
#
|
135
|
+
# self.nocolor = ENV["RBBT_NOCOLOR"] == 'true'
|
136
|
+
#
|
137
|
+
# self.ignore_stderr do
|
138
|
+
# self.tty_size = begin
|
139
|
+
# require "highline/system_extensions.rb"
|
140
|
+
# HighLine::SystemExtensions.terminal_size.first
|
141
|
+
# rescue Exception
|
142
|
+
# nil
|
143
|
+
# end
|
144
|
+
# end
|
145
|
+
#
|
146
|
+
# def self.with_severity(level)
|
147
|
+
# orig = Log.severity
|
148
|
+
# begin
|
149
|
+
# Log.severity = level
|
150
|
+
# yield
|
151
|
+
# ensure
|
152
|
+
# Log.severity = orig
|
153
|
+
# end
|
154
|
+
# end
|
155
|
+
#
|
156
|
+
# def self.logfile(file=nil)
|
157
|
+
# if file.nil?
|
158
|
+
# @logfile ||= nil
|
159
|
+
# else
|
160
|
+
# case file
|
161
|
+
# when String
|
162
|
+
# @logfile = File.open(file, :mode => 'a')
|
163
|
+
# when IO, File
|
164
|
+
# @logfile = file
|
165
|
+
# else
|
166
|
+
# raise "Unkown logfile format: #{file.inspect}"
|
167
|
+
# end
|
168
|
+
# end
|
169
|
+
# end
|
170
|
+
#
|
171
|
+
# WHITE, DARK, GREEN, YELLOW, RED = Color::SOLARIZED.values_at :base0, :base00, :green, :yellow, :magenta
|
172
|
+
#
|
173
|
+
# SEVERITY_COLOR = [reset, cyan, green, magenta, blue, yellow, red] #.collect{|e| "\033[#{e}"}
|
174
|
+
# HIGHLIGHT = "\033[1m"
|
175
|
+
#
|
176
|
+
# def self.uncolor(str)
|
177
|
+
# "" << Term::ANSIColor.uncolor(str)
|
178
|
+
# end
|
179
|
+
#
|
180
|
+
# def self.reset_color
|
181
|
+
# reset
|
182
|
+
# end
|
183
|
+
#
|
184
|
+
# def self.color(severity, str = nil, reset = false)
|
185
|
+
# return str.dup || "" if nocolor
|
186
|
+
# color = reset ? Term::ANSIColor.reset : ""
|
187
|
+
# color << SEVERITY_COLOR[severity] if Integer === severity
|
188
|
+
# color << Term::ANSIColor.send(severity) if Symbol === severity and Term::ANSIColor.respond_to? severity
|
189
|
+
# if str.nil?
|
190
|
+
# color
|
191
|
+
# else
|
192
|
+
# color + str.to_s + self.color(0)
|
193
|
+
# end
|
194
|
+
# end
|
195
|
+
#
|
196
|
+
# def self.up_lines(num = 1)
|
197
|
+
# nocolor ? "" : "\033[#{num+1}F\033[2K"
|
198
|
+
# end
|
199
|
+
#
|
200
|
+
# def self.down_lines(num = 1)
|
201
|
+
# nocolor ? "" : "\033[#{num+1}E"
|
202
|
+
# end
|
203
|
+
#
|
204
|
+
# def self.return_line
|
205
|
+
# nocolor ? "" : "\033[1A"
|
206
|
+
# end
|
207
|
+
#
|
208
|
+
# def self.clear_line(out = STDOUT)
|
209
|
+
# out.puts Log.return_line << " " * (Log.tty_size || 80) << Log.return_line unless nocolor
|
210
|
+
# end
|
211
|
+
#
|
212
|
+
# def self.highlight(str = nil)
|
213
|
+
# if str.nil?
|
214
|
+
# return "" if nocolor
|
215
|
+
# HIGHLIGHT
|
216
|
+
# else
|
217
|
+
# return str if nocolor
|
218
|
+
# HIGHLIGHT + str + color(0)
|
219
|
+
# end
|
220
|
+
# end
|
221
|
+
#
|
222
|
+
# LAST = "log"
|
223
|
+
# def self.logn(message = nil, severity = MEDIUM, &block)
|
224
|
+
# return if severity < self.severity
|
225
|
+
# message ||= block.call if block_given?
|
226
|
+
# return if message.nil?
|
227
|
+
#
|
228
|
+
# time = Time.now.strftime("%m/%d/%y-%H:%M:%S.%L")
|
229
|
+
#
|
230
|
+
# sev_str = severity.to_s
|
231
|
+
#
|
232
|
+
# prefix = time << color(severity) << "[" << sev_str << "]" << color(0)
|
233
|
+
# message = "" << highlight << message << color(0) if severity >= INFO
|
234
|
+
# str = prefix << " " << message.to_s
|
235
|
+
#
|
236
|
+
# LOG_MUTEX.synchronize do
|
237
|
+
# if logfile.nil?
|
238
|
+
# STDERR.write str
|
239
|
+
# else
|
240
|
+
# logfile.write str
|
241
|
+
# end
|
242
|
+
# Log::LAST.replace "log"
|
243
|
+
# nil
|
244
|
+
# end
|
245
|
+
# end
|
246
|
+
#
|
247
|
+
# def self.log(message = nil, severity = MEDIUM, &block)
|
248
|
+
# return if severity < self.severity
|
249
|
+
# message ||= block.call if block_given?
|
250
|
+
# return if message.nil?
|
251
|
+
# message = message + "\n" unless message[-1] == "\n"
|
252
|
+
# self.logn message, severity, &block
|
253
|
+
# end
|
254
|
+
#
|
255
|
+
# def self.log_obj_inspect(obj, level, file = $stdout)
|
256
|
+
# stack = caller
|
257
|
+
#
|
258
|
+
# line = Log.last_caller stack
|
259
|
+
#
|
260
|
+
# level = Log.get_level level
|
261
|
+
# name = Log::SEVERITY_NAMES[level] + ": "
|
262
|
+
# Log.log Log.color(level, name, true) << line, level
|
263
|
+
# Log.log "", level
|
264
|
+
# Log.log Log.color(level, "=> ", true) << obj.inspect, level
|
265
|
+
# Log.log "", level
|
266
|
+
# end
|
267
|
+
#
|
268
|
+
# def self.log_obj_fingerprint(obj, level, file = $stdout)
|
269
|
+
# stack = caller
|
270
|
+
#
|
271
|
+
# line = Log.last_caller stack
|
272
|
+
#
|
273
|
+
# level = Log.get_level level
|
274
|
+
# name = Log::SEVERITY_NAMES[level] + ": "
|
275
|
+
# Log.log Log.color(level, name, true) << line, level
|
276
|
+
# Log.log "", level
|
277
|
+
# Log.log Log.color(level, "=> ", true) << Misc.fingerprint(obj), level
|
278
|
+
# Log.log "", level
|
279
|
+
# end
|
280
|
+
#
|
281
|
+
# def self.debug(message = nil, &block)
|
282
|
+
# log(message, DEBUG, &block)
|
283
|
+
# end
|
284
|
+
#
|
285
|
+
# def self.low(message = nil, &block)
|
286
|
+
# log(message, LOW, &block)
|
287
|
+
# end
|
288
|
+
#
|
289
|
+
# def self.medium(message = nil, &block)
|
290
|
+
# log(message, MEDIUM, &block)
|
291
|
+
# end
|
292
|
+
#
|
293
|
+
# def self.high(message = nil, &block)
|
294
|
+
# log(message, HIGH, &block)
|
295
|
+
# end
|
296
|
+
#
|
297
|
+
# def self.info(message = nil, &block)
|
298
|
+
# log(message, INFO, &block)
|
299
|
+
# end
|
300
|
+
#
|
301
|
+
# def self.warn(message = nil, &block)
|
302
|
+
# log(message, WARN, &block)
|
303
|
+
# end
|
304
|
+
#
|
305
|
+
# def self.error(message = nil, &block)
|
306
|
+
# log(message, ERROR, &block)
|
307
|
+
# end
|
308
|
+
#
|
309
|
+
# def self.exception(e)
|
310
|
+
# stack = caller
|
311
|
+
# if ENV["RBBT_ORIGINAL_STACK"] == 'true'
|
312
|
+
# error([e.class.to_s, e.message].compact * ": " )
|
313
|
+
# error("BACKTRACE [#{Process.pid}]: " << Log.last_caller(stack) << "\n" + color_stack(e.backtrace)*"\n")
|
314
|
+
# else
|
315
|
+
# error("BACKTRACE [#{Process.pid}]: " << Log.last_caller(stack) << "\n" + color_stack(e.backtrace.reverse)*"\n")
|
316
|
+
# error([e.class.to_s, e.message].compact * ": " )
|
317
|
+
# end
|
318
|
+
# end
|
319
|
+
#
|
320
|
+
# def self.deprecated(m)
|
321
|
+
# stack = caller
|
322
|
+
# warn("DEPRECATED: " << Log.last_caller(stack))
|
323
|
+
# warn("* " << (m || "").to_s)
|
324
|
+
# end
|
325
|
+
#
|
326
|
+
# def self.color_stack(stack)
|
327
|
+
# stack.collect do |line|
|
328
|
+
# line = line.sub('`',"'")
|
329
|
+
# color = :green if line =~ /workflow/
|
330
|
+
# color = :blue if line =~ /rbbt-/
|
331
|
+
# Log.color color, line
|
332
|
+
# end unless stack.nil?
|
333
|
+
# end
|
334
|
+
#
|
335
|
+
# def self.tsv(tsv, example = false)
|
336
|
+
# STDERR.puts Log.color :magenta, "TSV log: " << Log.last_caller(caller).gsub('`',"'")
|
337
|
+
# STDERR.puts Log.color(:blue, "=> "<< Misc.fingerprint(tsv), true)
|
338
|
+
# STDERR.puts Log.color(:cyan, "=> " << tsv.summary)
|
339
|
+
# if example && ! tsv.empty?
|
340
|
+
# key = case example
|
341
|
+
# when TrueClass, :first, "first"
|
342
|
+
# tsv.keys.first
|
343
|
+
# when :random, "random"
|
344
|
+
# tsv.keys.shuffle.first
|
345
|
+
# else
|
346
|
+
# example
|
347
|
+
# end
|
348
|
+
#
|
349
|
+
# values = tsv[key]
|
350
|
+
# values = [values] if tsv.type == :flat || tsv.type == :single
|
351
|
+
# if values.nil?
|
352
|
+
# STDERR.puts Log.color(:blue, "Key (#{tsv.key_field}) not present: ") + key
|
353
|
+
# else
|
354
|
+
# STDERR.puts Log.color(:blue, "Key (#{tsv.key_field}): ") + key
|
355
|
+
# tsv.fields.zip(values).each do |field,value|
|
356
|
+
# STDERR.puts Log.color(:magenta, field + ": ") + (Array === value ? value * ", " : value.to_s)
|
357
|
+
# end
|
358
|
+
# end
|
359
|
+
# end
|
360
|
+
# end
|
361
|
+
#
|
362
|
+
# def self.stack(stack)
|
363
|
+
# LOG_MUTEX.synchronize do
|
364
|
+
# if ENV["RBBT_ORIGINAL_STACK"] == 'true'
|
365
|
+
# STDERR.puts Log.color :magenta, "Stack trace [#{Process.pid}]: " << Log.last_caller(caller)
|
366
|
+
# color_stack(stack).each do |line|
|
367
|
+
# STDERR.puts line
|
368
|
+
# end
|
369
|
+
# else
|
370
|
+
# STDERR.puts Log.color :magenta, "Stack trace [#{Process.pid}]: " << Log.last_caller(caller)
|
371
|
+
# color_stack(stack.reverse).each do |line|
|
372
|
+
# STDERR.puts line
|
373
|
+
# end
|
374
|
+
# end
|
375
|
+
# end
|
376
|
+
# end
|
377
|
+
#
|
378
|
+
# def self.count_stack
|
379
|
+
# if ! $count_stacks
|
380
|
+
# Log.debug "Counting stacks at: " << caller.first
|
381
|
+
# return
|
382
|
+
# end
|
383
|
+
# $stack_counts ||= {}
|
384
|
+
# head = $count_stacks_head
|
385
|
+
# stack = caller[1..head+1]
|
386
|
+
# stack.reverse.each do |line,i|
|
387
|
+
# $stack_counts[line] ||= 0
|
388
|
+
# $stack_counts[line] += 1
|
389
|
+
# end
|
390
|
+
# end
|
391
|
+
#
|
392
|
+
# def self.with_stack_counts(head = 10, total = 100)
|
393
|
+
# $count_stacks_head = head
|
394
|
+
# $count_stacks = true
|
395
|
+
# $stack_counts = {}
|
396
|
+
# res = yield
|
397
|
+
# $count_stacks = false
|
398
|
+
# Log.debug "STACK_COUNTS:\n" + $stack_counts.sort_by{|line,c| c}.reverse.collect{|line,c| [c, line] * " - "}[0..total] * "\n"
|
399
|
+
# $stack_counts = {}
|
400
|
+
# res
|
401
|
+
# end
|
402
|
+
#
|
403
|
+
# case ENV['RBBT_LOG']
|
404
|
+
# when 'DEBUG'
|
405
|
+
# self.severity = DEBUG
|
406
|
+
# when 'LOW'
|
407
|
+
# self.severity = LOW
|
408
|
+
# when 'MEDIUM'
|
409
|
+
# self.severity = MEDIUM
|
410
|
+
# when 'HIGH'
|
411
|
+
# self.severity = HIGH
|
412
|
+
# when nil
|
413
|
+
# self.severity = INFO
|
414
|
+
# else
|
415
|
+
# self.severity = ENV['RBBT_LOG'].to_i
|
416
|
+
# end
|
417
|
+
#end
|
418
|
+
#
|
419
|
+
#def ppp(message)
|
420
|
+
# stack = caller
|
421
|
+
# puts "#{Log.color :cyan, "PRINT:"} " << stack.first
|
422
|
+
# puts ""
|
423
|
+
# if message.length > 200 or message.include? "\n"
|
424
|
+
# puts Log.color(:cyan, "=>|") << "\n" << message.to_s
|
425
|
+
# else
|
426
|
+
# puts Log.color(:cyan, "=> ") << message.to_s
|
427
|
+
# end
|
428
|
+
# puts ""
|
429
|
+
#end
|
430
|
+
#
|
431
|
+
#def fff(object)
|
432
|
+
# stack = caller
|
433
|
+
# Log.debug{"#{Log.color :cyan, "FINGERPRINT:"} " << stack.first}
|
434
|
+
# Log.debug{""}
|
435
|
+
# Log.debug{require 'rbbt/util/misc'; "=> " << Misc.fingerprint(object) }
|
436
|
+
# Log.debug{""}
|
437
|
+
#end
|
438
|
+
#
|
439
|
+
#def ddd(obj, file = $stdout)
|
440
|
+
# Log.log_obj_inspect(obj, :debug, file)
|
441
|
+
#end
|
442
|
+
#
|
443
|
+
#def lll(obj, file = $stdout)
|
444
|
+
# Log.log_obj_inspect(obj, :low, file)
|
445
|
+
#end
|
446
|
+
#
|
447
|
+
#def mmm(obj, file = $stdout)
|
448
|
+
# Log.log_obj_inspect(obj, :medium, file)
|
449
|
+
#end
|
450
|
+
#
|
451
|
+
#def iii(obj=nil, file = $stdout)
|
452
|
+
# Log.log_obj_inspect(obj, :info, file)
|
453
|
+
#end
|
454
|
+
#
|
455
|
+
#def wwww(obj=nil, file = $stdout)
|
456
|
+
# Log.log_obj_inspect(obj, :warn, file)
|
457
|
+
#end
|
458
|
+
#
|
459
|
+
#def eee(obj=nil, file = $stdout)
|
460
|
+
# Log.log_obj_inspect(obj, :error, file)
|
461
|
+
#end
|
462
|
+
#
|
463
|
+
#def ddf(obj=nil, file = $stdout)
|
464
|
+
# Log.log_obj_fingerprint(obj, :debug, file)
|
465
|
+
#end
|
466
|
+
#
|
467
|
+
#def llf(obj=nil, file = $stdout)
|
468
|
+
# Log.log_obj_fingerprint(obj, :low, file)
|
469
|
+
#end
|
470
|
+
#
|
471
|
+
#def mmf(obj=nil, file = $stdout)
|
472
|
+
# Log.log_obj_fingerprint(obj, :medium, file)
|
473
|
+
#end
|
474
|
+
#
|
475
|
+
#def iif(obj=nil, file = $stdout)
|
476
|
+
# Log.log_obj_fingerprint(obj, :info, file)
|
477
|
+
#end
|
478
|
+
#
|
479
|
+
#def wwwf(obj=nil, file = $stdout)
|
480
|
+
# Log.log_obj_fingerprint(obj, :warn, file)
|
481
|
+
#end
|
482
|
+
#
|
483
|
+
#def eef(obj=nil, file = $stdout)
|
484
|
+
# Log.log_obj_fingerprint(obj, :error, file)
|
485
|
+
#end
|
486
|
+
#
|