scout-gear 1.1.1 → 2.0.0

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data/.gitmodules ADDED
@@ -0,0 +1,4 @@
1
+ [submodule "modules/rbbt-util"]
2
+ path = modules/rbbt-util
3
+ url = https://github.com/mikisvaz/rbbt-util.git
4
+ branch = scout
data/.vimproject CHANGED
@@ -1,12 +1,18 @@
1
1
  scout-gear=/$PWD filter="*.rb *.yaml" {
2
2
  Rakefile
3
3
  bin=bin {
4
+ scout
4
5
  }
5
6
  lib=lib {
6
7
  scout-gear.rb
7
8
  scout=scout{
8
- exceptions.rb
9
9
  meta_extension.rb
10
+ exceptions.rb
11
+
12
+ misc.rb
13
+ misc=misc{
14
+ format.rb
15
+ }
10
16
  tmpfile.rb
11
17
  indiferent_hash.rb
12
18
  indiferent_hash=indiferent_hash{
@@ -24,9 +30,18 @@ scout-gear=/$PWD filter="*.rb *.yaml" {
24
30
  util.rb
25
31
  }
26
32
  }
33
+ simple_opt.rb
34
+ simple_opt=simple_opt{
35
+ accessor.rb
36
+ doc.rb
37
+ parse.rb
38
+ get.rb
39
+ setup.rb
40
+ }
27
41
  path.rb
28
42
  path=path{
29
43
  find.rb
44
+ util.rb
30
45
  }
31
46
  }
32
47
  }
@@ -41,5 +56,593 @@ scout-gear=/$PWD filter="*.rb *.yaml" {
41
56
  test_tmpfile.rb
42
57
  }
43
58
  }
59
+
60
+ modules=modules{
61
+ rbbt-util=rbbt-util filter="*.rb *.rake Rakefile *.rdoc *.R *.sh *.js *.haml *.sass *.txt *.conf LICENSE" {
62
+ Migration-1.9.txt
63
+ Troubleshooting.txt
64
+ ToDo.txt
65
+ Rakefile
66
+ LICENSE
67
+ README.rdoc
68
+ bin=bin filter="*" {
69
+ excel2tsv.rb
70
+ rbbt
71
+ rbbt_Rutil.rb
72
+ rbbt_dangling_locks.rb
73
+ rbbt_exec.rb
74
+ rbbt_query.rb
75
+ rbbt_find.rb
76
+ }
77
+ lib=lib{
78
+ rbbt.rb
79
+
80
+ rbbt-util.rb
81
+
82
+ rbbt=rbbt{
83
+ refactor.rb
84
+
85
+ util=util{
86
+ misc.rb
87
+ misc=misc{
88
+ serialize.rb
89
+ exceptions.rb
90
+ concurrent_stream.rb
91
+ indiferent_hash.rb
92
+ pipes.rb
93
+ format.rb
94
+ omics.rb
95
+ inspect.rb
96
+ math.rb
97
+ development.rb
98
+ lock.rb
99
+ options.rb
100
+ system.rb
101
+ objects.rb
102
+ manipulation.rb
103
+ bgzf.rb
104
+ multipart_payload.rb
105
+ annotated_module.rb
106
+ communication.rb
107
+ }
108
+ version.rb
109
+ tar.rb
110
+ color.rb
111
+ colorize.rb
112
+ named_array.rb
113
+ cmd.rb
114
+ docker.rb
115
+ config.rb
116
+ log.rb
117
+ log=log{
118
+ refactor.rb
119
+ progress.rb
120
+ progress=progress{
121
+ util.rb
122
+ report.rb
123
+ }
124
+ }
125
+ open.rb
126
+ semaphore.rb
127
+
128
+ simpleopt.rb
129
+ simpleopt=simpleopt{
130
+ accessor.rb
131
+ doc.rb
132
+ parse.rb
133
+ get.rb
134
+ setup.rb
135
+ }
136
+
137
+ ssh.rb
138
+
139
+ simpleDSL.rb
140
+
141
+ chain_methods.rb
142
+
143
+ tmpfile.rb
144
+ tc_cache.rb
145
+ filecache.rb
146
+
147
+ R.rb
148
+ R=R{
149
+ eval.rb
150
+ model.rb
151
+ plot.rb
152
+ }
153
+
154
+ python.rb
155
+ python=python{
156
+ util.rb
157
+ }
158
+
159
+ excel2tsv.rb
160
+
161
+ concurrency.rb
162
+ concurrency=concurrency{
163
+ processes.rb
164
+ threads.rb
165
+ processes=processes{
166
+ socket.rb
167
+ worker.rb
168
+ }
169
+ }
170
+
171
+ procpath.rb
172
+
173
+ migrate.rb
174
+ }
175
+
176
+ monitor.rb
177
+
178
+ workflow.rb
179
+ workflow=workflow{
180
+ annotate.rb
181
+
182
+ definition.rb
183
+ dependencies.rb
184
+
185
+ accessor.rb
186
+
187
+ task.rb
188
+
189
+ step.rb
190
+ step=step{
191
+ accessor.rb
192
+ dependencies.rb
193
+ info.rb
194
+ prepare.rb
195
+ run.rb
196
+ save_load_inputs.rb
197
+ status.rb
198
+ }
199
+
200
+ examples.rb
201
+ doc.rb
202
+ usage.rb
203
+
204
+ soap.rb
205
+
206
+ util=util{
207
+ archive.rb
208
+ provenance.rb
209
+ orchestrator.rb
210
+ trace.rb
211
+ data.rb
212
+ }
213
+
214
+ remote_workflow.rb
215
+ remote_workflow=remote_workflow{
216
+ driver.rb
217
+ driver=driver{
218
+ rest.rb
219
+ ssh.rb
220
+ }
221
+
222
+ remote_step.rb
223
+ remote_step=remote_step{
224
+ rest.rb
225
+ ssh.rb
226
+ }
227
+ }
228
+
229
+ integration=integration{
230
+ cromwell.rb
231
+ nextflow.rb
232
+ ansible.rb
233
+ ansible=ansible{
234
+ workflow.rb
235
+ }
236
+ }
237
+ }
238
+
239
+ hpc.rb
240
+ hpc=hpc{
241
+ old=old{
242
+ slurm.rb
243
+ }
244
+ orchestrate.old.rb
245
+
246
+ batch.rb
247
+ slurm.rb
248
+ lsf.rb
249
+
250
+ orchestrate.rb
251
+ orchestrate=orchestrate{
252
+ rules.rb
253
+ chains.rb
254
+ batches.rb
255
+ }
256
+ trace.rb
257
+ }
258
+
259
+ tsv.rb
260
+ tsv=tsv{
261
+ parser.rb
262
+ dumper.rb
263
+
264
+ matrix.rb
265
+
266
+ accessor.rb
267
+ util.rb
268
+ marshal.rb
269
+ serializers.rb
270
+ manipulate.rb
271
+ index.rb
272
+ stream.rb
273
+ attach.rb
274
+ attach=attach{
275
+ util.rb
276
+ }
277
+ melt.rb
278
+ excel.rb
279
+ csv.rb
280
+ filter.rb
281
+ field_index.rb
282
+ change_id.rb
283
+ parallel.rb
284
+ parallel=parallel{
285
+ traverse.rb
286
+ through.rb
287
+ }
288
+ }
289
+
290
+ packed_index.rb
291
+ fix_width_table.rb
292
+
293
+ persist.rb
294
+ persist=persist{
295
+ tsv.rb
296
+ tsv=tsv{
297
+ adapter.rb
298
+
299
+ sharder.rb
300
+ tokyocabinet.rb
301
+ tokyocabinet=tokyocabinet{
302
+ marshal.rb
303
+ }
304
+ fix_width_table.rb
305
+ packed_index.rb
306
+ kyotocabinet.rb
307
+ lmdb.rb
308
+ cdb.rb
309
+ leveldb.rb
310
+ }
311
+ }
312
+
313
+ resource.rb
314
+ resource=resource{
315
+ path.rb
316
+ util.rb
317
+ with_key.rb
318
+ rake.rb
319
+ }
320
+
321
+ annotations.rb
322
+ annotations=annotations{
323
+ util.rb
324
+ annotated_array.rb
325
+ }
326
+
327
+ entity.rb
328
+ entity=entity{
329
+ identifiers.rb
330
+ }
331
+
332
+ association.rb
333
+ association=association{
334
+ util.rb
335
+ database.rb
336
+ open.rb
337
+ index.rb
338
+ item.rb
339
+ }
340
+
341
+ knowledge_base.rb
342
+ knowledge_base=knowledge_base{
343
+ enrichment.rb
344
+ entity.rb
345
+ query.rb
346
+ registry.rb
347
+ syndicate.rb
348
+ traverse.rb
349
+ }
350
+ }
351
+ }
352
+ test=test {
353
+ test_helper.rb
354
+ data=data filter="*"{
355
+ Test.xls
356
+ dose_response
357
+ dose_response2
358
+ dose_response3
359
+ example.pdf
360
+ gene_ages
361
+ identifiers
362
+ test.tsv
363
+ }
364
+ rbbt=rbbt{
365
+ test_annotations.rb
366
+ test_association.rb
367
+ test_entity.rb
368
+ test_fix_width_table.rb
369
+ test_knowledge_base.rb
370
+ test_monitor.rb
371
+ test_packed_index.rb
372
+ test_persist.rb
373
+ test_resource.rb
374
+ test_tsv.rb
375
+ test_workflow.rb
376
+ resource=resource{
377
+ test_path.rb
378
+ }
379
+ workflow=workflow{
380
+ _test_soap.rb
381
+ test_doc.rb
382
+ test_step.rb
383
+ test_task.rb
384
+ }
385
+ association=association{
386
+ test_database.rb
387
+ test_index.rb
388
+ test_item.rb
389
+ test_open.rb
390
+ test_util.rb
391
+ }
392
+ knowledge_base=knowledge_base{
393
+ test_enrichment.rb
394
+ test_query.rb
395
+ test_registry.rb
396
+ }
397
+ persist=persist{
398
+ tsv=tsv{
399
+ test_cdb.rb
400
+ test_kyotocabinet.rb
401
+ test_leveldb.rb
402
+ test_lmdb.rb
403
+ test_sharder.rb
404
+ test_tokyocabinet.rb
405
+ }
406
+ test_tsv.rb
407
+ }
408
+ tsv=tsv{
409
+ test_accessor.rb
410
+ test_attach.rb
411
+ test_change_id.rb
412
+ test_csv.rb
413
+ test_excel.rb
414
+ test_field_index.rb
415
+ test_filter.rb
416
+ test_index.rb
417
+ test_manipulate.rb
418
+ test_matrix.rb
419
+ test_parallel.rb
420
+ test_parser.rb
421
+ test_stream.rb
422
+ test_util.rb
423
+ parallel=parallel{
424
+ test_through.rb
425
+ test_traverse.rb
426
+ }
427
+ }
428
+ entity=entity{
429
+ test_identifiers.rb
430
+ }
431
+ util=util{
432
+ test_R.rb
433
+ test_chain_methods.rb
434
+ test_cmd.rb
435
+ test_colorize.rb
436
+ test_concurrency.rb
437
+ test_config.rb
438
+ test_excel2tsv.rb
439
+ test_filecache.rb
440
+ test_log.rb
441
+ test_misc.rb
442
+ test_open.rb
443
+ test_python.rb
444
+ test_semaphore.rb
445
+ test_simpleDSL.rb
446
+ test_simpleopt.rb
447
+ test_tmpfile.rb
448
+ R=R{
449
+ test_eval.rb
450
+ test_model.rb
451
+ test_plot.rb
452
+ }
453
+ misc=misc{
454
+ test_bgzf.rb
455
+ test_format.rb
456
+ test_lock.rb
457
+ test_multipart_payload.rb
458
+ test_omics.rb
459
+ test_pipes.rb
460
+ }
461
+ simpleopt=simpleopt{
462
+ test_get.rb
463
+ test_parse.rb
464
+ test_setup.rb
465
+ }
466
+ concurrency=concurrency{
467
+ test_processes.rb
468
+ test_threads.rb
469
+ }
470
+ }
471
+ }
472
+ }
473
+ python=python filter="*"{
474
+ rbbt.py
475
+ }
476
+ integration_test=integration_test{
477
+ test_bed.rb
478
+ test_helper.rb
479
+ test_namespaces.rb
480
+ test_workflow.rb
481
+ }
482
+ etc=etc filter="*"{
483
+ app.d=app.d{
484
+ init.rb
485
+
486
+ base.rb
487
+
488
+ requires.rb
489
+ entities.rb
490
+ finder.rb
491
+ foundation.rb
492
+ grid_system.rb
493
+ knowledge_bases.rb
494
+ resources.rb
495
+ workflows.rb
496
+ semaphores.rb
497
+ remote_workflow_tasks.rb
498
+ }
499
+ }
500
+ share=share{
501
+ config.ru
502
+ workflow_config.ru
503
+ unicorn.rb
504
+ color=color filter="*"{
505
+ diverging_colors.hex
506
+ color_names
507
+ }
508
+ rbbt_commands=rbbt_commands filter="*"{
509
+ alias
510
+ ansible
511
+ check_bgzf
512
+ cmd
513
+ color
514
+ log
515
+ migrate
516
+ migrate_job
517
+ purge_job
518
+ rsync
519
+ watch
520
+ system=system{
521
+ clean
522
+ deleted_files
523
+ optimize
524
+ purge
525
+ report
526
+ status
527
+ }
528
+ conf=conf{
529
+ web_user=web_user{
530
+ add
531
+ list
532
+ remove
533
+ }
534
+ }
535
+ resource=resource{
536
+ exists
537
+ find
538
+ glob
539
+ get
540
+ produce
541
+ read
542
+ }
543
+ workflow=workflow{
544
+ archive
545
+ archive_all
546
+ cmd
547
+ example
548
+ forget_deps
549
+ info
550
+ write_info
551
+ init
552
+ install
553
+ jobs
554
+ knowledge_base
555
+ list
556
+ monitor
557
+ prov
558
+ server
559
+ task
560
+ trace
561
+ remote=remote{
562
+ add
563
+ list
564
+ remove
565
+ }
566
+ }
567
+ hpc=hpc{
568
+ task
569
+ orchestrate
570
+ tail
571
+ list
572
+ clean
573
+ }
574
+ app=app{
575
+ install
576
+ start
577
+ template
578
+ }
579
+ association=association{
580
+ subset
581
+ }
582
+ tsv=tsv{
583
+ assemble_pdf_table
584
+ attach
585
+ change_id
586
+ collapse
587
+ get
588
+ head
589
+ info
590
+ json
591
+ keys
592
+ query
593
+ read
594
+ read_excel
595
+ slice
596
+ sort
597
+ subset
598
+ select
599
+ transpose
600
+ uncollapse
601
+ unzip
602
+ values
603
+ write_excel
604
+ zip
605
+ view
606
+ }
607
+ stat=stat{
608
+ abs
609
+ boxplot
610
+ compare_lists
611
+ density
612
+ heatmap
613
+ log
614
+ pvalue.qqplot
615
+ }
616
+ study=study{
617
+ maf2study
618
+ task
619
+ }
620
+ file_server=file_server{
621
+ add
622
+ list
623
+ remove
624
+ }
625
+ benchmark=benchmark{
626
+ pthrough
627
+ throughput
628
+ tsv
629
+ }
630
+ }
631
+ Rlib=Rlib{
632
+ plot.R
633
+ svg.R
634
+ util.R
635
+ }
636
+ software=install/software filter="*"{
637
+ zran=zran{
638
+ zran.c
639
+ }
640
+ lib=lib{
641
+ install_helpers
642
+ }
643
+ }
644
+ }
44
645
  }
45
646
 
647
+ }
648
+ }
data/Rakefile CHANGED
@@ -50,4 +50,5 @@ Rake::RDocTask.new do |rdoc|
50
50
  rdoc.title = "scout-gear #{version}"
51
51
  rdoc.rdoc_files.include('README*')
52
52
  rdoc.rdoc_files.include('lib/**/*.rb')
53
+ rdoc.rdoc_files.include('../modules/rbbt-util/lib/**/*.rb')
53
54
  end
data/VERSION CHANGED
@@ -1 +1 @@
1
- 1.1.1
1
+ 2.0.0
data/bin/scout CHANGED
@@ -0,0 +1,28 @@
1
+ #!/usr/bin/env ruby
2
+
3
+ require_relative '../lib/scout-gear'
4
+
5
+ $LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
6
+
7
+ case
8
+ when File.exist?(file = File.join(__dir__, '../modules/rbbt-util/bin/rbbt'))
9
+ $LOAD_PATH.unshift(lib_dir = File.join(file, '../..', 'lib'))
10
+ require_relative File.join(lib_dir,'rbbt-util')
11
+ Path.add_path(:rbbt, File.expand_path(File.join(File.dirname(lib_dir), "/{TOPLEVEL}/{SUBPATH}")))
12
+ Path.default_pkgdir = Rbbt
13
+ load file
14
+ when File.exist?(file = File.join(ENV["HOME"], 'git/scout-gear/modules/rbbt-util/bin/rbbt'))
15
+ $LOAD_PATH.unshift(lib_dir = File.join(file, '../..', 'lib'))
16
+ require_relative File.join(lib_dir,'rbbt-util')
17
+ Path.add_path(:rbbt, File.expand_path(File.join(File.dirname(lib_dir), "/{TOPLEVEL}/{SUBPATH}")))
18
+ Path.default_pkgdir = Rbbt
19
+ load file
20
+ when File.exist?(file = File.join(ENV["HOME"], 'git/rbbt-util/bin/rbbt'))
21
+ $LOAD_PATH.unshift(lib_dir = File.join(file, '../..', 'lib'))
22
+ require_relative File.join(lib_dir,'rbbt-util')
23
+ Path.add_path(:rbbt, File.expand_path(File.join(File.dirname(lib_dir), "/{TOPLEVEL}/{SUBPATH}")))
24
+ Path.default_pkgdir = Rbbt
25
+ load file
26
+ else
27
+ raise "Cant find rbbt"
28
+ end
@@ -75,33 +75,3 @@ module IndiferentHash
75
75
  end
76
76
  end
77
77
 
78
- module CaseInsensitiveHash
79
-
80
- def self.setup(hash)
81
- hash.extend CaseInsensitiveHash
82
- end
83
-
84
- def downcase_keys
85
- @downcase_keys ||= begin
86
- down = {}
87
- keys.collect{|key|
88
- down[key.to_s.downcase] = key
89
- }
90
- down
91
- end
92
- end
93
-
94
- def [](key, *rest)
95
- value = super(key, *rest)
96
- return value unless value.nil?
97
- key_downcase = key.to_s.downcase
98
- super(downcase_keys[key_downcase])
99
- end
100
-
101
- def values_at(*keys)
102
- keys.collect do |key|
103
- self[key]
104
- end
105
- end
106
-
107
- end
@@ -208,7 +208,7 @@ module Log
208
208
  done_msg << Log.color(:magenta, " · " << desc)
209
209
  print(io, Log.up_lines(@depth) << done_msg << Log.down_lines(@depth))
210
210
 
211
- FileUtils.rm file if file and File.exists?(file)
211
+ FileUtils.rm file if file and File.exist?(file)
212
212
 
213
213
  @callback.call self if @callback
214
214
  end