rbbt-util 5.21.33 → 5.21.34

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data/lib/rbbt/workflow.rb CHANGED
@@ -36,7 +36,7 @@ module Workflow
36
36
  end
37
37
 
38
38
  def self.init_remote_tasks
39
- return if @@init_remote_tasks
39
+ return if defined? @@init_remote_tasks and @@init_remote_tasks
40
40
  load_remote_tasks(Rbbt.root.etc.remote_tasks.find) if Rbbt.root.etc.remote_tasks.exists?
41
41
  @@init_remote_tasks = true
42
42
  end
@@ -99,7 +99,7 @@ TSV.traverse jobs, :_bar => "Checking job status" do |file,i|
99
99
  status = status.to_s
100
100
  end
101
101
 
102
- next unless (force and status !~ /done/) or status =~ /\bnopid/ or status =~ /\berror$/ or status =~ /\bmissing$/ or status =~ /\baborted$/ or status =~ /\bdead$/ or status =~ /\bsync$/ or status == "" or (force and status == 'noinfo')
102
+ next unless (force and status !~ /done/) or status =~ /\bnopid/ or status =~ /\berror$/ or status =~ /\bmissing$/ or status =~ /\baborted$/ or status =~ /\bdead$/ or status =~ /\bsync$/ or status == ""
103
103
  puts " Removing #{ file } - #{status}"
104
104
  Step.clean(file)
105
105
  end
metadata CHANGED
@@ -1,7 +1,7 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: rbbt-util
3
3
  version: !ruby/object:Gem::Version
4
- version: 5.21.33
4
+ version: 5.21.34
5
5
  platform: ruby
6
6
  authors:
7
7
  - Miguel Vazquez
@@ -487,82 +487,82 @@ signing_key:
487
487
  specification_version: 4
488
488
  summary: Utilities for the Ruby Bioinformatics Toolkit (rbbt)
489
489
  test_files:
490
- - test/rbbt/test_workflow.rb
490
+ - test/test_helper.rb
491
491
  - test/rbbt/resource/test_path.rb
492
- - test/rbbt/util/test_cmd.rb
493
- - test/rbbt/util/simpleopt/test_setup.rb
494
- - test/rbbt/util/simpleopt/test_get.rb
495
- - test/rbbt/util/simpleopt/test_parse.rb
496
- - test/rbbt/util/test_chain_methods.rb
497
- - test/rbbt/util/test_simpleDSL.rb
492
+ - test/rbbt/association/test_item.rb
493
+ - test/rbbt/association/test_database.rb
494
+ - test/rbbt/association/test_open.rb
495
+ - test/rbbt/association/test_index.rb
496
+ - test/rbbt/association/test_util.rb
497
+ - test/rbbt/util/test_concurrency.rb
498
498
  - test/rbbt/util/test_log.rb
499
+ - test/rbbt/util/test_chain_methods.rb
500
+ - test/rbbt/util/test_simpleopt.rb
501
+ - test/rbbt/util/simpleopt/test_parse.rb
502
+ - test/rbbt/util/simpleopt/test_get.rb
503
+ - test/rbbt/util/simpleopt/test_setup.rb
504
+ - test/rbbt/util/test_cmd.rb
505
+ - test/rbbt/util/test_semaphore.rb
506
+ - test/rbbt/util/concurrency/test_threads.rb
507
+ - test/rbbt/util/concurrency/processes/test_socket.rb
508
+ - test/rbbt/util/concurrency/test_processes.rb
509
+ - test/rbbt/util/test_tmpfile.rb
499
510
  - test/rbbt/util/test_open.rb
511
+ - test/rbbt/util/test_filecache.rb
512
+ - test/rbbt/util/R/test_eval.rb
513
+ - test/rbbt/util/R/test_model.rb
514
+ - test/rbbt/util/test_simpleDSL.rb
515
+ - test/rbbt/util/log/test_progress.rb
516
+ - test/rbbt/util/test_colorize.rb
517
+ - test/rbbt/util/test_R.rb
500
518
  - test/rbbt/util/misc/test_lock.rb
501
- - test/rbbt/util/misc/test_multipart_payload.rb
502
- - test/rbbt/util/misc/test_bgzf.rb
503
519
  - test/rbbt/util/misc/test_pipes.rb
520
+ - test/rbbt/util/misc/test_bgzf.rb
504
521
  - test/rbbt/util/misc/test_omics.rb
505
- - test/rbbt/util/test_concurrency.rb
506
- - test/rbbt/util/test_R.rb
507
- - test/rbbt/util/log/test_progress.rb
508
- - test/rbbt/util/test_colorize.rb
509
- - test/rbbt/util/test_simpleopt.rb
522
+ - test/rbbt/util/misc/test_multipart_payload.rb
510
523
  - test/rbbt/util/test_excel2tsv.rb
511
- - test/rbbt/util/test_filecache.rb
512
- - test/rbbt/util/concurrency/test_processes.rb
513
- - test/rbbt/util/concurrency/test_threads.rb
514
- - test/rbbt/util/concurrency/processes/test_socket.rb
515
- - test/rbbt/util/test_semaphore.rb
516
524
  - test/rbbt/util/test_misc.rb
517
- - test/rbbt/util/test_tmpfile.rb
518
- - test/rbbt/util/R/test_model.rb
519
- - test/rbbt/util/R/test_eval.rb
520
- - test/rbbt/test_packed_index.rb
521
- - test/rbbt/entity/test_identifiers.rb
522
- - test/rbbt/test_association.rb
523
- - test/rbbt/knowledge_base/test_traverse.rb
524
- - test/rbbt/knowledge_base/test_registry.rb
525
- - test/rbbt/knowledge_base/test_entity.rb
526
- - test/rbbt/knowledge_base/test_enrichment.rb
527
- - test/rbbt/knowledge_base/test_syndicate.rb
528
- - test/rbbt/knowledge_base/test_query.rb
529
- - test/rbbt/test_resource.rb
530
525
  - test/rbbt/test_entity.rb
531
- - test/rbbt/test_knowledge_base.rb
532
- - test/rbbt/annotations/test_util.rb
533
- - test/rbbt/association/test_index.rb
534
- - test/rbbt/association/test_item.rb
535
- - test/rbbt/association/test_open.rb
536
- - test/rbbt/association/test_util.rb
537
- - test/rbbt/association/test_database.rb
538
- - test/rbbt/test_tsv.rb
539
526
  - test/rbbt/workflow/step/test_dependencies.rb
540
- - test/rbbt/workflow/test_task.rb
541
- - test/rbbt/workflow/test_step.rb
542
527
  - test/rbbt/workflow/test_doc.rb
543
- - test/rbbt/test_monitor.rb
544
- - test/rbbt/test_persist.rb
545
- - test/rbbt/test_annotations.rb
546
- - test/rbbt/persist/test_tsv.rb
547
- - test/rbbt/persist/tsv/test_lmdb.rb
548
- - test/rbbt/persist/tsv/test_kyotocabinet.rb
549
- - test/rbbt/persist/tsv/test_sharder.rb
550
- - test/rbbt/persist/tsv/test_cdb.rb
551
- - test/rbbt/persist/tsv/test_tokyocabinet.rb
552
- - test/rbbt/persist/tsv/test_leveldb.rb
553
- - test/rbbt/tsv/test_field_index.rb
528
+ - test/rbbt/workflow/test_step.rb
529
+ - test/rbbt/workflow/test_task.rb
530
+ - test/rbbt/test_association.rb
531
+ - test/rbbt/test_knowledge_base.rb
532
+ - test/rbbt/tsv/parallel/test_traverse.rb
533
+ - test/rbbt/tsv/parallel/test_through.rb
554
534
  - test/rbbt/tsv/test_parallel.rb
555
- - test/rbbt/tsv/test_index.rb
556
- - test/rbbt/tsv/test_matrix.rb
535
+ - test/rbbt/tsv/test_accessor.rb
557
536
  - test/rbbt/tsv/test_change_id.rb
558
- - test/rbbt/tsv/test_parser.rb
559
537
  - test/rbbt/tsv/test_stream.rb
560
- - test/rbbt/tsv/test_util.rb
561
- - test/rbbt/tsv/test_accessor.rb
562
538
  - test/rbbt/tsv/test_filter.rb
539
+ - test/rbbt/tsv/test_matrix.rb
563
540
  - test/rbbt/tsv/test_attach.rb
564
541
  - test/rbbt/tsv/test_manipulate.rb
565
- - test/rbbt/tsv/parallel/test_through.rb
566
- - test/rbbt/tsv/parallel/test_traverse.rb
542
+ - test/rbbt/tsv/test_field_index.rb
543
+ - test/rbbt/tsv/test_index.rb
544
+ - test/rbbt/tsv/test_util.rb
545
+ - test/rbbt/tsv/test_parser.rb
546
+ - test/rbbt/test_packed_index.rb
547
+ - test/rbbt/test_persist.rb
567
548
  - test/rbbt/test_fix_width_table.rb
568
- - test/test_helper.rb
549
+ - test/rbbt/knowledge_base/test_traverse.rb
550
+ - test/rbbt/knowledge_base/test_entity.rb
551
+ - test/rbbt/knowledge_base/test_query.rb
552
+ - test/rbbt/knowledge_base/test_enrichment.rb
553
+ - test/rbbt/knowledge_base/test_syndicate.rb
554
+ - test/rbbt/knowledge_base/test_registry.rb
555
+ - test/rbbt/entity/test_identifiers.rb
556
+ - test/rbbt/test_monitor.rb
557
+ - test/rbbt/test_workflow.rb
558
+ - test/rbbt/test_annotations.rb
559
+ - test/rbbt/annotations/test_util.rb
560
+ - test/rbbt/test_resource.rb
561
+ - test/rbbt/persist/tsv/test_tokyocabinet.rb
562
+ - test/rbbt/persist/tsv/test_kyotocabinet.rb
563
+ - test/rbbt/persist/tsv/test_lmdb.rb
564
+ - test/rbbt/persist/tsv/test_leveldb.rb
565
+ - test/rbbt/persist/tsv/test_cdb.rb
566
+ - test/rbbt/persist/tsv/test_sharder.rb
567
+ - test/rbbt/persist/test_tsv.rb
568
+ - test/rbbt/test_tsv.rb