rbbt-util 5.31.14 → 5.32.4
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- checksums.yaml +4 -4
- data/lib/rbbt/hpc/batch.rb +35 -3
- data/lib/rbbt/hpc/lsf.rb +7 -4
- data/lib/rbbt/hpc/orchestrate.rb +8 -1
- data/lib/rbbt/hpc/slurm.rb +7 -3
- data/lib/rbbt/persist/tsv/adapter.rb +1 -1
- data/lib/rbbt/resource.rb +9 -10
- data/lib/rbbt/tsv/csv.rb +5 -0
- data/lib/rbbt/tsv/parser.rb +2 -2
- data/lib/rbbt/tsv/stream.rb +1 -0
- data/lib/rbbt/util/misc/pipes.rb +1 -1
- data/lib/rbbt/workflow.rb +10 -6
- data/lib/rbbt/workflow/definition.rb +1 -0
- data/lib/rbbt/workflow/doc.rb +18 -3
- data/lib/rbbt/workflow/step.rb +4 -0
- data/lib/rbbt/workflow/step/accessor.rb +1 -0
- data/lib/rbbt/workflow/usage.rb +2 -2
- data/lib/rbbt/workflow/util/archive.rb +1 -1
- data/lib/rbbt/workflow/util/trace.rb +141 -90
- data/share/rbbt_commands/hpc/clean +1 -27
- data/share/rbbt_commands/hpc/list +4 -28
- data/share/rbbt_commands/hpc/orchestrate +1 -27
- data/share/rbbt_commands/hpc/tail +1 -27
- data/share/rbbt_commands/hpc/task +1 -27
- data/share/rbbt_commands/workflow/forget_deps +17 -5
- data/share/rbbt_commands/workflow/trace +9 -195
- data/share/rbbt_commands/workflow/write_info +17 -3
- data/test/rbbt/persist/tsv/test_tokyocabinet.rb +1 -1
- metadata +81 -80
@@ -46,7 +46,21 @@ pid = step.info[:pid]
|
|
46
46
|
host = step.info[:pid_hostname]
|
47
47
|
|
48
48
|
step.rec_dependencies.each do |dep|
|
49
|
-
|
50
|
-
|
51
|
-
|
49
|
+
begin
|
50
|
+
dep.set_info key, value if (force || ! dep.info.include?(key)) && (!check_pid || dep.info[:pid].to_s == pid and dep.info[:pid_hostname] == host)
|
51
|
+
rescue
|
52
|
+
Log.warn "Could no set info #{key} for #{dep.path}: #{$!.message}"
|
53
|
+
end
|
52
54
|
end if recursive
|
55
|
+
|
56
|
+
if recursive && step.info[:archived_info]
|
57
|
+
ad = step.info[:archived_info]
|
58
|
+
ad.each do |d,info|
|
59
|
+
begin
|
60
|
+
info[key] = value if (force || ! info.include?(key)) && (!check_pid || info[:pid].to_s == pid and info[:pid_hostname] == host)
|
61
|
+
rescue
|
62
|
+
Log.warn "Could no set info #{key} for archived_dep #{info[:path]}: #{$!.message}"
|
63
|
+
end
|
64
|
+
end
|
65
|
+
step.set_info :archived_info, ad
|
66
|
+
end
|
metadata
CHANGED
@@ -1,14 +1,14 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: rbbt-util
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 5.
|
4
|
+
version: 5.32.4
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- Miguel Vazquez
|
8
|
-
autorequire:
|
8
|
+
autorequire:
|
9
9
|
bindir: bin
|
10
10
|
cert_chain: []
|
11
|
-
date: 2021-04-
|
11
|
+
date: 2021-04-29 00:00:00.000000000 Z
|
12
12
|
dependencies:
|
13
13
|
- !ruby/object:Gem::Dependency
|
14
14
|
name: rake
|
@@ -542,7 +542,7 @@ homepage: http://github.com/mikisvaz/rbbt-util
|
|
542
542
|
licenses:
|
543
543
|
- MIT
|
544
544
|
metadata: {}
|
545
|
-
post_install_message:
|
545
|
+
post_install_message:
|
546
546
|
rdoc_options: []
|
547
547
|
require_paths:
|
548
548
|
- lib
|
@@ -557,101 +557,102 @@ required_rubygems_version: !ruby/object:Gem::Requirement
|
|
557
557
|
- !ruby/object:Gem::Version
|
558
558
|
version: '0'
|
559
559
|
requirements: []
|
560
|
-
|
561
|
-
|
560
|
+
rubyforge_project:
|
561
|
+
rubygems_version: 2.7.6
|
562
|
+
signing_key:
|
562
563
|
specification_version: 4
|
563
564
|
summary: Utilities for the Ruby Bioinformatics Toolkit (rbbt)
|
564
565
|
test_files:
|
566
|
+
- test/test_helper.rb
|
567
|
+
- test/rbbt/entity/test_identifiers.rb
|
568
|
+
- test/rbbt/test_resource.rb
|
569
|
+
- test/rbbt/test_association.rb
|
570
|
+
- test/rbbt/hpc/test_slurm.rb
|
571
|
+
- test/rbbt/hpc/test_batch.rb
|
572
|
+
- test/rbbt/persist/test_tsv.rb
|
573
|
+
- test/rbbt/persist/tsv/test_kyotocabinet.rb
|
574
|
+
- test/rbbt/persist/tsv/test_lmdb.rb
|
575
|
+
- test/rbbt/persist/tsv/test_tokyocabinet.rb
|
576
|
+
- test/rbbt/persist/tsv/test_cdb.rb
|
577
|
+
- test/rbbt/persist/tsv/test_leveldb.rb
|
578
|
+
- test/rbbt/persist/tsv/test_sharder.rb
|
579
|
+
- test/rbbt/test_packed_index.rb
|
565
580
|
- test/rbbt/test_entity.rb
|
581
|
+
- test/rbbt/test_fix_width_table.rb
|
566
582
|
- test/rbbt/workflow/test_remote_workflow.rb
|
567
|
-
- test/rbbt/workflow/util/test_orchestrator.rb
|
568
583
|
- test/rbbt/workflow/test_doc.rb
|
569
|
-
- test/rbbt/workflow/test_schedule.rb
|
570
|
-
- test/rbbt/workflow/test_step.rb
|
571
584
|
- test/rbbt/workflow/step/test_dependencies.rb
|
585
|
+
- test/rbbt/workflow/test_schedule.rb
|
586
|
+
- test/rbbt/workflow/util/test_orchestrator.rb
|
572
587
|
- test/rbbt/workflow/test_task.rb
|
573
|
-
- test/rbbt/
|
574
|
-
- test/rbbt/
|
588
|
+
- test/rbbt/workflow/test_step.rb
|
589
|
+
- test/rbbt/test_tsv.rb
|
590
|
+
- test/rbbt/test_annotations.rb
|
591
|
+
- test/rbbt/test_knowledge_base.rb
|
592
|
+
- test/rbbt/util/test_simpleDSL.rb
|
593
|
+
- test/rbbt/util/concurrency/processes/test_socket.rb
|
594
|
+
- test/rbbt/util/concurrency/test_processes.rb
|
595
|
+
- test/rbbt/util/concurrency/test_threads.rb
|
596
|
+
- test/rbbt/util/test_filecache.rb
|
597
|
+
- test/rbbt/util/simpleopt/test_get.rb
|
598
|
+
- test/rbbt/util/simpleopt/test_parse.rb
|
599
|
+
- test/rbbt/util/simpleopt/test_setup.rb
|
600
|
+
- test/rbbt/util/test_misc.rb
|
601
|
+
- test/rbbt/util/test_excel2tsv.rb
|
602
|
+
- test/rbbt/util/test_semaphore.rb
|
575
603
|
- test/rbbt/util/test_procpath.rb
|
576
|
-
- test/rbbt/util/misc/test_development.rb
|
577
|
-
- test/rbbt/util/misc/test_omics.rb
|
578
|
-
- test/rbbt/util/misc/test_pipes.rb
|
579
|
-
- test/rbbt/util/misc/test_format.rb
|
580
|
-
- test/rbbt/util/misc/test_lock.rb
|
581
|
-
- test/rbbt/util/misc/test_multipart_payload.rb
|
582
|
-
- test/rbbt/util/misc/test_bgzf.rb
|
583
|
-
- test/rbbt/util/test_concurrency.rb
|
584
|
-
- test/rbbt/util/test_cmd.rb
|
585
|
-
- test/rbbt/util/R/test_plot.rb
|
586
|
-
- test/rbbt/util/R/test_eval.rb
|
587
604
|
- test/rbbt/util/R/test_model.rb
|
605
|
+
- test/rbbt/util/R/test_eval.rb
|
606
|
+
- test/rbbt/util/R/test_plot.rb
|
607
|
+
- test/rbbt/util/test_open.rb
|
608
|
+
- test/rbbt/util/test_tmpfile.rb
|
609
|
+
- test/rbbt/util/test_cmd.rb
|
610
|
+
- test/rbbt/util/test_concurrency.rb
|
611
|
+
- test/rbbt/util/test_colorize.rb
|
588
612
|
- test/rbbt/util/test_config.rb
|
589
613
|
- test/rbbt/util/test_log.rb
|
590
|
-
- test/rbbt/util/test_simpleDSL.rb
|
591
|
-
- test/rbbt/util/log/test_progress.rb
|
592
|
-
- test/rbbt/util/test_tmpfile.rb
|
593
|
-
- test/rbbt/util/test_R.rb
|
594
|
-
- test/rbbt/util/test_excel2tsv.rb
|
595
|
-
- test/rbbt/util/test_misc.rb
|
596
|
-
- test/rbbt/util/test_open.rb
|
597
614
|
- test/rbbt/util/test_simpleopt.rb
|
598
|
-
- test/rbbt/util/simpleopt/test_parse.rb
|
599
|
-
- test/rbbt/util/simpleopt/test_setup.rb
|
600
|
-
- test/rbbt/util/simpleopt/test_get.rb
|
601
615
|
- test/rbbt/util/test_python.rb
|
602
|
-
- test/rbbt/util/test_filecache.rb
|
603
|
-
- test/rbbt/util/concurrency/test_processes.rb
|
604
|
-
- test/rbbt/util/concurrency/test_threads.rb
|
605
|
-
- test/rbbt/util/concurrency/processes/test_socket.rb
|
606
|
-
- test/rbbt/util/test_semaphore.rb
|
607
616
|
- test/rbbt/util/test_chain_methods.rb
|
608
|
-
- test/rbbt/
|
609
|
-
- test/rbbt/
|
610
|
-
- test/rbbt/
|
611
|
-
- test/rbbt/
|
612
|
-
- test/rbbt/
|
617
|
+
- test/rbbt/util/misc/test_omics.rb
|
618
|
+
- test/rbbt/util/misc/test_lock.rb
|
619
|
+
- test/rbbt/util/misc/test_multipart_payload.rb
|
620
|
+
- test/rbbt/util/misc/test_bgzf.rb
|
621
|
+
- test/rbbt/util/misc/test_development.rb
|
622
|
+
- test/rbbt/util/misc/test_format.rb
|
623
|
+
- test/rbbt/util/misc/test_pipes.rb
|
624
|
+
- test/rbbt/util/log/test_progress.rb
|
625
|
+
- test/rbbt/util/test_R.rb
|
626
|
+
- test/rbbt/test_workflow.rb
|
627
|
+
- test/rbbt/knowledge_base/test_entity.rb
|
628
|
+
- test/rbbt/knowledge_base/test_enrichment.rb
|
629
|
+
- test/rbbt/knowledge_base/test_traverse.rb
|
630
|
+
- test/rbbt/knowledge_base/test_syndicate.rb
|
631
|
+
- test/rbbt/knowledge_base/test_registry.rb
|
632
|
+
- test/rbbt/knowledge_base/test_query.rb
|
633
|
+
- test/rbbt/association/test_item.rb
|
634
|
+
- test/rbbt/association/test_util.rb
|
635
|
+
- test/rbbt/association/test_open.rb
|
636
|
+
- test/rbbt/association/test_database.rb
|
637
|
+
- test/rbbt/association/test_index.rb
|
638
|
+
- test/rbbt/annotations/test_util.rb
|
639
|
+
- test/rbbt/test_monitor.rb
|
640
|
+
- test/rbbt/resource/test_path.rb
|
641
|
+
- test/rbbt/test_hpc.rb
|
642
|
+
- test/rbbt/test_persist.rb
|
613
643
|
- test/rbbt/tsv/test_parser.rb
|
614
644
|
- test/rbbt/tsv/test_csv.rb
|
615
|
-
- test/rbbt/tsv/
|
616
|
-
- test/rbbt/tsv/test_matrix.rb
|
645
|
+
- test/rbbt/tsv/test_manipulate.rb
|
617
646
|
- test/rbbt/tsv/test_field_index.rb
|
618
647
|
- test/rbbt/tsv/test_util.rb
|
619
|
-
- test/rbbt/tsv/
|
648
|
+
- test/rbbt/tsv/test_accessor.rb
|
649
|
+
- test/rbbt/tsv/test_filter.rb
|
650
|
+
- test/rbbt/tsv/test_stream.rb
|
620
651
|
- test/rbbt/tsv/test_parallel.rb
|
621
|
-
- test/rbbt/tsv/
|
652
|
+
- test/rbbt/tsv/test_matrix.rb
|
653
|
+
- test/rbbt/tsv/test_attach.rb
|
622
654
|
- test/rbbt/tsv/test_excel.rb
|
623
|
-
- test/rbbt/tsv/
|
655
|
+
- test/rbbt/tsv/test_change_id.rb
|
656
|
+
- test/rbbt/tsv/test_index.rb
|
624
657
|
- test/rbbt/tsv/parallel/test_traverse.rb
|
625
|
-
- test/rbbt/tsv/
|
626
|
-
- test/rbbt/test_association.rb
|
627
|
-
- test/rbbt/hpc/test_batch.rb
|
628
|
-
- test/rbbt/hpc/test_slurm.rb
|
629
|
-
- test/rbbt/association/test_database.rb
|
630
|
-
- test/rbbt/association/test_item.rb
|
631
|
-
- test/rbbt/association/test_open.rb
|
632
|
-
- test/rbbt/association/test_util.rb
|
633
|
-
- test/rbbt/association/test_index.rb
|
634
|
-
- test/rbbt/test_knowledge_base.rb
|
635
|
-
- test/rbbt/persist/tsv/test_kyotocabinet.rb
|
636
|
-
- test/rbbt/persist/tsv/test_cdb.rb
|
637
|
-
- test/rbbt/persist/tsv/test_lmdb.rb
|
638
|
-
- test/rbbt/persist/tsv/test_sharder.rb
|
639
|
-
- test/rbbt/persist/tsv/test_leveldb.rb
|
640
|
-
- test/rbbt/persist/tsv/test_tokyocabinet.rb
|
641
|
-
- test/rbbt/persist/test_tsv.rb
|
642
|
-
- test/rbbt/test_tsv.rb
|
643
|
-
- test/rbbt/test_annotations.rb
|
644
|
-
- test/rbbt/test_fix_width_table.rb
|
645
|
-
- test/rbbt/test_workflow.rb
|
646
|
-
- test/rbbt/entity/test_identifiers.rb
|
647
|
-
- test/rbbt/annotations/test_util.rb
|
648
|
-
- test/rbbt/test_hpc.rb
|
649
|
-
- test/rbbt/test_monitor.rb
|
650
|
-
- test/rbbt/test_persist.rb
|
651
|
-
- test/rbbt/knowledge_base/test_entity.rb
|
652
|
-
- test/rbbt/knowledge_base/test_registry.rb
|
653
|
-
- test/rbbt/knowledge_base/test_syndicate.rb
|
654
|
-
- test/rbbt/knowledge_base/test_query.rb
|
655
|
-
- test/rbbt/knowledge_base/test_enrichment.rb
|
656
|
-
- test/rbbt/knowledge_base/test_traverse.rb
|
657
|
-
- test/test_helper.rb
|
658
|
+
- test/rbbt/tsv/parallel/test_through.rb
|