rbbt-util 5.38.0 → 5.39.0
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- checksums.yaml +4 -4
- data/lib/rbbt/annotations.rb +2 -0
- data/lib/rbbt/persist.rb +2 -2
- data/lib/rbbt/resource.rb +12 -3
- data/lib/rbbt/tsv/excel.rb +5 -1
- data/lib/rbbt/tsv/parser.rb +2 -2
- data/lib/rbbt/tsv/util.rb +4 -0
- data/lib/rbbt/util/cmd.rb +8 -4
- data/lib/rbbt/util/concurrency/processes.rb +1 -1
- data/lib/rbbt/util/migrate.rb +1 -2
- data/lib/rbbt/util/misc/development.rb +0 -2
- data/lib/rbbt/util/misc/format.rb +3 -0
- data/lib/rbbt/util/misc/indiferent_hash.rb +9 -6
- data/lib/rbbt/util/misc/inspect.rb +23 -8
- data/lib/rbbt/util/misc/options.rb +1 -1
- data/lib/rbbt/util/misc/pipes.rb +3 -3
- data/lib/rbbt/util/open.rb +6 -1
- data/lib/rbbt/util/ssh.rb +46 -4
- data/lib/rbbt/workflow/remote_workflow/driver/ssh.rb +7 -7
- data/lib/rbbt/workflow/remote_workflow/remote_step/ssh.rb +4 -3
- data/lib/rbbt/workflow/remote_workflow/remote_step.rb +1 -0
- data/lib/rbbt/workflow/step/dependencies.rb +9 -9
- data/lib/rbbt/workflow/step/info.rb +1 -1
- data/lib/rbbt/workflow/step/save_load_inputs.rb +4 -5
- data/lib/rbbt/workflow/step.rb +9 -4
- data/lib/rbbt/workflow/usage.rb +1 -1
- data/lib/rbbt/workflow/util/trace.rb +2 -1
- data/lib/rbbt/workflow.rb +4 -3
- data/share/rbbt_commands/resource/claims +57 -0
- data/share/rbbt_commands/resource/find +1 -1
- data/share/rbbt_commands/resource/glob +1 -1
- data/share/rbbt_commands/workflow/task +58 -11
- data/test/rbbt/test_resource.rb +7 -2
- data/test/rbbt/test_tsv.rb +16 -1
- data/test/rbbt/tsv/parallel/test_traverse.rb +2 -2
- data/test/rbbt/tsv/test_accessor.rb +21 -4
- data/test/rbbt/tsv/test_parser.rb +28 -0
- data/test/rbbt/tsv/test_util.rb +14 -0
- data/test/rbbt/util/misc/test_indiferent_hash.rb +14 -0
- data/test/rbbt/util/test_cmd.rb +7 -1
- data/test/rbbt/util/test_migrate.rb +2 -2
- data/test/rbbt/util/test_open.rb +3 -3
- data/test/rbbt/util/test_ssh.rb +10 -0
- metadata +99 -94
metadata
CHANGED
@@ -1,14 +1,14 @@
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|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
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name: rbbt-util
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 5.
|
4
|
+
version: 5.39.0
|
5
5
|
platform: ruby
|
6
6
|
authors:
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7
7
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- Miguel Vazquez
|
8
8
|
autorequire:
|
9
9
|
bindir: bin
|
10
10
|
cert_chain: []
|
11
|
-
date: 2023-
|
11
|
+
date: 2023-08-02 00:00:00.000000000 Z
|
12
12
|
dependencies:
|
13
13
|
- !ruby/object:Gem::Dependency
|
14
14
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name: rake
|
@@ -390,6 +390,7 @@ files:
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|
390
390
|
- share/rbbt_commands/migrate
|
391
391
|
- share/rbbt_commands/migrate_job
|
392
392
|
- share/rbbt_commands/purge_job
|
393
|
+
- share/rbbt_commands/resource/claims
|
393
394
|
- share/rbbt_commands/resource/exists
|
394
395
|
- share/rbbt_commands/resource/find
|
395
396
|
- share/rbbt_commands/resource/get
|
@@ -530,6 +531,7 @@ files:
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|
530
531
|
- test/rbbt/util/misc/test_communication.rb
|
531
532
|
- test/rbbt/util/misc/test_development.rb
|
532
533
|
- test/rbbt/util/misc/test_format.rb
|
534
|
+
- test/rbbt/util/misc/test_indiferent_hash.rb
|
533
535
|
- test/rbbt/util/misc/test_lock.rb
|
534
536
|
- test/rbbt/util/misc/test_multipart_payload.rb
|
535
537
|
- test/rbbt/util/misc/test_omics.rb
|
@@ -556,6 +558,7 @@ files:
|
|
556
558
|
- test/rbbt/util/test_semaphore.rb
|
557
559
|
- test/rbbt/util/test_simpleDSL.rb
|
558
560
|
- test/rbbt/util/test_simpleopt.rb
|
561
|
+
- test/rbbt/util/test_ssh.rb
|
559
562
|
- test/rbbt/util/test_tmpfile.rb
|
560
563
|
- test/rbbt/workflow/step/test_dependencies.rb
|
561
564
|
- test/rbbt/workflow/step/test_save_load_inputs.rb
|
@@ -587,113 +590,115 @@ required_rubygems_version: !ruby/object:Gem::Requirement
|
|
587
590
|
- !ruby/object:Gem::Version
|
588
591
|
version: '0'
|
589
592
|
requirements: []
|
590
|
-
rubygems_version: 3.4.
|
593
|
+
rubygems_version: 3.4.13
|
591
594
|
signing_key:
|
592
595
|
specification_version: 4
|
593
596
|
summary: Utilities for the Ruby Bioinformatics Toolkit (rbbt)
|
594
597
|
test_files:
|
595
|
-
- test/rbbt/
|
596
|
-
- test/rbbt/workflow/test_remote_workflow.rb
|
597
|
-
- test/rbbt/workflow/util/test_archive.rb
|
598
|
-
- test/rbbt/workflow/util/test_orchestrator.rb
|
599
|
-
- test/rbbt/workflow/util/test_data.rb
|
600
|
-
- test/rbbt/workflow/test_doc.rb
|
601
|
-
- test/rbbt/workflow/test_schedule.rb
|
602
|
-
- test/rbbt/workflow/test_step.rb
|
603
|
-
- test/rbbt/workflow/step/test_dependencies.rb
|
604
|
-
- test/rbbt/workflow/step/test_save_load_inputs.rb
|
605
|
-
- test/rbbt/workflow/test_task.rb
|
606
|
-
- test/rbbt/resource/test_path.rb
|
607
|
-
- test/rbbt/util/test_colorize.rb
|
608
|
-
- test/rbbt/util/test_procpath.rb
|
609
|
-
- test/rbbt/util/python/test_util.rb
|
610
|
-
- test/rbbt/util/misc/test_development.rb
|
611
|
-
- test/rbbt/util/misc/test_omics.rb
|
612
|
-
- test/rbbt/util/misc/test_pipes.rb
|
613
|
-
- test/rbbt/util/misc/test_serialize.rb
|
614
|
-
- test/rbbt/util/misc/test_format.rb
|
615
|
-
- test/rbbt/util/misc/test_communication.rb
|
616
|
-
- test/rbbt/util/misc/test_lock.rb
|
617
|
-
- test/rbbt/util/misc/test_multipart_payload.rb
|
618
|
-
- test/rbbt/util/misc/test_bgzf.rb
|
619
|
-
- test/rbbt/util/test_concurrency.rb
|
620
|
-
- test/rbbt/util/test_cmd.rb
|
621
|
-
- test/rbbt/util/R/test_plot.rb
|
622
|
-
- test/rbbt/util/R/test_eval.rb
|
623
|
-
- test/rbbt/util/R/test_model.rb
|
624
|
-
- test/rbbt/util/test_config.rb
|
625
|
-
- test/rbbt/util/test_log.rb
|
626
|
-
- test/rbbt/util/test_simpleDSL.rb
|
627
|
-
- test/rbbt/util/log/test_progress.rb
|
628
|
-
- test/rbbt/util/test_tmpfile.rb
|
629
|
-
- test/rbbt/util/test_R.rb
|
630
|
-
- test/rbbt/util/test_excel2tsv.rb
|
631
|
-
- test/rbbt/util/test_misc.rb
|
632
|
-
- test/rbbt/util/test_open.rb
|
633
|
-
- test/rbbt/util/test_simpleopt.rb
|
634
|
-
- test/rbbt/util/simpleopt/test_parse.rb
|
635
|
-
- test/rbbt/util/simpleopt/test_setup.rb
|
636
|
-
- test/rbbt/util/simpleopt/test_get.rb
|
637
|
-
- test/rbbt/util/test_python.rb
|
638
|
-
- test/rbbt/util/test_filecache.rb
|
639
|
-
- test/rbbt/util/concurrency/test_processes.rb
|
640
|
-
- test/rbbt/util/concurrency/test_threads.rb
|
641
|
-
- test/rbbt/util/concurrency/processes/test_socket.rb
|
642
|
-
- test/rbbt/util/test_semaphore.rb
|
643
|
-
- test/rbbt/util/test_chain_methods.rb
|
644
|
-
- test/rbbt/util/test_migrate.rb
|
645
|
-
- test/rbbt/test_resource.rb
|
646
|
-
- test/rbbt/test_packed_index.rb
|
647
|
-
- test/rbbt/tsv/test_change_id.rb
|
648
|
-
- test/rbbt/tsv/test_attach.rb
|
649
|
-
- test/rbbt/tsv/test_filter.rb
|
650
|
-
- test/rbbt/tsv/test_marshal.rb
|
651
|
-
- test/rbbt/tsv/test_parser.rb
|
652
|
-
- test/rbbt/tsv/test_csv.rb
|
653
|
-
- test/rbbt/tsv/test_accessor.rb
|
654
|
-
- test/rbbt/tsv/test_matrix.rb
|
655
|
-
- test/rbbt/tsv/test_field_index.rb
|
656
|
-
- test/rbbt/tsv/test_util.rb
|
657
|
-
- test/rbbt/tsv/test_index.rb
|
658
|
-
- test/rbbt/tsv/test_parallel.rb
|
659
|
-
- test/rbbt/tsv/test_manipulate.rb
|
660
|
-
- test/rbbt/tsv/test_excel.rb
|
661
|
-
- test/rbbt/tsv/parallel/test_through.rb
|
662
|
-
- test/rbbt/tsv/parallel/test_traverse.rb
|
663
|
-
- test/rbbt/tsv/test_stream.rb
|
664
|
-
- test/rbbt/test_association.rb
|
665
|
-
- test/rbbt/hpc/test_batch.rb
|
666
|
-
- test/rbbt/hpc/orchestrate/test_chains.rb
|
667
|
-
- test/rbbt/hpc/orchestrate/test_rules.rb
|
668
|
-
- test/rbbt/hpc/orchestrate/test_batches.rb
|
669
|
-
- test/rbbt/hpc/test_slurm.rb
|
670
|
-
- test/rbbt/hpc/test_orchestrate.rb
|
598
|
+
- test/rbbt/annotations/test_util.rb
|
671
599
|
- test/rbbt/association/test_database.rb
|
600
|
+
- test/rbbt/association/test_index.rb
|
672
601
|
- test/rbbt/association/test_item.rb
|
673
602
|
- test/rbbt/association/test_open.rb
|
674
603
|
- test/rbbt/association/test_util.rb
|
675
|
-
- test/rbbt/
|
676
|
-
- test/rbbt/
|
677
|
-
- test/rbbt/
|
604
|
+
- test/rbbt/entity/test_identifiers.rb
|
605
|
+
- test/rbbt/hpc/orchestrate/test_batches.rb
|
606
|
+
- test/rbbt/hpc/orchestrate/test_chains.rb
|
607
|
+
- test/rbbt/hpc/orchestrate/test_rules.rb
|
608
|
+
- test/rbbt/hpc/test_batch.rb
|
609
|
+
- test/rbbt/hpc/test_orchestrate.rb
|
610
|
+
- test/rbbt/hpc/test_slurm.rb
|
611
|
+
- test/rbbt/knowledge_base/test_enrichment.rb
|
612
|
+
- test/rbbt/knowledge_base/test_entity.rb
|
613
|
+
- test/rbbt/knowledge_base/test_query.rb
|
614
|
+
- test/rbbt/knowledge_base/test_registry.rb
|
615
|
+
- test/rbbt/knowledge_base/test_syndicate.rb
|
616
|
+
- test/rbbt/knowledge_base/test_traverse.rb
|
617
|
+
- test/rbbt/persist/test_tsv.rb
|
678
618
|
- test/rbbt/persist/tsv/test_cdb.rb
|
619
|
+
- test/rbbt/persist/tsv/test_kyotocabinet.rb
|
620
|
+
- test/rbbt/persist/tsv/test_leveldb.rb
|
679
621
|
- test/rbbt/persist/tsv/test_lmdb.rb
|
680
622
|
- test/rbbt/persist/tsv/test_sharder.rb
|
681
|
-
- test/rbbt/persist/tsv/test_leveldb.rb
|
682
623
|
- test/rbbt/persist/tsv/test_tokyocabinet.rb
|
683
|
-
- test/rbbt/
|
684
|
-
- test/rbbt/test_tsv.rb
|
624
|
+
- test/rbbt/resource/test_path.rb
|
685
625
|
- test/rbbt/test_annotations.rb
|
626
|
+
- test/rbbt/test_association.rb
|
627
|
+
- test/rbbt/test_entity.rb
|
686
628
|
- test/rbbt/test_fix_width_table.rb
|
687
|
-
- test/rbbt/test_workflow.rb
|
688
|
-
- test/rbbt/entity/test_identifiers.rb
|
689
|
-
- test/rbbt/annotations/test_util.rb
|
690
629
|
- test/rbbt/test_hpc.rb
|
630
|
+
- test/rbbt/test_knowledge_base.rb
|
691
631
|
- test/rbbt/test_monitor.rb
|
632
|
+
- test/rbbt/test_packed_index.rb
|
692
633
|
- test/rbbt/test_persist.rb
|
693
|
-
- test/rbbt/
|
694
|
-
- test/rbbt/
|
695
|
-
- test/rbbt/
|
696
|
-
- test/rbbt/
|
697
|
-
- test/rbbt/
|
698
|
-
- test/rbbt/
|
634
|
+
- test/rbbt/test_resource.rb
|
635
|
+
- test/rbbt/test_tsv.rb
|
636
|
+
- test/rbbt/test_workflow.rb
|
637
|
+
- test/rbbt/tsv/parallel/test_through.rb
|
638
|
+
- test/rbbt/tsv/parallel/test_traverse.rb
|
639
|
+
- test/rbbt/tsv/test_accessor.rb
|
640
|
+
- test/rbbt/tsv/test_attach.rb
|
641
|
+
- test/rbbt/tsv/test_change_id.rb
|
642
|
+
- test/rbbt/tsv/test_csv.rb
|
643
|
+
- test/rbbt/tsv/test_excel.rb
|
644
|
+
- test/rbbt/tsv/test_field_index.rb
|
645
|
+
- test/rbbt/tsv/test_filter.rb
|
646
|
+
- test/rbbt/tsv/test_index.rb
|
647
|
+
- test/rbbt/tsv/test_manipulate.rb
|
648
|
+
- test/rbbt/tsv/test_marshal.rb
|
649
|
+
- test/rbbt/tsv/test_matrix.rb
|
650
|
+
- test/rbbt/tsv/test_parallel.rb
|
651
|
+
- test/rbbt/tsv/test_parser.rb
|
652
|
+
- test/rbbt/tsv/test_stream.rb
|
653
|
+
- test/rbbt/tsv/test_util.rb
|
654
|
+
- test/rbbt/util/R/test_eval.rb
|
655
|
+
- test/rbbt/util/R/test_model.rb
|
656
|
+
- test/rbbt/util/R/test_plot.rb
|
657
|
+
- test/rbbt/util/concurrency/processes/test_socket.rb
|
658
|
+
- test/rbbt/util/concurrency/test_processes.rb
|
659
|
+
- test/rbbt/util/concurrency/test_threads.rb
|
660
|
+
- test/rbbt/util/log/test_progress.rb
|
661
|
+
- test/rbbt/util/misc/test_bgzf.rb
|
662
|
+
- test/rbbt/util/misc/test_communication.rb
|
663
|
+
- test/rbbt/util/misc/test_development.rb
|
664
|
+
- test/rbbt/util/misc/test_format.rb
|
665
|
+
- test/rbbt/util/misc/test_indiferent_hash.rb
|
666
|
+
- test/rbbt/util/misc/test_lock.rb
|
667
|
+
- test/rbbt/util/misc/test_multipart_payload.rb
|
668
|
+
- test/rbbt/util/misc/test_omics.rb
|
669
|
+
- test/rbbt/util/misc/test_pipes.rb
|
670
|
+
- test/rbbt/util/misc/test_serialize.rb
|
671
|
+
- test/rbbt/util/python/test_util.rb
|
672
|
+
- test/rbbt/util/simpleopt/test_get.rb
|
673
|
+
- test/rbbt/util/simpleopt/test_parse.rb
|
674
|
+
- test/rbbt/util/simpleopt/test_setup.rb
|
675
|
+
- test/rbbt/util/test_R.rb
|
676
|
+
- test/rbbt/util/test_chain_methods.rb
|
677
|
+
- test/rbbt/util/test_cmd.rb
|
678
|
+
- test/rbbt/util/test_colorize.rb
|
679
|
+
- test/rbbt/util/test_concurrency.rb
|
680
|
+
- test/rbbt/util/test_config.rb
|
681
|
+
- test/rbbt/util/test_excel2tsv.rb
|
682
|
+
- test/rbbt/util/test_filecache.rb
|
683
|
+
- test/rbbt/util/test_log.rb
|
684
|
+
- test/rbbt/util/test_migrate.rb
|
685
|
+
- test/rbbt/util/test_misc.rb
|
686
|
+
- test/rbbt/util/test_open.rb
|
687
|
+
- test/rbbt/util/test_procpath.rb
|
688
|
+
- test/rbbt/util/test_python.rb
|
689
|
+
- test/rbbt/util/test_semaphore.rb
|
690
|
+
- test/rbbt/util/test_simpleDSL.rb
|
691
|
+
- test/rbbt/util/test_simpleopt.rb
|
692
|
+
- test/rbbt/util/test_ssh.rb
|
693
|
+
- test/rbbt/util/test_tmpfile.rb
|
694
|
+
- test/rbbt/workflow/step/test_dependencies.rb
|
695
|
+
- test/rbbt/workflow/step/test_save_load_inputs.rb
|
696
|
+
- test/rbbt/workflow/test_doc.rb
|
697
|
+
- test/rbbt/workflow/test_remote_workflow.rb
|
698
|
+
- test/rbbt/workflow/test_schedule.rb
|
699
|
+
- test/rbbt/workflow/test_step.rb
|
700
|
+
- test/rbbt/workflow/test_task.rb
|
701
|
+
- test/rbbt/workflow/util/test_archive.rb
|
702
|
+
- test/rbbt/workflow/util/test_data.rb
|
703
|
+
- test/rbbt/workflow/util/test_orchestrator.rb
|
699
704
|
- test/test_helper.rb
|