rbbt-util 5.32.24 → 5.32.28
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- checksums.yaml +4 -4
- data/bin/rbbt_find.rb +74 -0
- data/lib/rbbt/annotations/annotated_array.rb +4 -0
- data/lib/rbbt/annotations/util.rb +29 -0
- data/lib/rbbt/entity.rb +3 -1
- data/lib/rbbt/hpc/orchestrate/batches.rb +140 -0
- data/lib/rbbt/hpc/orchestrate/chains.rb +173 -0
- data/lib/rbbt/hpc/orchestrate/rules.rb +70 -0
- data/lib/rbbt/hpc/orchestrate.old.rb +220 -0
- data/lib/rbbt/hpc/orchestrate.rb +24 -200
- data/lib/rbbt/hpc/slurm.rb +1 -0
- data/lib/rbbt/persist/tsv.rb +1 -1
- data/lib/rbbt/tsv/excel.rb +16 -8
- data/lib/rbbt/util/log.rb +6 -2
- data/lib/rbbt/util/migrate.rb +6 -1
- data/lib/rbbt/util/misc/inspect.rb +4 -1
- data/lib/rbbt/util/misc.rb +5 -0
- data/lib/rbbt/util/python.rb +1 -1
- data/lib/rbbt/workflow/definition.rb +1 -1
- data/lib/rbbt/workflow/examples.rb +0 -65
- data/lib/rbbt/workflow/integration/nextflow.rb +74 -14
- data/lib/rbbt/workflow/step/accessor.rb +0 -70
- data/lib/rbbt/workflow/step/dependencies.rb +8 -2
- data/lib/rbbt/workflow/step/run.rb +1 -1
- data/lib/rbbt/workflow/step/save_load_inputs.rb +162 -0
- data/lib/rbbt/workflow/step.rb +2 -1
- data/lib/rbbt/workflow/task.rb +2 -2
- data/lib/rbbt/workflow.rb +9 -2
- data/share/rbbt_commands/hpc/tail +0 -13
- data/share/rbbt_commands/lsf/tail +0 -13
- data/share/rbbt_commands/slurm/tail +0 -13
- data/share/rbbt_commands/tsv/keys +14 -15
- data/share/rbbt_commands/tsv/read_excel +2 -2
- data/share/rbbt_commands/workflow/task +11 -5
- data/test/rbbt/annotations/test_util.rb +11 -0
- data/test/rbbt/hpc/orchestrate/test_batches.rb +113 -0
- data/test/rbbt/hpc/orchestrate/test_chains.rb +139 -0
- data/test/rbbt/hpc/orchestrate/test_rules.rb +92 -0
- data/test/rbbt/hpc/test_orchestrate.rb +144 -0
- data/test/rbbt/tsv/test_excel.rb +38 -4
- data/test/rbbt/util/test_misc.rb +4 -0
- data/test/rbbt/workflow/step/test_dependencies.rb +14 -13
- data/test/rbbt/workflow/step/test_save_load_inputs.rb +46 -0
- metadata +19 -2
metadata
CHANGED
@@ -1,14 +1,14 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
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2
2
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name: rbbt-util
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3
3
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version: !ruby/object:Gem::Version
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4
|
-
version: 5.32.
|
4
|
+
version: 5.32.28
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- Miguel Vazquez
|
8
8
|
autorequire:
|
9
9
|
bindir: bin
|
10
10
|
cert_chain: []
|
11
|
-
date:
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11
|
+
date: 2022-02-11 00:00:00.000000000 Z
|
12
12
|
dependencies:
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13
13
|
- !ruby/object:Gem::Dependency
|
14
14
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name: rake
|
@@ -172,6 +172,7 @@ executables:
|
|
172
172
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- rbbt_Rutil.rb
|
173
173
|
- rbbt
|
174
174
|
- rbbt_dangling_locks.rb
|
175
|
+
- rbbt_find.rb
|
175
176
|
extensions: []
|
176
177
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extra_rdoc_files:
|
177
178
|
- LICENSE
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@@ -183,6 +184,7 @@ files:
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|
183
184
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- bin/rbbt_Rutil.rb
|
184
185
|
- bin/rbbt_dangling_locks.rb
|
185
186
|
- bin/rbbt_exec.rb
|
187
|
+
- bin/rbbt_find.rb
|
186
188
|
- bin/rbbt_query.rb
|
187
189
|
- etc/app.d/base.rb
|
188
190
|
- etc/app.d/entities.rb
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@@ -213,7 +215,11 @@ files:
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|
213
215
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- lib/rbbt/hpc.rb
|
214
216
|
- lib/rbbt/hpc/batch.rb
|
215
217
|
- lib/rbbt/hpc/lsf.rb
|
218
|
+
- lib/rbbt/hpc/orchestrate.old.rb
|
216
219
|
- lib/rbbt/hpc/orchestrate.rb
|
220
|
+
- lib/rbbt/hpc/orchestrate/batches.rb
|
221
|
+
- lib/rbbt/hpc/orchestrate/chains.rb
|
222
|
+
- lib/rbbt/hpc/orchestrate/rules.rb
|
217
223
|
- lib/rbbt/hpc/slurm.rb
|
218
224
|
- lib/rbbt/knowledge_base.rb
|
219
225
|
- lib/rbbt/knowledge_base/enrichment.rb
|
@@ -343,6 +349,7 @@ files:
|
|
343
349
|
- lib/rbbt/workflow/step/info.rb
|
344
350
|
- lib/rbbt/workflow/step/prepare.rb
|
345
351
|
- lib/rbbt/workflow/step/run.rb
|
352
|
+
- lib/rbbt/workflow/step/save_load_inputs.rb
|
346
353
|
- lib/rbbt/workflow/step/status.rb
|
347
354
|
- lib/rbbt/workflow/task.rb
|
348
355
|
- lib/rbbt/workflow/usage.rb
|
@@ -468,7 +475,11 @@ files:
|
|
468
475
|
- test/rbbt/association/test_open.rb
|
469
476
|
- test/rbbt/association/test_util.rb
|
470
477
|
- test/rbbt/entity/test_identifiers.rb
|
478
|
+
- test/rbbt/hpc/orchestrate/test_batches.rb
|
479
|
+
- test/rbbt/hpc/orchestrate/test_chains.rb
|
480
|
+
- test/rbbt/hpc/orchestrate/test_rules.rb
|
471
481
|
- test/rbbt/hpc/test_batch.rb
|
482
|
+
- test/rbbt/hpc/test_orchestrate.rb
|
472
483
|
- test/rbbt/hpc/test_slurm.rb
|
473
484
|
- test/rbbt/knowledge_base/test_enrichment.rb
|
474
485
|
- test/rbbt/knowledge_base/test_entity.rb
|
@@ -548,6 +559,7 @@ files:
|
|
548
559
|
- test/rbbt/util/test_simpleopt.rb
|
549
560
|
- test/rbbt/util/test_tmpfile.rb
|
550
561
|
- test/rbbt/workflow/step/test_dependencies.rb
|
562
|
+
- test/rbbt/workflow/step/test_save_load_inputs.rb
|
551
563
|
- test/rbbt/workflow/test_doc.rb
|
552
564
|
- test/rbbt/workflow/test_remote_workflow.rb
|
553
565
|
- test/rbbt/workflow/test_schedule.rb
|
@@ -590,6 +602,7 @@ test_files:
|
|
590
602
|
- test/rbbt/workflow/test_schedule.rb
|
591
603
|
- test/rbbt/workflow/test_step.rb
|
592
604
|
- test/rbbt/workflow/step/test_dependencies.rb
|
605
|
+
- test/rbbt/workflow/step/test_save_load_inputs.rb
|
593
606
|
- test/rbbt/workflow/test_task.rb
|
594
607
|
- test/rbbt/resource/test_path.rb
|
595
608
|
- test/rbbt/util/test_colorize.rb
|
@@ -647,7 +660,11 @@ test_files:
|
|
647
660
|
- test/rbbt/tsv/test_stream.rb
|
648
661
|
- test/rbbt/test_association.rb
|
649
662
|
- test/rbbt/hpc/test_batch.rb
|
663
|
+
- test/rbbt/hpc/orchestrate/test_chains.rb
|
664
|
+
- test/rbbt/hpc/orchestrate/test_rules.rb
|
665
|
+
- test/rbbt/hpc/orchestrate/test_batches.rb
|
650
666
|
- test/rbbt/hpc/test_slurm.rb
|
667
|
+
- test/rbbt/hpc/test_orchestrate.rb
|
651
668
|
- test/rbbt/association/test_database.rb
|
652
669
|
- test/rbbt/association/test_item.rb
|
653
670
|
- test/rbbt/association/test_open.rb
|