rbbt-util 5.32.24 → 5.32.28

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Files changed (44) hide show
  1. checksums.yaml +4 -4
  2. data/bin/rbbt_find.rb +74 -0
  3. data/lib/rbbt/annotations/annotated_array.rb +4 -0
  4. data/lib/rbbt/annotations/util.rb +29 -0
  5. data/lib/rbbt/entity.rb +3 -1
  6. data/lib/rbbt/hpc/orchestrate/batches.rb +140 -0
  7. data/lib/rbbt/hpc/orchestrate/chains.rb +173 -0
  8. data/lib/rbbt/hpc/orchestrate/rules.rb +70 -0
  9. data/lib/rbbt/hpc/orchestrate.old.rb +220 -0
  10. data/lib/rbbt/hpc/orchestrate.rb +24 -200
  11. data/lib/rbbt/hpc/slurm.rb +1 -0
  12. data/lib/rbbt/persist/tsv.rb +1 -1
  13. data/lib/rbbt/tsv/excel.rb +16 -8
  14. data/lib/rbbt/util/log.rb +6 -2
  15. data/lib/rbbt/util/migrate.rb +6 -1
  16. data/lib/rbbt/util/misc/inspect.rb +4 -1
  17. data/lib/rbbt/util/misc.rb +5 -0
  18. data/lib/rbbt/util/python.rb +1 -1
  19. data/lib/rbbt/workflow/definition.rb +1 -1
  20. data/lib/rbbt/workflow/examples.rb +0 -65
  21. data/lib/rbbt/workflow/integration/nextflow.rb +74 -14
  22. data/lib/rbbt/workflow/step/accessor.rb +0 -70
  23. data/lib/rbbt/workflow/step/dependencies.rb +8 -2
  24. data/lib/rbbt/workflow/step/run.rb +1 -1
  25. data/lib/rbbt/workflow/step/save_load_inputs.rb +162 -0
  26. data/lib/rbbt/workflow/step.rb +2 -1
  27. data/lib/rbbt/workflow/task.rb +2 -2
  28. data/lib/rbbt/workflow.rb +9 -2
  29. data/share/rbbt_commands/hpc/tail +0 -13
  30. data/share/rbbt_commands/lsf/tail +0 -13
  31. data/share/rbbt_commands/slurm/tail +0 -13
  32. data/share/rbbt_commands/tsv/keys +14 -15
  33. data/share/rbbt_commands/tsv/read_excel +2 -2
  34. data/share/rbbt_commands/workflow/task +11 -5
  35. data/test/rbbt/annotations/test_util.rb +11 -0
  36. data/test/rbbt/hpc/orchestrate/test_batches.rb +113 -0
  37. data/test/rbbt/hpc/orchestrate/test_chains.rb +139 -0
  38. data/test/rbbt/hpc/orchestrate/test_rules.rb +92 -0
  39. data/test/rbbt/hpc/test_orchestrate.rb +144 -0
  40. data/test/rbbt/tsv/test_excel.rb +38 -4
  41. data/test/rbbt/util/test_misc.rb +4 -0
  42. data/test/rbbt/workflow/step/test_dependencies.rb +14 -13
  43. data/test/rbbt/workflow/step/test_save_load_inputs.rb +46 -0
  44. metadata +19 -2
metadata CHANGED
@@ -1,14 +1,14 @@
1
1
  --- !ruby/object:Gem::Specification
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2
  name: rbbt-util
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3
  version: !ruby/object:Gem::Version
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- version: 5.32.24
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+ version: 5.32.28
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  platform: ruby
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  authors:
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  - Miguel Vazquez
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  autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2021-11-09 00:00:00.000000000 Z
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+ date: 2022-02-11 00:00:00.000000000 Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: rake
@@ -172,6 +172,7 @@ executables:
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  - rbbt_Rutil.rb
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  - rbbt
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  - rbbt_dangling_locks.rb
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+ - rbbt_find.rb
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  extensions: []
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  extra_rdoc_files:
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  - LICENSE
@@ -183,6 +184,7 @@ files:
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  - bin/rbbt_Rutil.rb
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  - bin/rbbt_dangling_locks.rb
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  - bin/rbbt_exec.rb
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+ - bin/rbbt_find.rb
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  - bin/rbbt_query.rb
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  - etc/app.d/base.rb
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  - etc/app.d/entities.rb
@@ -213,7 +215,11 @@ files:
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  - lib/rbbt/hpc.rb
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  - lib/rbbt/hpc/batch.rb
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  - lib/rbbt/hpc/lsf.rb
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+ - lib/rbbt/hpc/orchestrate.old.rb
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  - lib/rbbt/hpc/orchestrate.rb
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+ - lib/rbbt/hpc/orchestrate/batches.rb
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+ - lib/rbbt/hpc/orchestrate/chains.rb
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+ - lib/rbbt/hpc/orchestrate/rules.rb
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  - lib/rbbt/hpc/slurm.rb
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  - lib/rbbt/knowledge_base.rb
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  - lib/rbbt/knowledge_base/enrichment.rb
@@ -343,6 +349,7 @@ files:
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  - lib/rbbt/workflow/step/info.rb
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  - lib/rbbt/workflow/step/prepare.rb
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  - lib/rbbt/workflow/step/run.rb
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+ - lib/rbbt/workflow/step/save_load_inputs.rb
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  - lib/rbbt/workflow/step/status.rb
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  - lib/rbbt/workflow/task.rb
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  - lib/rbbt/workflow/usage.rb
@@ -468,7 +475,11 @@ files:
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  - test/rbbt/association/test_open.rb
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  - test/rbbt/association/test_util.rb
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  - test/rbbt/entity/test_identifiers.rb
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+ - test/rbbt/hpc/orchestrate/test_batches.rb
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+ - test/rbbt/hpc/orchestrate/test_chains.rb
480
+ - test/rbbt/hpc/orchestrate/test_rules.rb
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  - test/rbbt/hpc/test_batch.rb
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+ - test/rbbt/hpc/test_orchestrate.rb
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  - test/rbbt/hpc/test_slurm.rb
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  - test/rbbt/knowledge_base/test_enrichment.rb
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  - test/rbbt/knowledge_base/test_entity.rb
@@ -548,6 +559,7 @@ files:
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  - test/rbbt/util/test_simpleopt.rb
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  - test/rbbt/util/test_tmpfile.rb
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  - test/rbbt/workflow/step/test_dependencies.rb
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+ - test/rbbt/workflow/step/test_save_load_inputs.rb
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  - test/rbbt/workflow/test_doc.rb
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  - test/rbbt/workflow/test_remote_workflow.rb
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  - test/rbbt/workflow/test_schedule.rb
@@ -590,6 +602,7 @@ test_files:
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  - test/rbbt/workflow/test_schedule.rb
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  - test/rbbt/workflow/test_step.rb
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  - test/rbbt/workflow/step/test_dependencies.rb
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+ - test/rbbt/workflow/step/test_save_load_inputs.rb
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  - test/rbbt/workflow/test_task.rb
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  - test/rbbt/resource/test_path.rb
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  - test/rbbt/util/test_colorize.rb
@@ -647,7 +660,11 @@ test_files:
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  - test/rbbt/tsv/test_stream.rb
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  - test/rbbt/test_association.rb
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  - 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
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  - test/rbbt/hpc/test_slurm.rb
667
+ - test/rbbt/hpc/test_orchestrate.rb
651
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  - test/rbbt/association/test_database.rb
652
669
  - test/rbbt/association/test_item.rb
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670
  - test/rbbt/association/test_open.rb