rbbt-util 5.2.4 → 5.3.0

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Files changed (47) hide show
  1. checksums.yaml +8 -8
  2. data/bin/rbbt +23 -10
  3. data/bin/rbbt_monitor.rb +8 -8
  4. data/lib/rbbt/annotations.rb +22 -1
  5. data/lib/rbbt/annotations/util.rb +1 -1
  6. data/lib/rbbt/entity.rb +162 -0
  7. data/lib/rbbt/fix_width_table.rb +7 -0
  8. data/lib/rbbt/persist.rb +16 -9
  9. data/lib/rbbt/persist/tsv.rb +14 -8
  10. data/lib/rbbt/resource.rb +1 -6
  11. data/lib/rbbt/resource/path.rb +23 -27
  12. data/lib/rbbt/tsv.rb +33 -4
  13. data/lib/rbbt/tsv/accessor.rb +100 -57
  14. data/lib/rbbt/tsv/attach.rb +3 -1
  15. data/lib/rbbt/tsv/attach/util.rb +34 -10
  16. data/lib/rbbt/tsv/index.rb +12 -3
  17. data/lib/rbbt/tsv/manipulate.rb +25 -1
  18. data/lib/rbbt/tsv/parser.rb +1 -0
  19. data/lib/rbbt/util/R.rb +36 -6
  20. data/lib/rbbt/util/cmd.rb +2 -1
  21. data/lib/rbbt/util/color.rb +250 -0
  22. data/lib/rbbt/util/colorize.rb +57 -0
  23. data/lib/rbbt/util/misc.rb +57 -19
  24. data/lib/rbbt/util/named_array.rb +66 -14
  25. data/lib/rbbt/util/open.rb +134 -10
  26. data/lib/rbbt/util/semaphore.rb +71 -0
  27. data/lib/rbbt/workflow.rb +34 -7
  28. data/lib/rbbt/workflow/accessor.rb +12 -8
  29. data/lib/rbbt/workflow/step.rb +44 -28
  30. data/lib/rbbt/workflow/usage.rb +3 -0
  31. data/share/lib/R/util.R +31 -0
  32. data/share/rbbt_commands/app/start +5 -4
  33. data/share/rbbt_commands/study/task +222 -0
  34. data/share/rbbt_commands/tsv/attach +13 -0
  35. data/share/rbbt_commands/tsv/change_id +15 -0
  36. data/share/rbbt_commands/tsv/info +3 -1
  37. data/share/rbbt_commands/workflow/task +14 -15
  38. data/test/rbbt/test_entity.rb +221 -0
  39. data/test/rbbt/test_tsv.rb +2 -1
  40. data/test/rbbt/test_workflow.rb +0 -2
  41. data/test/rbbt/tsv/test_accessor.rb +2 -2
  42. data/test/rbbt/util/test_R.rb +9 -2
  43. data/test/rbbt/util/test_colorize.rb +12 -0
  44. data/test/rbbt/util/test_misc.rb +0 -5
  45. data/test/rbbt/util/test_open.rb +31 -0
  46. data/test/rbbt/workflow/test_step.rb +32 -0
  47. metadata +13 -2
data/test/rbbt/workflow/test_step.rb CHANGED
@@ -178,5 +178,37 @@ class TestStep < Test::Unit::TestCase
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  end
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  end
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+ def test_semaphore
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+ TmpFile.with_file do |semaphore|
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+ begin
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+ semaphore = "/" << semaphore.gsub('/','_')
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+ RbbtSemaphore.create_semaphore(semaphore, 2)
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+
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+ task = Task.setup do
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+ 5.times do
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+ puts "Process: #{Process.pid}"
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+ sleep rand * 2
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+ end
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+ end
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+
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+ jobs = []
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+ 10.times do
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+ TmpFile.with_file do |tmp|
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+ step = Step.new tmp, task
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+ jobs << step.fork(semaphore)
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+ end
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+ end
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+ jobs.each do |job|
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+ while not job.done?
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+ sleep 1
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+ end
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+ end
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+ ensure
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+ RbbtSemaphore.delete_semaphore(semaphore)
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+ end
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+ end
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+
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+ end
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+
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  end
metadata CHANGED
@@ -1,14 +1,14 @@
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  --- !ruby/object:Gem::Specification
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  name: rbbt-util
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  version: !ruby/object:Gem::Version
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- version: 5.2.4
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+ version: 5.3.0
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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: 2013-05-27 00:00:00.000000000 Z
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+ date: 2013-08-01 00:00:00.000000000 Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: rake
@@ -173,6 +173,7 @@ files:
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  - lib/rbbt/annotations.rb
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  - lib/rbbt/annotations/annotated_array.rb
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  - lib/rbbt/annotations/util.rb
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+ - lib/rbbt/entity.rb
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  - lib/rbbt/fix_width_table.rb
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  - lib/rbbt/persist.rb
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  - lib/rbbt/persist/tsv.rb
@@ -195,12 +196,15 @@ files:
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  - lib/rbbt/util/R.rb
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197
  - lib/rbbt/util/chain_methods.rb
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  - lib/rbbt/util/cmd.rb
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+ - lib/rbbt/util/color.rb
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+ - lib/rbbt/util/colorize.rb
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201
  - lib/rbbt/util/excel2tsv.rb
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  - lib/rbbt/util/filecache.rb
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  - lib/rbbt/util/log.rb
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  - lib/rbbt/util/misc.rb
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  - lib/rbbt/util/named_array.rb
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  - lib/rbbt/util/open.rb
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+ - lib/rbbt/util/semaphore.rb
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  - lib/rbbt/util/simpleDSL.rb
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  - lib/rbbt/util/simpleopt.rb
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  - lib/rbbt/util/task/job.rb
@@ -219,6 +223,9 @@ files:
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  - share/rbbt_commands/conf/web_user/add
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  - share/rbbt_commands/conf/web_user/list
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  - share/rbbt_commands/conf/web_user/remove
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+ - share/rbbt_commands/study/task
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+ - share/rbbt_commands/tsv/attach
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+ - share/rbbt_commands/tsv/change_id
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  - share/rbbt_commands/tsv/info
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  - share/rbbt_commands/workflow/remote/add
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  - share/rbbt_commands/workflow/remote/list
@@ -241,11 +248,13 @@ files:
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  - test/rbbt/test_tsv.rb
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  - test/rbbt/test_resource.rb
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  - test/rbbt/test_annotations.rb
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+ - test/rbbt/test_entity.rb
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  - test/rbbt/test_persist.rb
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  - test/rbbt/util/test_filecache.rb
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  - test/rbbt/util/test_tmpfile.rb
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  - test/rbbt/util/test_excel2tsv.rb
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  - test/rbbt/util/test_simpleopt.rb
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+ - test/rbbt/util/test_colorize.rb
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  - test/rbbt/util/test_misc.rb
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  - test/rbbt/util/test_open.rb
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  - test/rbbt/util/test_cmd.rb
@@ -302,11 +311,13 @@ test_files:
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  - test/rbbt/test_tsv.rb
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  - test/rbbt/test_resource.rb
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  - test/rbbt/test_annotations.rb
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+ - test/rbbt/test_entity.rb
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  - test/rbbt/test_persist.rb
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  - test/rbbt/util/test_filecache.rb
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  - test/rbbt/util/test_tmpfile.rb
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  - test/rbbt/util/test_excel2tsv.rb
309
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  - test/rbbt/util/test_simpleopt.rb
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+ - test/rbbt/util/test_colorize.rb
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  - test/rbbt/util/test_misc.rb
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  - test/rbbt/util/test_open.rb
312
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  - test/rbbt/util/test_cmd.rb