scout-gear 10.4.0 → 10.6.1

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Files changed (145) hide show
  1. checksums.yaml +4 -4
  2. data/.vimproject +100 -656
  3. data/Rakefile +1 -0
  4. data/VERSION +1 -1
  5. data/bin/scout +1 -3
  6. data/lib/scout/association/fields.rb +170 -0
  7. data/lib/scout/association/index.rb +229 -0
  8. data/lib/scout/association/item.rb +227 -0
  9. data/lib/scout/association/util.rb +7 -0
  10. data/lib/scout/association.rb +100 -0
  11. data/lib/scout/entity/format.rb +62 -0
  12. data/lib/scout/entity/identifiers.rb +111 -0
  13. data/lib/scout/entity/object.rb +20 -0
  14. data/lib/scout/entity/property.rb +165 -0
  15. data/lib/scout/entity.rb +40 -0
  16. data/lib/scout/offsite/step.rb +2 -2
  17. data/lib/scout/{tsv/persist → persist/engine}/fix_width_table.rb +25 -33
  18. data/lib/scout/persist/engine/packed_index.rb +100 -0
  19. data/lib/scout/persist/engine/sharder.rb +219 -0
  20. data/lib/scout/{tsv/persist → persist/engine}/tkrzw.rb +0 -17
  21. data/lib/scout/{tsv/persist → persist/engine}/tokyocabinet.rb +55 -31
  22. data/lib/scout/persist/engine.rb +4 -0
  23. data/lib/scout/{tsv/persist/adapter.rb → persist/tsv/adapter/base.rb} +80 -51
  24. data/lib/scout/persist/tsv/adapter/fix_width_table.rb +106 -0
  25. data/lib/scout/persist/tsv/adapter/packed_index.rb +95 -0
  26. data/lib/scout/persist/tsv/adapter/sharder.rb +54 -0
  27. data/lib/scout/persist/tsv/adapter/tkrzw.rb +18 -0
  28. data/lib/scout/persist/tsv/adapter/tokyocabinet.rb +65 -0
  29. data/lib/scout/persist/tsv/adapter.rb +6 -0
  30. data/lib/scout/{tsv/persist → persist/tsv}/serialize.rb +5 -0
  31. data/lib/scout/persist/tsv.rb +107 -0
  32. data/lib/scout/tsv/annotation/repo.rb +83 -0
  33. data/lib/scout/tsv/annotation.rb +169 -0
  34. data/lib/scout/tsv/attach.rb +95 -19
  35. data/lib/scout/tsv/change_id/translate.rb +148 -0
  36. data/lib/scout/tsv/change_id.rb +3 -0
  37. data/lib/scout/tsv/csv.rb +85 -0
  38. data/lib/scout/tsv/dumper.rb +113 -25
  39. data/lib/scout/tsv/entity.rb +5 -0
  40. data/lib/scout/tsv/index.rb +88 -36
  41. data/lib/scout/tsv/open.rb +21 -8
  42. data/lib/scout/tsv/parser.rb +153 -90
  43. data/lib/scout/tsv/path.rb +7 -2
  44. data/lib/scout/tsv/stream.rb +48 -6
  45. data/lib/scout/tsv/transformer.rb +4 -3
  46. data/lib/scout/tsv/traverse.rb +26 -18
  47. data/lib/scout/tsv/util/process.rb +7 -0
  48. data/lib/scout/tsv/util/reorder.rb +25 -15
  49. data/lib/scout/tsv/util/select.rb +9 -1
  50. data/lib/scout/tsv/util/sort.rb +90 -2
  51. data/lib/scout/tsv/util/unzip.rb +56 -0
  52. data/lib/scout/tsv/util.rb +52 -5
  53. data/lib/scout/tsv.rb +45 -27
  54. data/lib/scout/work_queue/socket.rb +8 -0
  55. data/lib/scout/work_queue/worker.rb +22 -5
  56. data/lib/scout/work_queue.rb +38 -24
  57. data/lib/scout/workflow/definition.rb +11 -10
  58. data/lib/scout/workflow/deployment/orchestrator.rb +20 -3
  59. data/lib/scout/workflow/deployment/trace.rb +205 -0
  60. data/lib/scout/workflow/deployment.rb +1 -0
  61. data/lib/scout/workflow/documentation.rb +1 -1
  62. data/lib/scout/workflow/step/archive.rb +42 -0
  63. data/lib/scout/workflow/step/children.rb +51 -0
  64. data/lib/scout/workflow/step/config.rb +1 -1
  65. data/lib/scout/workflow/step/dependencies.rb +24 -7
  66. data/lib/scout/workflow/step/file.rb +19 -0
  67. data/lib/scout/workflow/step/info.rb +37 -9
  68. data/lib/scout/workflow/step/progress.rb +11 -2
  69. data/lib/scout/workflow/step/status.rb +8 -1
  70. data/lib/scout/workflow/step.rb +80 -25
  71. data/lib/scout/workflow/task/dependencies.rb +4 -1
  72. data/lib/scout/workflow/task/inputs.rb +91 -41
  73. data/lib/scout/workflow/task.rb +54 -57
  74. data/lib/scout/workflow/usage.rb +1 -1
  75. data/lib/scout/workflow/util.rb +4 -0
  76. data/lib/scout/workflow.rb +110 -13
  77. data/lib/scout-gear.rb +2 -0
  78. data/lib/scout.rb +0 -1
  79. data/scout-gear.gemspec +80 -23
  80. data/scout_commands/rbbt +2 -0
  81. data/test/data/person/brothers +4 -0
  82. data/test/data/person/identifiers +10 -0
  83. data/test/data/person/marriages +3 -0
  84. data/test/data/person/parents +6 -0
  85. data/test/scout/association/test_fields.rb +105 -0
  86. data/test/scout/association/test_index.rb +70 -0
  87. data/test/scout/association/test_item.rb +21 -0
  88. data/test/scout/entity/test_format.rb +19 -0
  89. data/test/scout/entity/test_identifiers.rb +58 -0
  90. data/test/scout/entity/test_object.rb +0 -0
  91. data/test/scout/entity/test_property.rb +345 -0
  92. data/test/scout/{tsv/persist → persist/engine}/test_fix_width_table.rb +0 -1
  93. data/test/scout/persist/engine/test_packed_index.rb +99 -0
  94. data/test/scout/persist/engine/test_sharder.rb +31 -0
  95. data/test/scout/persist/engine/test_tkrzw.rb +0 -0
  96. data/test/scout/persist/engine/test_tokyocabinet.rb +17 -0
  97. data/test/scout/persist/test_tsv.rb +146 -0
  98. data/test/scout/{tsv/persist/test_adapter.rb → persist/tsv/adapter/test_base.rb} +3 -4
  99. data/test/scout/persist/tsv/adapter/test_fix_width_table.rb +46 -0
  100. data/test/scout/persist/tsv/adapter/test_packed_index.rb +37 -0
  101. data/test/scout/persist/tsv/adapter/test_serialize.rb +0 -0
  102. data/test/scout/persist/tsv/adapter/test_sharder.rb +290 -0
  103. data/test/scout/{tsv/persist → persist/tsv/adapter}/test_tkrzw.rb +3 -6
  104. data/test/scout/persist/tsv/adapter/test_tokyocabinet.rb +282 -0
  105. data/test/scout/persist/tsv/test_serialize.rb +12 -0
  106. data/test/scout/test_association.rb +51 -0
  107. data/test/scout/test_entity.rb +40 -0
  108. data/test/scout/test_tsv.rb +33 -4
  109. data/test/scout/test_work_queue.rb +3 -2
  110. data/test/scout/test_workflow.rb +16 -15
  111. data/test/scout/tsv/annotation/test_repo.rb +150 -0
  112. data/test/scout/tsv/change_id/test_translate.rb +178 -0
  113. data/test/scout/tsv/test_annotation.rb +52 -0
  114. data/test/scout/tsv/test_attach.rb +226 -1
  115. data/test/scout/tsv/test_change_id.rb +25 -0
  116. data/test/scout/tsv/test_csv.rb +50 -0
  117. data/test/scout/tsv/test_dumper.rb +38 -0
  118. data/test/scout/tsv/test_entity.rb +0 -0
  119. data/test/scout/tsv/test_index.rb +82 -0
  120. data/test/scout/tsv/test_open.rb +44 -0
  121. data/test/scout/tsv/test_parser.rb +70 -0
  122. data/test/scout/tsv/test_stream.rb +22 -0
  123. data/test/scout/tsv/test_transformer.rb +27 -3
  124. data/test/scout/tsv/test_traverse.rb +78 -0
  125. data/test/scout/tsv/util/test_process.rb +16 -0
  126. data/test/scout/tsv/util/test_reorder.rb +67 -0
  127. data/test/scout/tsv/util/test_sort.rb +28 -1
  128. data/test/scout/tsv/util/test_unzip.rb +32 -0
  129. data/test/scout/work_queue/test_socket.rb +4 -1
  130. data/test/scout/workflow/deployment/test_orchestrator.rb +17 -26
  131. data/test/scout/workflow/deployment/test_trace.rb +25 -0
  132. data/test/scout/workflow/step/test_archive.rb +28 -0
  133. data/test/scout/workflow/step/test_children.rb +25 -0
  134. data/test/scout/workflow/step/test_info.rb +16 -0
  135. data/test/scout/workflow/task/test_dependencies.rb +16 -16
  136. data/test/scout/workflow/task/test_inputs.rb +45 -1
  137. data/test/scout/workflow/test_definition.rb +52 -0
  138. data/test/scout/workflow/test_step.rb +57 -0
  139. data/test/scout/workflow/test_task.rb +26 -1
  140. data/test/scout/workflow/test_usage.rb +4 -4
  141. data/test/test_helper.rb +23 -1
  142. metadata +71 -14
  143. data/lib/scout/tsv/persist.rb +0 -27
  144. data/test/scout/tsv/persist/test_tokyocabinet.rb +0 -120
  145. data/test/scout/tsv/test_persist.rb +0 -45
data/.vimproject CHANGED
@@ -3,38 +3,7 @@ scout-gear=/$PWD filter="*.rb *.yaml" {
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  bin=bin filter="*"{
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  scout
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  }
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- scout_commands=scout_commands filter="*"{
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- rbbt
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- alias
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- find
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- glob
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- log
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- doc
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- update
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- template
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- offsite
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- workflow=workflow{
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- task
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- list
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- info
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- write_info
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- install
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- trace
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- prov
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- }
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- batch=batch{
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- list
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- clean
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- }
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- resource=resource{
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- produce
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- }
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- }
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  lib=lib {
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- scout-gear.rb
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- workflow-scout.rb
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- rbbt-scout.rb
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- scout.rb
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  scout=scout{
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  workflow.rb
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  workflow=workflow{
@@ -51,8 +20,10 @@ scout-gear=/$PWD filter="*.rb *.yaml" {
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  load.rb
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  progress.rb
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  provenance.rb
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+ children.rb
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  status.rb
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  inputs.rb
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+ archive.rb
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  }
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  task.rb
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  task=task{
@@ -61,6 +32,7 @@ scout-gear=/$PWD filter="*.rb *.yaml" {
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  }
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  deployment.rb
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  deployment=deployment{
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+ trace.rb
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  orchestrator.rb
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  }
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  }
@@ -70,36 +42,78 @@ scout-gear=/$PWD filter="*.rb *.yaml" {
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  socket.rb
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  worker.rb
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  }
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+
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+ persist=persist{
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+ engine.rb
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+ engine=engine{
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+ tokyocabinet.rb
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+ fix_width_table.rb
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+ tkrzw.rb
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+ packed_index.rb
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+ sharder.rb
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+ }
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+ tsv.rb
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+ tsv=tsv{
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+ adapter.rb
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+ serialize.rb
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+ adapter=adapter{
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+ base.rb
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+
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+ fix_width_table.rb
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+ packed_index.rb
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+ tkrzw.rb
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+ tokyocabinet.rb
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+ sharder.rb
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+ }
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+ }
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+ }
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+
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  tsv.rb
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  tsv=tsv{
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  util.rb
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  util=util{
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- select.rb
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+ filter.rb
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+ melt.rb
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  process.rb
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- unzip.rb
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  reorder.rb
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+ select.rb
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  sort.rb
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- melt.rb
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+ unzip.rb
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  }
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+ entity.rb
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  parser.rb
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  dumper.rb
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  transformer.rb
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- persist.rb
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- persist=persist{
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- adapter.rb
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- serialize.rb
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- tokyocabinet.rb
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- tkrzw.rb
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- fix_width_table.rb
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- }
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  index.rb
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  traverse.rb
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  attach.rb
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  change_id.rb
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+ change_id=change_id{
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+ translate.rb
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+ }
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+ annotation.rb
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+ annotation=annotation{
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+ repo.rb
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+ }
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  path.rb
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  stream.rb
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  open.rb
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+ csv.rb
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+ }
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+ entity.rb
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+ entity=entity{
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+ property.rb
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+ object.rb
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+ format.rb
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+ identifiers.rb
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  }
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+ association.rb
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+ association=association{
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+ fields.rb
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+ index.rb
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+ item.rb
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+ }
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+
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  offsite.rb
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  offsite=offsite{
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  ssh.rb
@@ -107,28 +121,54 @@ scout-gear=/$PWD filter="*.rb *.yaml" {
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  step.rb
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  }
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  }
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+ scout-gear.rb
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+ workflow-scout.rb
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+ rbbt-scout.rb
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+ scout.rb
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+ }
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+ scout_commands=scout_commands filter="*"{
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+ rbbt
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+ alias
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+ find
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+ glob
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+ log
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+ doc
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+ update
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+ template
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+ offsite
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+ workflow=workflow{
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+ task
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+ list
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+ info
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+ write_info
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+ install
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+ trace
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+ prov
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+ }
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+ batch=batch{
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+ list
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+ clean
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+ }
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+ resource=resource{
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+ produce
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+ }
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  }
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  test=test {
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  test_helper.rb
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  test_scout-gear.rb
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+ test_scout.rb
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+ data=data{
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+ person=person{
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+ }
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+ }
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  scout=scout{
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- test_cmd.rb
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- test_concurrent_stream.rb
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- test_config.rb
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- test_indiferent_hash.rb
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- test_log.rb
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- test_meta_extension.rb
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- test_misc.rb
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- test_named_array.rb
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- test_open.rb
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- test_path.rb
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- test_persist.rb
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- test_resource.rb
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+ test_association.rb
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+ test_entity.rb
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+ test_offsite.rb
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  test_semaphore.rb
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- test_tmpfile.rb
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  test_tsv.rb
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- test_work_queue.rb
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  test_workflow.rb
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+ test_work_queue.rb
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  work_queue=work_queue{
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  test_socket.rb
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  test_worker.rb
@@ -156,9 +196,12 @@ scout-gear=/$PWD filter="*.rb *.yaml" {
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  }
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  }
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  tsv=tsv{
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+ test_annotation.rb
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  test_attach.rb
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  test_change_id.rb
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+ test_csv.rb
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  test_dumper.rb
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+ test_entity.rb
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  test_index.rb
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  test_open.rb
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  test_parser.rb
@@ -179,6 +222,7 @@ scout-gear=/$PWD filter="*.rb *.yaml" {
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  persist=persist{
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  test_adapter.rb
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  test_fix_width_table.rb
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+ test_tkrzw.rb
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  test_tokyocabinet.rb
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  }
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  }
@@ -198,604 +242,4 @@ scout-gear=/$PWD filter="*.rb *.yaml" {
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  workflow.rb
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  }
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  }
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-
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-
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-
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- modules=modules{
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- rbbt-util=rbbt-util filter="*.rb *.rake Rakefile *.rdoc *.R *.sh *.js *.haml *.sass *.txt *.conf LICENSE" {
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- Migration-1.9.txt
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- Troubleshooting.txt
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- ToDo.txt
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- Rakefile
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- LICENSE
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- README.rdoc
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- bin=bin filter="*" {
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- excel2tsv.rb
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- rbbt
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- rbbt_Rutil.rb
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- rbbt_dangling_locks.rb
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- rbbt_exec.rb
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- rbbt_query.rb
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- rbbt_find.rb
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- }
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- lib=lib{
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- rbbt.rb
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-
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- rbbt-util.rb
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-
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- rbbt=rbbt{
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- refactor.rb
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-
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- util=util{
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- misc.rb
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- misc=misc{
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- refactor.rb
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-
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- serialize.rb
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- exceptions.rb
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- concurrent_stream.rb
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- indiferent_hash.rb
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- pipes.rb
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- format.rb
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- omics.rb
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- inspect.rb
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- math.rb
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- development.rb
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- lock.rb
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- options.rb
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- system.rb
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- objects.rb
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- manipulation.rb
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- bgzf.rb
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- multipart_payload.rb
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- annotated_module.rb
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- communication.rb
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- }
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- version.rb
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- tar.rb
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- color.rb
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- colorize.rb
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- named_array.rb
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- cmd.rb
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- docker.rb
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- config.rb
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- log.rb
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- log=log{
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- refactor.rb
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- progress.rb
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- progress=progress{
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- util.rb
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- report.rb
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- }
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- }
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- open.rb
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- semaphore.rb
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-
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- simpleopt.rb
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- simpleopt=simpleopt{
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- accessor.rb
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- doc.rb
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- parse.rb
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- get.rb
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- setup.rb
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- }
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-
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- ssh.rb
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-
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- simpleDSL.rb
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-
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- chain_methods.rb
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-
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- tmpfile.rb
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- tc_cache.rb
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- filecache.rb
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-
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- R.rb
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- R=R{
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- eval.rb
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- model.rb
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- plot.rb
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- }
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-
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- python.rb
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- python=python{
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- util.rb
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- }
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-
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- excel2tsv.rb
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-
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- concurrency.rb
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- concurrency=concurrency{
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- processes.rb
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- threads.rb
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- processes=processes{
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- socket.rb
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- worker.rb
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- }
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- }
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-
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- procpath.rb
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-
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- migrate.rb
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- }
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-
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- monitor.rb
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-
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- workflow.rb
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- workflow=workflow{
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- refactor.rb
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- annotate.rb
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-
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- definition.rb
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- dependencies.rb
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-
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- accessor.rb
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-
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- task.rb
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-
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- step.rb
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- step=step{
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- accessor.rb
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- dependencies.rb
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- info.rb
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- prepare.rb
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- run.rb
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- save_load_inputs.rb
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- status.rb
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- }
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-
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- examples.rb
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- doc.rb
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- usage.rb
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-
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- soap.rb
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-
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- util=util{
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- archive.rb
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- provenance.rb
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- orchestrator.rb
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- trace.rb
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- data.rb
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- }
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-
361
- remote_workflow.rb
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- remote_workflow=remote_workflow{
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- driver.rb
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- driver=driver{
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- rest.rb
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- ssh.rb
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- }
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-
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- remote_step.rb
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- remote_step=remote_step{
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- rest.rb
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- ssh.rb
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- }
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- }
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-
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- integration=integration{
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- cromwell.rb
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- nextflow.rb
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- ansible.rb
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- ansible=ansible{
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- workflow.rb
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- }
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- }
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- }
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-
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- hpc.rb
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- hpc=hpc{
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- old=old{
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- slurm.rb
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- }
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- orchestrate.old.rb
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-
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- batch.rb
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- slurm.rb
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- lsf.rb
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-
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- orchestrate.rb
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- orchestrate=orchestrate{
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- rules.rb
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- chains.rb
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- batches.rb
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- }
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- trace.rb
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- }
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-
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- tsv.rb
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- tsv=tsv{
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- refactor.rb
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- parser.rb
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- dumper.rb
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-
412
- matrix.rb
413
-
414
- accessor.rb
415
- util.rb
416
- marshal.rb
417
- serializers.rb
418
- manipulate.rb
419
- index.rb
420
- stream.rb
421
- attach.rb
422
- attach=attach{
423
- util.rb
424
- }
425
- melt.rb
426
- excel.rb
427
- csv.rb
428
- filter.rb
429
- field_index.rb
430
- change_id.rb
431
- parallel.rb
432
- parallel=parallel{
433
- traverse.rb
434
- through.rb
435
- }
436
- }
437
-
438
- packed_index.rb
439
- fix_width_table.rb
440
-
441
- persist.rb
442
- persist=persist{
443
- refactor.rb
444
- tsv.rb
445
- tsv=tsv{
446
- adapter.rb
447
-
448
- sharder.rb
449
- tokyocabinet.rb
450
- tokyocabinet=tokyocabinet{
451
- marshal.rb
452
- }
453
- fix_width_table.rb
454
- packed_index.rb
455
- kyotocabinet.rb
456
- lmdb.rb
457
- cdb.rb
458
- leveldb.rb
459
- }
460
- }
461
-
462
- resource.rb
463
- resource=resource{
464
- path.rb
465
- path=path{
466
- refactor.rb
467
- }
468
- util.rb
469
- with_key.rb
470
- rake.rb
471
- }
472
-
473
- annotations.rb
474
- annotations=annotations{
475
- util.rb
476
- annotated_array.rb
477
- }
478
-
479
- entity.rb
480
- entity=entity{
481
- identifiers.rb
482
- }
483
-
484
- association.rb
485
- association=association{
486
- util.rb
487
- database.rb
488
- open.rb
489
- index.rb
490
- item.rb
491
- }
492
-
493
- knowledge_base.rb
494
- knowledge_base=knowledge_base{
495
- enrichment.rb
496
- entity.rb
497
- query.rb
498
- registry.rb
499
- syndicate.rb
500
- traverse.rb
501
- }
502
- }
503
- }
504
- test=test {
505
- test_helper.rb
506
- data=data filter="*"{
507
- Test.xls
508
- dose_response
509
- dose_response2
510
- dose_response3
511
- example.pdf
512
- gene_ages
513
- identifiers
514
- test.tsv
515
- }
516
- rbbt=rbbt{
517
- test_annotations.rb
518
- test_association.rb
519
- test_entity.rb
520
- test_fix_width_table.rb
521
- test_knowledge_base.rb
522
- test_monitor.rb
523
- test_packed_index.rb
524
- test_persist.rb
525
- test_resource.rb
526
- test_tsv.rb
527
- test_workflow.rb
528
- resource=resource{
529
- test_path.rb
530
- }
531
- workflow=workflow{
532
- test_soap.rb
533
- test_doc.rb
534
- test_step.rb
535
- test_task.rb
536
- }
537
- association=association{
538
- test_database.rb
539
- test_index.rb
540
- test_item.rb
541
- test_open.rb
542
- test_util.rb
543
- }
544
- knowledge_base=knowledge_base{
545
- test_enrichment.rb
546
- test_query.rb
547
- test_registry.rb
548
- }
549
- persist=persist{
550
- tsv=tsv{
551
- test_cdb.rb
552
- test_kyotocabinet.rb
553
- test_leveldb.rb
554
- test_lmdb.rb
555
- test_sharder.rb
556
- test_tokyocabinet.rb
557
- }
558
- test_tsv.rb
559
- }
560
- tsv=tsv{
561
- test_accessor.rb
562
- test_attach.rb
563
- test_change_id.rb
564
- test_csv.rb
565
- test_excel.rb
566
- test_field_index.rb
567
- test_filter.rb
568
- test_index.rb
569
- test_manipulate.rb
570
- test_marshal.rb
571
- test_matrix.rb
572
- test_parallel.rb
573
- test_parser.rb
574
- test_stream.rb
575
- test_util.rb
576
- parallel=parallel{
577
- test_through.rb
578
- test_traverse.rb
579
- }
580
- }
581
- entity=entity{
582
- test_identifiers.rb
583
- }
584
- util=util{
585
- test_R.rb
586
- test_chain_methods.rb
587
- test_cmd.rb
588
- test_colorize.rb
589
- test_concurrency.rb
590
- test_config.rb
591
- test_excel2tsv.rb
592
- test_filecache.rb
593
- test_log.rb
594
- test_misc.rb
595
- test_open.rb
596
- test_python.rb
597
- test_semaphore.rb
598
- test_simpleDSL.rb
599
- test_simpleopt.rb
600
- test_tmpfile.rb
601
- R=R{
602
- test_eval.rb
603
- test_model.rb
604
- test_plot.rb
605
- }
606
- misc=misc{
607
- test_bgzf.rb
608
- test_format.rb
609
- test_lock.rb
610
- test_multipart_payload.rb
611
- test_omics.rb
612
- test_pipes.rb
613
- }
614
- simpleopt=simpleopt{
615
- test_get.rb
616
- test_parse.rb
617
- test_setup.rb
618
- }
619
- concurrency=concurrency{
620
- test_processes.rb
621
- test_threads.rb
622
- }
623
- }
624
- }
625
- }
626
- python=python filter="*"{
627
- rbbt.py
628
- }
629
- integration_test=integration_test{
630
- test_bed.rb
631
- test_helper.rb
632
- test_namespaces.rb
633
- test_workflow.rb
634
- }
635
- etc=etc filter="*"{
636
- app.d=app.d{
637
- init.rb
638
-
639
- base.rb
640
-
641
- requires.rb
642
- entities.rb
643
- finder.rb
644
- foundation.rb
645
- grid_system.rb
646
- knowledge_bases.rb
647
- resources.rb
648
- workflows.rb
649
- semaphores.rb
650
- remote_workflow_tasks.rb
651
- }
652
- }
653
- share=share{
654
- config.ru
655
- workflow_config.ru
656
- unicorn.rb
657
- color=color filter="*"{
658
- diverging_colors.hex
659
- color_names
660
- }
661
- rbbt_commands=rbbt_commands filter="*"{
662
- alias
663
- ansible
664
- check_bgzf
665
- cmd
666
- color
667
- log
668
- migrate
669
- migrate_job
670
- purge_job
671
- rsync
672
- watch
673
- system=system{
674
- clean
675
- deleted_files
676
- optimize
677
- purge
678
- report
679
- status
680
- }
681
- conf=conf{
682
- web_user=web_user{
683
- add
684
- list
685
- remove
686
- }
687
- }
688
- resource=resource{
689
- exists
690
- find
691
- glob
692
- get
693
- produce
694
- read
695
- }
696
- workflow=workflow{
697
- archive
698
- archive_all
699
- cmd
700
- example
701
- forget_deps
702
- info
703
- write_info
704
- init
705
- install
706
- jobs
707
- knowledge_base
708
- list
709
- monitor
710
- prov
711
- server
712
- task
713
- trace
714
- remote=remote{
715
- add
716
- list
717
- remove
718
- }
719
- }
720
- hpc=hpc{
721
- task
722
- orchestrate
723
- tail
724
- list
725
- clean
726
- }
727
- app=app{
728
- install
729
- start
730
- template
731
- }
732
- association=association{
733
- subset
734
- }
735
- tsv=tsv{
736
- assemble_pdf_table
737
- attach
738
- change_id
739
- collapse
740
- get
741
- head
742
- info
743
- json
744
- keys
745
- query
746
- read
747
- read_excel
748
- slice
749
- sort
750
- subset
751
- select
752
- transpose
753
- uncollapse
754
- unzip
755
- values
756
- write_excel
757
- zip
758
- view
759
- }
760
- stat=stat{
761
- abs
762
- boxplot
763
- compare_lists
764
- density
765
- heatmap
766
- log
767
- pvalue.qqplot
768
- }
769
- study=study{
770
- maf2study
771
- task
772
- }
773
- file_server=file_server{
774
- add
775
- list
776
- remove
777
- }
778
- benchmark=benchmark{
779
- pthrough
780
- throughput
781
- tsv
782
- }
783
- }
784
- Rlib=Rlib{
785
- plot.R
786
- svg.R
787
- util.R
788
- }
789
- software=install/software filter="*"{
790
- zran=zran{
791
- zran.c
792
- }
793
- lib=lib{
794
- install_helpers
795
- }
796
- }
797
- }
798
- }
799
-
800
- }
801
245
  }