rbbt-util 5.44.0 → 6.0.3

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Files changed (169) hide show
  1. checksums.yaml +4 -4
  2. data/bin/rbbt +67 -90
  3. data/etc/app.d/base.rb +3 -3
  4. data/etc/app.d/semaphores.rb +3 -3
  5. data/lib/rbbt/annotations/annotated_array.rb +207 -207
  6. data/lib/rbbt/annotations/refactor.rb +27 -0
  7. data/lib/rbbt/annotations/util.rb +282 -282
  8. data/lib/rbbt/annotations.rb +343 -320
  9. data/lib/rbbt/association/database.rb +200 -225
  10. data/lib/rbbt/association/index.rb +294 -291
  11. data/lib/rbbt/association/item.rb +227 -227
  12. data/lib/rbbt/association/open.rb +35 -34
  13. data/lib/rbbt/association/util.rb +0 -169
  14. data/lib/rbbt/association.rb +2 -4
  15. data/lib/rbbt/entity/identifiers.rb +119 -118
  16. data/lib/rbbt/entity/refactor.rb +12 -0
  17. data/lib/rbbt/entity.rb +319 -315
  18. data/lib/rbbt/hpc/batch.rb +72 -53
  19. data/lib/rbbt/hpc/lsf.rb +2 -2
  20. data/lib/rbbt/hpc/orchestrate/batches.rb +2 -2
  21. data/lib/rbbt/hpc/orchestrate/chains.rb +25 -5
  22. data/lib/rbbt/hpc/orchestrate/rules.rb +2 -2
  23. data/lib/rbbt/hpc/orchestrate.rb +19 -13
  24. data/lib/rbbt/hpc/slurm.rb +18 -18
  25. data/lib/rbbt/knowledge_base/entity.rb +13 -5
  26. data/lib/rbbt/knowledge_base/query.rb +2 -2
  27. data/lib/rbbt/knowledge_base/registry.rb +32 -31
  28. data/lib/rbbt/knowledge_base/traverse.rb +1 -1
  29. data/lib/rbbt/knowledge_base.rb +1 -1
  30. data/lib/rbbt/monitor.rb +36 -25
  31. data/lib/rbbt/persist/refactor.rb +166 -0
  32. data/lib/rbbt/persist/tsv/sharder.rb +1 -1
  33. data/lib/rbbt/persist/tsv/tokyocabinet.rb +105 -105
  34. data/lib/rbbt/persist/tsv.rb +187 -185
  35. data/lib/rbbt/persist.rb +556 -551
  36. data/lib/rbbt/refactor.rb +20 -0
  37. data/lib/rbbt/resource/path/refactor.rb +178 -0
  38. data/lib/rbbt/resource/path.rb +317 -497
  39. data/lib/rbbt/resource/util.rb +0 -48
  40. data/lib/rbbt/resource.rb +3 -390
  41. data/lib/rbbt/tsv/accessor.rb +2 -838
  42. data/lib/rbbt/tsv/attach.rb +303 -299
  43. data/lib/rbbt/tsv/change_id.rb +244 -245
  44. data/lib/rbbt/tsv/csv.rb +87 -85
  45. data/lib/rbbt/tsv/dumper.rb +2 -100
  46. data/lib/rbbt/tsv/excel.rb +26 -24
  47. data/lib/rbbt/tsv/field_index.rb +4 -1
  48. data/lib/rbbt/tsv/filter.rb +3 -2
  49. data/lib/rbbt/tsv/index.rb +2 -284
  50. data/lib/rbbt/tsv/manipulate.rb +750 -747
  51. data/lib/rbbt/tsv/marshal.rb +3 -3
  52. data/lib/rbbt/tsv/matrix.rb +2 -2
  53. data/lib/rbbt/tsv/parallel/through.rb +2 -1
  54. data/lib/rbbt/tsv/parallel/traverse.rb +783 -781
  55. data/lib/rbbt/tsv/parser.rb +678 -678
  56. data/lib/rbbt/tsv/refactor.rb +195 -0
  57. data/lib/rbbt/tsv/stream.rb +253 -251
  58. data/lib/rbbt/tsv/util.rb +420 -420
  59. data/lib/rbbt/tsv.rb +210 -208
  60. data/lib/rbbt/util/R/eval.rb +4 -4
  61. data/lib/rbbt/util/R/plot.rb +62 -166
  62. data/lib/rbbt/util/R.rb +21 -18
  63. data/lib/rbbt/util/cmd.rb +2 -318
  64. data/lib/rbbt/util/color.rb +269 -269
  65. data/lib/rbbt/util/colorize.rb +89 -89
  66. data/lib/rbbt/util/concurrency/processes/refactor.rb +22 -0
  67. data/lib/rbbt/util/concurrency/processes/worker.rb +2 -2
  68. data/lib/rbbt/util/concurrency/processes.rb +389 -386
  69. data/lib/rbbt/util/config.rb +169 -167
  70. data/lib/rbbt/util/iruby.rb +20 -0
  71. data/lib/rbbt/util/log/progress/report.rb +241 -241
  72. data/lib/rbbt/util/log/progress/util.rb +99 -99
  73. data/lib/rbbt/util/log/progress.rb +102 -102
  74. data/lib/rbbt/util/log/refactor.rb +49 -0
  75. data/lib/rbbt/util/log.rb +486 -532
  76. data/lib/rbbt/util/migrate.rb +1 -1
  77. data/lib/rbbt/util/misc/concurrent_stream.rb +248 -246
  78. data/lib/rbbt/util/misc/development.rb +12 -11
  79. data/lib/rbbt/util/misc/exceptions.rb +117 -112
  80. data/lib/rbbt/util/misc/format.rb +2 -230
  81. data/lib/rbbt/util/misc/indiferent_hash.rb +2 -107
  82. data/lib/rbbt/util/misc/inspect.rb +2 -476
  83. data/lib/rbbt/util/misc/lock.rb +109 -106
  84. data/lib/rbbt/util/misc/omics.rb +10 -1
  85. data/lib/rbbt/util/misc/pipes.rb +765 -793
  86. data/lib/rbbt/util/misc/refactor.rb +20 -0
  87. data/lib/rbbt/util/misc/ssw.rb +308 -0
  88. data/lib/rbbt/util/misc/system.rb +0 -15
  89. data/lib/rbbt/util/misc.rb +39 -20
  90. data/lib/rbbt/util/named_array/refactor.rb +4 -0
  91. data/lib/rbbt/util/named_array.rb +3 -220
  92. data/lib/rbbt/util/open/refactor.rb +7 -0
  93. data/lib/rbbt/util/open.rb +3 -857
  94. data/lib/rbbt/util/procpath.rb +6 -6
  95. data/lib/rbbt/util/python/paths.rb +27 -0
  96. data/lib/rbbt/util/python/run.rb +115 -0
  97. data/lib/rbbt/util/python/script.rb +110 -0
  98. data/lib/rbbt/util/python/util.rb +3 -3
  99. data/lib/rbbt/util/python.rb +22 -81
  100. data/lib/rbbt/util/semaphore.rb +152 -148
  101. data/lib/rbbt/util/simpleopt.rb +9 -8
  102. data/lib/rbbt/util/ssh/refactor.rb +19 -0
  103. data/lib/rbbt/util/ssh.rb +122 -118
  104. data/lib/rbbt/util/tar.rb +117 -115
  105. data/lib/rbbt/util/tmpfile.rb +69 -67
  106. data/lib/rbbt/util/version.rb +2 -0
  107. data/lib/rbbt/workflow/refactor/entity.rb +11 -0
  108. data/lib/rbbt/workflow/refactor/export.rb +66 -0
  109. data/lib/rbbt/workflow/refactor/inputs.rb +24 -0
  110. data/lib/rbbt/workflow/refactor/recursive.rb +64 -0
  111. data/lib/rbbt/workflow/refactor/task_info.rb +65 -0
  112. data/lib/rbbt/workflow/refactor.rb +153 -0
  113. data/lib/rbbt/workflow/remote_workflow/driver/ssh.rb +55 -32
  114. data/lib/rbbt/workflow/remote_workflow/remote_step/rest.rb +3 -1
  115. data/lib/rbbt/workflow/remote_workflow/remote_step/ssh.rb +14 -5
  116. data/lib/rbbt/workflow/remote_workflow/remote_step.rb +19 -7
  117. data/lib/rbbt/workflow/remote_workflow.rb +6 -1
  118. data/lib/rbbt/workflow/step/info.rb +2 -2
  119. data/lib/rbbt/workflow/step/run.rb +766 -766
  120. data/lib/rbbt/workflow/step/save_load_inputs.rb +254 -254
  121. data/lib/rbbt/workflow/step.rb +2 -362
  122. data/lib/rbbt/workflow/task.rb +118 -118
  123. data/lib/rbbt/workflow/usage.rb +289 -287
  124. data/lib/rbbt/workflow/util/archive.rb +6 -5
  125. data/lib/rbbt/workflow/util/data.rb +1 -1
  126. data/lib/rbbt/workflow/util/orchestrator.rb +249 -246
  127. data/lib/rbbt/workflow/util/trace.rb +79 -44
  128. data/lib/rbbt/workflow.rb +4 -882
  129. data/lib/rbbt-util.rb +21 -13
  130. data/lib/rbbt.rb +16 -3
  131. data/python/rbbt/__init__.py +19 -1
  132. data/share/Rlib/plot.R +37 -37
  133. data/share/Rlib/svg.R +22 -5
  134. data/share/install/software/lib/install_helpers +1 -1
  135. data/share/rbbt_commands/hpc/list +2 -3
  136. data/share/rbbt_commands/hpc/orchestrate +4 -4
  137. data/share/rbbt_commands/hpc/tail +2 -0
  138. data/share/rbbt_commands/hpc/task +10 -7
  139. data/share/rbbt_commands/lsf/list +2 -3
  140. data/share/rbbt_commands/lsf/orchestrate +4 -4
  141. data/share/rbbt_commands/lsf/tail +2 -0
  142. data/share/rbbt_commands/lsf/task +10 -7
  143. data/share/rbbt_commands/migrate +1 -1
  144. data/share/rbbt_commands/pbs/list +2 -3
  145. data/share/rbbt_commands/pbs/orchestrate +4 -4
  146. data/share/rbbt_commands/pbs/tail +2 -0
  147. data/share/rbbt_commands/pbs/task +10 -7
  148. data/share/rbbt_commands/resource/produce +8 -1
  149. data/share/rbbt_commands/slurm/list +2 -3
  150. data/share/rbbt_commands/slurm/orchestrate +4 -4
  151. data/share/rbbt_commands/slurm/tail +2 -0
  152. data/share/rbbt_commands/slurm/task +10 -7
  153. data/share/rbbt_commands/system/clean +5 -5
  154. data/share/rbbt_commands/system/status +5 -5
  155. data/share/rbbt_commands/tsv/get +2 -3
  156. data/share/rbbt_commands/tsv/info +10 -13
  157. data/share/rbbt_commands/tsv/keys +18 -14
  158. data/share/rbbt_commands/tsv/slice +2 -2
  159. data/share/rbbt_commands/tsv/transpose +6 -2
  160. data/share/rbbt_commands/workflow/info +20 -24
  161. data/share/rbbt_commands/workflow/list +1 -1
  162. data/share/rbbt_commands/workflow/prov +20 -13
  163. data/share/rbbt_commands/workflow/server +16 -1
  164. data/share/rbbt_commands/workflow/task +76 -71
  165. data/share/rbbt_commands/workflow/write_info +26 -9
  166. data/share/software/opt/ssw/ssw.c +861 -0
  167. data/share/software/opt/ssw/ssw.h +130 -0
  168. data/share/workflow_config.ru +3 -3
  169. metadata +42 -3
data/lib/rbbt/tsv/marshal.rb CHANGED
@@ -3,15 +3,15 @@ module TSV
3
3
  if defined?(Persist::TCAdapter) && Persist::TCAdapter === self
4
4
  super
5
5
  else
6
- [info, to_hash]
6
+ [options, Annotation.purge(self)]
7
7
  end
8
8
  end
9
9
  end
10
10
 
11
11
  class Hash
12
12
  def marshal_load(array)
13
- info, to_hash = array
13
+ options, to_hash = array
14
14
  self.merge! to_hash
15
- TSV.setup(self)
15
+ TSV.setup(self, options)
16
16
  end
17
17
  end
data/lib/rbbt/tsv/matrix.rb CHANGED
@@ -1,5 +1,3 @@
1
- require 'rbbt/association'
2
-
3
1
  module TSV
4
2
  def self.read_matrix(tsv, field_format = "ID", value_format = "Value", *others)
5
3
  tsv = TSV.open(tsv) unless TSV === tsv
@@ -32,6 +30,8 @@ module TSV
32
30
  end
33
31
 
34
32
  def matrix_melt(*args)
33
+ require 'rbbt/association'
34
+
35
35
  tsv = TSV.read_matrix(self, *args)
36
36
 
37
37
  melt = Association.index tsv, :persist => false, :recycle => true
data/lib/rbbt/tsv/parallel/through.rb CHANGED
@@ -1,3 +1,4 @@
1
+ require 'scout/tsv'
1
2
  module TSV
2
3
 
3
4
  def pthrough(num_threads = 10, new_key_field = nil, new_fields = nil, uniq = false, zipped = false, &block)
@@ -6,7 +7,7 @@ module TSV
6
7
  q.init(true, &block)
7
8
 
8
9
  begin
9
- res = through(new_key_field, new_fields, uniq, zipped) do |*p|
10
+ res = through(new_key_field, new_fields, one2one: zipped) do |*p|
10
11
  q.process p
11
12
  end
12
13
  q.join