rbbt-util 5.44.1 → 6.0.3
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- checksums.yaml +4 -4
- data/bin/rbbt +67 -90
- data/etc/app.d/base.rb +2 -2
- data/etc/app.d/semaphores.rb +3 -3
- data/lib/rbbt/annotations/annotated_array.rb +207 -207
- data/lib/rbbt/annotations/refactor.rb +27 -0
- data/lib/rbbt/annotations/util.rb +282 -282
- data/lib/rbbt/annotations.rb +343 -320
- data/lib/rbbt/association/database.rb +200 -225
- data/lib/rbbt/association/index.rb +294 -291
- data/lib/rbbt/association/item.rb +227 -227
- data/lib/rbbt/association/open.rb +35 -34
- data/lib/rbbt/association/util.rb +0 -169
- data/lib/rbbt/association.rb +2 -4
- data/lib/rbbt/entity/identifiers.rb +119 -118
- data/lib/rbbt/entity/refactor.rb +12 -0
- data/lib/rbbt/entity.rb +319 -315
- data/lib/rbbt/hpc/batch.rb +72 -53
- data/lib/rbbt/hpc/lsf.rb +2 -2
- data/lib/rbbt/hpc/orchestrate/batches.rb +2 -2
- data/lib/rbbt/hpc/orchestrate/chains.rb +25 -5
- data/lib/rbbt/hpc/orchestrate/rules.rb +2 -2
- data/lib/rbbt/hpc/orchestrate.rb +19 -13
- data/lib/rbbt/hpc/slurm.rb +18 -18
- data/lib/rbbt/knowledge_base/entity.rb +13 -5
- data/lib/rbbt/knowledge_base/query.rb +2 -2
- data/lib/rbbt/knowledge_base/registry.rb +32 -31
- data/lib/rbbt/knowledge_base/traverse.rb +1 -1
- data/lib/rbbt/knowledge_base.rb +1 -1
- data/lib/rbbt/monitor.rb +36 -25
- data/lib/rbbt/persist/refactor.rb +166 -0
- data/lib/rbbt/persist/tsv/tokyocabinet.rb +105 -105
- data/lib/rbbt/persist/tsv.rb +187 -185
- data/lib/rbbt/persist.rb +556 -551
- data/lib/rbbt/refactor.rb +20 -0
- data/lib/rbbt/resource/path/refactor.rb +178 -0
- data/lib/rbbt/resource/path.rb +317 -497
- data/lib/rbbt/resource/util.rb +0 -48
- data/lib/rbbt/resource.rb +3 -390
- data/lib/rbbt/tsv/accessor.rb +2 -838
- data/lib/rbbt/tsv/attach.rb +303 -299
- data/lib/rbbt/tsv/change_id.rb +244 -245
- data/lib/rbbt/tsv/csv.rb +87 -85
- data/lib/rbbt/tsv/dumper.rb +2 -100
- data/lib/rbbt/tsv/excel.rb +26 -24
- data/lib/rbbt/tsv/field_index.rb +4 -1
- data/lib/rbbt/tsv/filter.rb +3 -2
- data/lib/rbbt/tsv/index.rb +2 -284
- data/lib/rbbt/tsv/manipulate.rb +750 -747
- data/lib/rbbt/tsv/marshal.rb +3 -3
- data/lib/rbbt/tsv/matrix.rb +2 -2
- data/lib/rbbt/tsv/parallel/through.rb +2 -1
- data/lib/rbbt/tsv/parallel/traverse.rb +783 -781
- data/lib/rbbt/tsv/parser.rb +678 -678
- data/lib/rbbt/tsv/refactor.rb +195 -0
- data/lib/rbbt/tsv/stream.rb +253 -251
- data/lib/rbbt/tsv/util.rb +420 -420
- data/lib/rbbt/tsv.rb +210 -208
- data/lib/rbbt/util/R/eval.rb +4 -4
- data/lib/rbbt/util/R/plot.rb +62 -166
- data/lib/rbbt/util/R.rb +21 -18
- data/lib/rbbt/util/cmd.rb +2 -318
- data/lib/rbbt/util/color.rb +269 -269
- data/lib/rbbt/util/colorize.rb +89 -89
- data/lib/rbbt/util/concurrency/processes/refactor.rb +22 -0
- data/lib/rbbt/util/concurrency/processes/worker.rb +2 -2
- data/lib/rbbt/util/concurrency/processes.rb +389 -386
- data/lib/rbbt/util/config.rb +169 -167
- data/lib/rbbt/util/iruby.rb +20 -0
- data/lib/rbbt/util/log/progress/report.rb +241 -241
- data/lib/rbbt/util/log/progress/util.rb +99 -99
- data/lib/rbbt/util/log/progress.rb +102 -102
- data/lib/rbbt/util/log/refactor.rb +49 -0
- data/lib/rbbt/util/log.rb +486 -532
- data/lib/rbbt/util/migrate.rb +1 -1
- data/lib/rbbt/util/misc/concurrent_stream.rb +248 -246
- data/lib/rbbt/util/misc/development.rb +12 -11
- data/lib/rbbt/util/misc/exceptions.rb +117 -112
- data/lib/rbbt/util/misc/format.rb +2 -230
- data/lib/rbbt/util/misc/indiferent_hash.rb +2 -107
- data/lib/rbbt/util/misc/inspect.rb +2 -476
- data/lib/rbbt/util/misc/lock.rb +109 -106
- data/lib/rbbt/util/misc/omics.rb +9 -1
- data/lib/rbbt/util/misc/pipes.rb +765 -793
- data/lib/rbbt/util/misc/refactor.rb +20 -0
- data/lib/rbbt/util/misc/ssw.rb +27 -17
- data/lib/rbbt/util/misc/system.rb +0 -15
- data/lib/rbbt/util/misc.rb +39 -20
- data/lib/rbbt/util/named_array/refactor.rb +4 -0
- data/lib/rbbt/util/named_array.rb +3 -220
- data/lib/rbbt/util/open/refactor.rb +7 -0
- data/lib/rbbt/util/open.rb +3 -857
- data/lib/rbbt/util/procpath.rb +6 -6
- data/lib/rbbt/util/python/paths.rb +27 -0
- data/lib/rbbt/util/python/run.rb +115 -0
- data/lib/rbbt/util/python/script.rb +110 -0
- data/lib/rbbt/util/python/util.rb +3 -3
- data/lib/rbbt/util/python.rb +22 -81
- data/lib/rbbt/util/semaphore.rb +152 -148
- data/lib/rbbt/util/simpleopt.rb +9 -8
- data/lib/rbbt/util/ssh/refactor.rb +19 -0
- data/lib/rbbt/util/ssh.rb +122 -118
- data/lib/rbbt/util/tar.rb +117 -115
- data/lib/rbbt/util/tmpfile.rb +69 -67
- data/lib/rbbt/util/version.rb +2 -0
- data/lib/rbbt/workflow/refactor/entity.rb +11 -0
- data/lib/rbbt/workflow/refactor/export.rb +66 -0
- data/lib/rbbt/workflow/refactor/inputs.rb +24 -0
- data/lib/rbbt/workflow/refactor/recursive.rb +64 -0
- data/lib/rbbt/workflow/refactor/task_info.rb +65 -0
- data/lib/rbbt/workflow/refactor.rb +153 -0
- data/lib/rbbt/workflow/remote_workflow/driver/ssh.rb +55 -32
- data/lib/rbbt/workflow/remote_workflow/remote_step/rest.rb +3 -1
- data/lib/rbbt/workflow/remote_workflow/remote_step/ssh.rb +14 -5
- data/lib/rbbt/workflow/remote_workflow/remote_step.rb +19 -7
- data/lib/rbbt/workflow/remote_workflow.rb +6 -1
- data/lib/rbbt/workflow/step/run.rb +766 -766
- data/lib/rbbt/workflow/step/save_load_inputs.rb +254 -254
- data/lib/rbbt/workflow/step.rb +2 -362
- data/lib/rbbt/workflow/task.rb +118 -118
- data/lib/rbbt/workflow/usage.rb +289 -287
- data/lib/rbbt/workflow/util/archive.rb +6 -5
- data/lib/rbbt/workflow/util/data.rb +1 -1
- data/lib/rbbt/workflow/util/orchestrator.rb +249 -246
- data/lib/rbbt/workflow/util/trace.rb +79 -44
- data/lib/rbbt/workflow.rb +4 -882
- data/lib/rbbt-util.rb +21 -13
- data/lib/rbbt.rb +16 -3
- data/python/rbbt/__init__.py +19 -1
- data/share/Rlib/plot.R +37 -37
- data/share/Rlib/svg.R +22 -5
- data/share/install/software/lib/install_helpers +1 -1
- data/share/rbbt_commands/hpc/list +2 -3
- data/share/rbbt_commands/hpc/orchestrate +4 -4
- data/share/rbbt_commands/hpc/tail +2 -0
- data/share/rbbt_commands/hpc/task +10 -7
- data/share/rbbt_commands/lsf/list +2 -3
- data/share/rbbt_commands/lsf/orchestrate +4 -4
- data/share/rbbt_commands/lsf/tail +2 -0
- data/share/rbbt_commands/lsf/task +10 -7
- data/share/rbbt_commands/migrate +1 -1
- data/share/rbbt_commands/pbs/list +2 -3
- data/share/rbbt_commands/pbs/orchestrate +4 -4
- data/share/rbbt_commands/pbs/tail +2 -0
- data/share/rbbt_commands/pbs/task +10 -7
- data/share/rbbt_commands/resource/produce +8 -1
- data/share/rbbt_commands/slurm/list +2 -3
- data/share/rbbt_commands/slurm/orchestrate +4 -4
- data/share/rbbt_commands/slurm/tail +2 -0
- data/share/rbbt_commands/slurm/task +10 -7
- data/share/rbbt_commands/system/clean +5 -5
- data/share/rbbt_commands/system/status +5 -5
- data/share/rbbt_commands/tsv/get +2 -3
- data/share/rbbt_commands/tsv/info +10 -13
- data/share/rbbt_commands/tsv/keys +18 -14
- data/share/rbbt_commands/tsv/slice +2 -2
- data/share/rbbt_commands/tsv/transpose +6 -2
- data/share/rbbt_commands/workflow/info +20 -24
- data/share/rbbt_commands/workflow/list +1 -1
- data/share/rbbt_commands/workflow/prov +20 -13
- data/share/rbbt_commands/workflow/server +11 -1
- data/share/rbbt_commands/workflow/task +76 -71
- data/share/rbbt_commands/workflow/write_info +26 -9
- data/share/software/opt/ssw/ssw.c +861 -0
- data/share/software/opt/ssw/ssw.h +130 -0
- data/share/workflow_config.ru +3 -3
- metadata +40 -2
@@ -1,99 +1,99 @@
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module Log
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class ProgressBar
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BAR_MUTEX = Mutex.new
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BARS = []
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REMOVE = []
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SILENCED = []
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def self.add_offset(value = 1)
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value = 1 if TrueClass === value
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@@offset = offset + value.to_i
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@@offset = 0 if @@offset < 0
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@@offset
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end
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def self.remove_offset(value = 1)
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value = 1 if TrueClass === value
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@@offset = offset - value.to_i
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@@offset = 0 if @@offset < 0
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@@offset
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end
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def self.offset
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@@offset ||= 0
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@@offset = 0 if @@offset < 0
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@@offset
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end
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def self.new_bar(max, options = {})
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cleanup_bars
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BAR_MUTEX.synchronize do
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Log::LAST.replace "new_bar" if Log::LAST == "progress"
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options = Misc.add_defaults options, :depth => BARS.length + Log::ProgressBar.offset
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BARS << (bar = ProgressBar.new(max, options))
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bar
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end
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end
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def self.cleanup_bars
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BAR_MUTEX.synchronize do
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REMOVE.each do |bar|
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index = BARS.index bar
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if index
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BARS.delete_at index
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BARS.each_with_index do |bar,i|
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bar.depth = i
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end
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end
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index = SILENCED.index bar
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if index
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SILENCED.delete_at index
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SILENCED.each_with_index do |bar,i|
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bar.depth = i
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end
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end
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end
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REMOVE.clear
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BARS.length
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end
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end
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def self.remove_bar(bar, error = false)
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BAR_MUTEX.synchronize do
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return if REMOVE.include? bar
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end
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if error
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bar.error if bar.respond_to? :error
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else
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bar.done if bar.respond_to? :done
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end
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BAR_MUTEX.synchronize do
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REMOVE << bar
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end
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Log::LAST.replace "remove_bar" if Log::LAST == "progress"
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end
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def remove(error = false)
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Log::ProgressBar.remove_bar self, error
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end
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def self.with_bar(max, options = {})
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bar = new_bar(max, options)
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res = nil
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begin
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error = false
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keep = false
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yield bar
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rescue KeepBar
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keep = true
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rescue
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error = true
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raise $!
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ensure
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remove_bar(bar, error) if bar
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end
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end
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end
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end
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#module Log
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# class ProgressBar
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# BAR_MUTEX = Mutex.new
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# BARS = []
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# REMOVE = []
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# SILENCED = []
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#
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# def self.add_offset(value = 1)
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# value = 1 if TrueClass === value
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# @@offset = offset + value.to_i
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# @@offset = 0 if @@offset < 0
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# @@offset
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# end
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#
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# def self.remove_offset(value = 1)
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# value = 1 if TrueClass === value
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# @@offset = offset - value.to_i
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# @@offset = 0 if @@offset < 0
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# @@offset
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# end
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#
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#
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# def self.offset
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# @@offset ||= 0
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# @@offset = 0 if @@offset < 0
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# @@offset
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# end
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#
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# def self.new_bar(max, options = {})
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# cleanup_bars
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# BAR_MUTEX.synchronize do
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# Log::LAST.replace "new_bar" if Log::LAST == "progress"
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# options = Misc.add_defaults options, :depth => BARS.length + Log::ProgressBar.offset
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# BARS << (bar = ProgressBar.new(max, options))
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# bar
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# end
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# end
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#
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# def self.cleanup_bars
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# BAR_MUTEX.synchronize do
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# REMOVE.each do |bar|
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# index = BARS.index bar
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# if index
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# BARS.delete_at index
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# BARS.each_with_index do |bar,i|
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# bar.depth = i
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# end
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# end
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# index = SILENCED.index bar
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# if index
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# SILENCED.delete_at index
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# SILENCED.each_with_index do |bar,i|
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# bar.depth = i
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# end
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# end
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# end
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# REMOVE.clear
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# BARS.length
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# end
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# end
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#
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# def self.remove_bar(bar, error = false)
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# BAR_MUTEX.synchronize do
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# return if REMOVE.include? bar
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# end
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# if error
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# bar.error if bar.respond_to? :error
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# else
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# bar.done if bar.respond_to? :done
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# end
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# BAR_MUTEX.synchronize do
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# REMOVE << bar
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# end
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# Log::LAST.replace "remove_bar" if Log::LAST == "progress"
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# end
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#
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# def remove(error = false)
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# Log::ProgressBar.remove_bar self, error
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# end
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#
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# def self.with_bar(max, options = {})
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# bar = new_bar(max, options)
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# res = nil
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# begin
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# error = false
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# keep = false
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# yield bar
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# rescue KeepBar
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# keep = true
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# rescue
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# error = true
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# raise $!
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# ensure
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# remove_bar(bar, error) if bar
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# end
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# end
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# end
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#end
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#
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@@ -1,102 +1,102 @@
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require 'rbbt/util/log'
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require 'rbbt/util/log/progress/util'
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require 'rbbt/util/log/progress/report'
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module Log
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def self.no_bar=(value)
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@@no_bar = value
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end
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def self.no_bar
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@@no_bar = false unless defined?(@@no_bar)
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end
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class ProgressBar
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class << self
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attr_accessor :default_file
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end
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attr_accessor :max, :ticks, :frequency, :depth, :desc, :file, :bytes, :process, :callback
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def initialize(max = nil, options = {})
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options = Misc.add_defaults options, :depth => 0, :num_reports => 100, :io => STDERR, :severity => Log.severity, :frequency => 2
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depth, num_reports, desc, io, severity, file, bytes, frequency, process, callback = Misc.process_options options, :depth, :num_reports, :desc, :io, :severity, :file, :bytes, :frequency, :process, :callback
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@max = max
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@ticks = 0
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@frequency = frequency
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@last_time = nil
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@last_count = nil
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@last_percent = nil
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@depth = depth
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@desc = desc.nil? ? "" : desc.gsub(/\n/,' ')
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@file = file
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36
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-
@bytes = bytes
|
37
|
-
@process = process
|
38
|
-
@callback = callback
|
39
|
-
end
|
40
|
-
|
41
|
-
def percent
|
42
|
-
return 0 if @ticks == 0
|
43
|
-
return 100 if @max == 0
|
44
|
-
(@ticks * 100) / @max
|
45
|
-
end
|
46
|
-
|
47
|
-
def file
|
48
|
-
@file || ProgressBar.default_file
|
49
|
-
end
|
50
|
-
|
51
|
-
def init
|
52
|
-
@ticks, @bytes = 0
|
53
|
-
@last_time = @last_count = @last_percent = nil
|
54
|
-
@history, @mean_max, @max_history = nil
|
55
|
-
@start = @last_time = Time.now
|
56
|
-
@last_count = 0
|
57
|
-
report
|
58
|
-
end
|
59
|
-
|
60
|
-
def tick(step = 1)
|
61
|
-
return if Log.no_bar
|
62
|
-
@ticks += step
|
63
|
-
|
64
|
-
time = Time.now
|
65
|
-
if @last_time.nil?
|
66
|
-
@last_time = time
|
67
|
-
@last_count = @ticks
|
68
|
-
@start = time
|
69
|
-
return
|
70
|
-
end
|
71
|
-
|
72
|
-
diff = time - @last_time
|
73
|
-
report and return if diff >= @frequency
|
74
|
-
return unless max and max > 0
|
75
|
-
|
76
|
-
percent = self.percent
|
77
|
-
if @last_percent.nil?
|
78
|
-
@last_percent = percent
|
79
|
-
return
|
80
|
-
end
|
81
|
-
report and return if percent > @last_percent and diff > 0.3
|
82
|
-
end
|
83
|
-
|
84
|
-
def pos(pos)
|
85
|
-
step = pos - (@ticks || 0)
|
86
|
-
tick(step)
|
87
|
-
end
|
88
|
-
|
89
|
-
def process(elem)
|
90
|
-
case res = @process.call(elem)
|
91
|
-
when FalseClass
|
92
|
-
nil
|
93
|
-
when TrueClass
|
94
|
-
tick
|
95
|
-
when Integer
|
96
|
-
pos(res)
|
97
|
-
when Float
|
98
|
-
pos(res * max)
|
99
|
-
end
|
100
|
-
end
|
101
|
-
end
|
102
|
-
end
|
1
|
+
#require 'rbbt/util/log'
|
2
|
+
#require 'rbbt/util/log/progress/util'
|
3
|
+
#require 'rbbt/util/log/progress/report'
|
4
|
+
#module Log
|
5
|
+
#
|
6
|
+
# def self.no_bar=(value)
|
7
|
+
# @@no_bar = value
|
8
|
+
# end
|
9
|
+
#
|
10
|
+
# def self.no_bar
|
11
|
+
# @@no_bar = false unless defined?(@@no_bar)
|
12
|
+
# @@no_bar || ENV["RBBT_NO_PROGRESS"] == "true"
|
13
|
+
# end
|
14
|
+
#
|
15
|
+
# class ProgressBar
|
16
|
+
#
|
17
|
+
# class << self
|
18
|
+
# attr_accessor :default_file
|
19
|
+
# end
|
20
|
+
#
|
21
|
+
# attr_accessor :max, :ticks, :frequency, :depth, :desc, :file, :bytes, :process, :callback
|
22
|
+
#
|
23
|
+
# def initialize(max = nil, options = {})
|
24
|
+
# options = Misc.add_defaults options, :depth => 0, :num_reports => 100, :io => STDERR, :severity => Log.severity, :frequency => 2
|
25
|
+
# depth, num_reports, desc, io, severity, file, bytes, frequency, process, callback = Misc.process_options options, :depth, :num_reports, :desc, :io, :severity, :file, :bytes, :frequency, :process, :callback
|
26
|
+
#
|
27
|
+
# @max = max
|
28
|
+
# @ticks = 0
|
29
|
+
# @frequency = frequency
|
30
|
+
# @last_time = nil
|
31
|
+
# @last_count = nil
|
32
|
+
# @last_percent = nil
|
33
|
+
# @depth = depth
|
34
|
+
# @desc = desc.nil? ? "" : desc.gsub(/\n/,' ')
|
35
|
+
# @file = file
|
36
|
+
# @bytes = bytes
|
37
|
+
# @process = process
|
38
|
+
# @callback = callback
|
39
|
+
# end
|
40
|
+
#
|
41
|
+
# def percent
|
42
|
+
# return 0 if @ticks == 0
|
43
|
+
# return 100 if @max == 0
|
44
|
+
# (@ticks * 100) / @max
|
45
|
+
# end
|
46
|
+
#
|
47
|
+
# def file
|
48
|
+
# @file || ProgressBar.default_file
|
49
|
+
# end
|
50
|
+
#
|
51
|
+
# def init
|
52
|
+
# @ticks, @bytes = 0
|
53
|
+
# @last_time = @last_count = @last_percent = nil
|
54
|
+
# @history, @mean_max, @max_history = nil
|
55
|
+
# @start = @last_time = Time.now
|
56
|
+
# @last_count = 0
|
57
|
+
# report
|
58
|
+
# end
|
59
|
+
#
|
60
|
+
# def tick(step = 1)
|
61
|
+
# return if Log.no_bar
|
62
|
+
# @ticks += step
|
63
|
+
#
|
64
|
+
# time = Time.now
|
65
|
+
# if @last_time.nil?
|
66
|
+
# @last_time = time
|
67
|
+
# @last_count = @ticks
|
68
|
+
# @start = time
|
69
|
+
# return
|
70
|
+
# end
|
71
|
+
#
|
72
|
+
# diff = time - @last_time
|
73
|
+
# report and return if diff >= @frequency
|
74
|
+
# return unless max and max > 0
|
75
|
+
#
|
76
|
+
# percent = self.percent
|
77
|
+
# if @last_percent.nil?
|
78
|
+
# @last_percent = percent
|
79
|
+
# return
|
80
|
+
# end
|
81
|
+
# report and return if percent > @last_percent and diff > 0.3
|
82
|
+
# end
|
83
|
+
#
|
84
|
+
# def pos(pos)
|
85
|
+
# step = pos - (@ticks || 0)
|
86
|
+
# tick(step)
|
87
|
+
# end
|
88
|
+
#
|
89
|
+
# def process(elem)
|
90
|
+
# case res = @process.call(elem)
|
91
|
+
# when FalseClass
|
92
|
+
# nil
|
93
|
+
# when TrueClass
|
94
|
+
# tick
|
95
|
+
# when Integer
|
96
|
+
# pos(res)
|
97
|
+
# when Float
|
98
|
+
# pos(res * max)
|
99
|
+
# end
|
100
|
+
# end
|
101
|
+
# end
|
102
|
+
#end
|
@@ -0,0 +1,49 @@
|
|
1
|
+
module Log
|
2
|
+
|
3
|
+
def self._ignore_stderr
|
4
|
+
begin
|
5
|
+
File.open('/dev/null', 'w') do |f|
|
6
|
+
backup_stderr = STDERR.dup
|
7
|
+
STDERR.reopen(f)
|
8
|
+
begin
|
9
|
+
yield
|
10
|
+
ensure
|
11
|
+
STDERR.reopen backup_stderr
|
12
|
+
backup_stderr.close
|
13
|
+
end
|
14
|
+
end
|
15
|
+
rescue Errno::ENOENT
|
16
|
+
yield
|
17
|
+
end
|
18
|
+
end
|
19
|
+
|
20
|
+
|
21
|
+
def self.ignore_stderr(&block)
|
22
|
+
_ignore_stderr &block
|
23
|
+
end
|
24
|
+
|
25
|
+
def self._ignore_stdout
|
26
|
+
begin
|
27
|
+
File.open('/dev/null', 'w') do |f|
|
28
|
+
backup_stdout = STDOUT.dup
|
29
|
+
STDOUT.reopen(f)
|
30
|
+
begin
|
31
|
+
yield
|
32
|
+
ensure
|
33
|
+
STDOUT.reopen backup_stdout
|
34
|
+
backup_stdout.close
|
35
|
+
end
|
36
|
+
end
|
37
|
+
rescue Errno::ENOENT
|
38
|
+
yield
|
39
|
+
end
|
40
|
+
end
|
41
|
+
|
42
|
+
|
43
|
+
def self.ignore_stdout(&block)
|
44
|
+
_ignore_stdout &block
|
45
|
+
end
|
46
|
+
|
47
|
+
end
|
48
|
+
|
49
|
+
Rbbt.relay_module_method Misc, :fingerprint, Log, :fingerprint
|