rbbt-util 5.44.0 → 6.0.3
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- checksums.yaml +4 -4
- data/bin/rbbt +67 -90
- data/etc/app.d/base.rb +3 -3
- 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/sharder.rb +1 -1
- 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 +10 -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 +308 -0
- 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/info.rb +2 -2
- 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 +16 -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 +42 -3
data/lib/rbbt/util/colorize.rb
CHANGED
@@ -1,89 +1,89 @@
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require 'rbbt/util/color'
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module Colorize
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def self.from_name(color)
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return color if color =~ /^#?[0-9A-F]+$/i
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colors = Rbbt.share.color.color_names.tsv :type => :single
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case color.to_s
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when "white"
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'#000'
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when "black"
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'#fff'
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when 'green'
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colors["green3"]
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when 'red'
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colors["red3"]
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when 'yellow'
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colors["gold1"]
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when 'blue'
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colors["RoyalBlue"]
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else
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colors[color.to_s] || color
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end
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end
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def self.continuous(array, start = "#40324F", eend = "#EABD5D", percent = false)
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start_color = Color.new from_name(start)
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end_color = Color.new from_name(eend)
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if percent
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array = array.collect{|v| n = v.to_f; n = n > 100 ? 100 : n; n < 0.001 ? 0.001 : n}
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else
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array = array.collect{|v| n = v.to_f; }
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end
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max = array.max
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min = array.min
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range = max - min
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array.collect do |v|
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ratio = (v.to_f-min) / range
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start_color.blend end_color, ratio
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end
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end
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def self.gradient(array, value, start = :green, eend = :red, percent = false)
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index = array.index value
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colors = continuous(array, start, eend, percent)
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colors[index]
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end
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def self.rank_gradient(array, value, start = :green, eend = :red, percent = false)
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index = array.index value
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sorted = array.sort
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array = array.collect{|e| sorted.index e}
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colors = continuous(array, start, eend, percent)
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colors[index]
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end
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def self.distinct(array)
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colors = Rbbt.share.color["diverging_colors.hex"].list.collect{|c| Color.new c}
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num = array.uniq.length
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times = num / 12
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all_colors = colors.dup
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factor = 0.3 / times
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times.times do
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all_colors.concat colors.collect{|n| n.darken(factor) }
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end
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value_color = Hash[*array.uniq.zip(all_colors).flatten]
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value_color.values_at *array
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end
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def self.tsv(tsv, options = {})
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values = tsv.values.flatten
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if Numeric === values.first or (values.first.to_f != 0 and values[0] != "0" and values[0] != "0.0")
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value_colors = Misc.process_to_hash(values){continuous(values)}
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else
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value_colors = Misc.process_to_hash(values){distinct(values)}
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end
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if tsv.type == :single
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Hash[*tsv.keys.zip(value_colors.values_at(*values)).flatten]
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else
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Hash[*tsv.keys.zip(values.collect{|vs| value_colors.values_at(*vs)}).flatten]
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end
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end
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end
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#require 'rbbt/util/color'
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#
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#module Colorize
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# def self.from_name(color)
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# return color if color =~ /^#?[0-9A-F]+$/i
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# colors = Rbbt.share.color.color_names.tsv :type => :single
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# case color.to_s
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# when "white"
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# '#000'
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# when "black"
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# '#fff'
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# when 'green'
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# colors["green3"]
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# when 'red'
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# colors["red3"]
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# when 'yellow'
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# colors["gold1"]
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# when 'blue'
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# colors["RoyalBlue"]
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# else
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# colors[color.to_s] || color
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# end
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# end
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#
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# def self.continuous(array, start = "#40324F", eend = "#EABD5D", percent = false)
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# start_color = Color.new from_name(start)
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# end_color = Color.new from_name(eend)
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#
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# if percent
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# array = array.collect{|v| n = v.to_f; n = n > 100 ? 100 : n; n < 0.001 ? 0.001 : n}
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# else
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# array = array.collect{|v| n = v.to_f; }
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# end
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# max = array.max
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# min = array.min
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# range = max - min
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# array.collect do |v|
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# ratio = (v.to_f-min) / range
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# start_color.blend end_color, ratio
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# end
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# end
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#
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# def self.gradient(array, value, start = :green, eend = :red, percent = false)
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# index = array.index value
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# colors = continuous(array, start, eend, percent)
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# colors[index]
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# end
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#
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# def self.rank_gradient(array, value, start = :green, eend = :red, percent = false)
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# index = array.index value
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# sorted = array.sort
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# array = array.collect{|e| sorted.index e}
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# colors = continuous(array, start, eend, percent)
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# colors[index]
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# end
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#
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#
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# def self.distinct(array)
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# colors = Rbbt.share.color["diverging_colors.hex"].list.collect{|c| Color.new c}
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#
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# num = array.uniq.length
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# times = num / 12
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#
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# all_colors = colors.dup
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# factor = 0.3 / times
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# times.times do
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# all_colors.concat colors.collect{|n| n.darken(factor) }
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# end
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#
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# value_color = Hash[*array.uniq.zip(all_colors).flatten]
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#
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# value_color.values_at *array
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# end
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#
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# def self.tsv(tsv, options = {})
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# values = tsv.values.flatten
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# if Numeric === values.first or (values.first.to_f != 0 and values[0] != "0" and values[0] != "0.0")
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# value_colors = Misc.process_to_hash(values){continuous(values)}
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# else
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# value_colors = Misc.process_to_hash(values){distinct(values)}
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# end
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#
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# if tsv.type == :single
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# Hash[*tsv.keys.zip(value_colors.values_at(*values)).flatten]
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# else
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# Hash[*tsv.keys.zip(values.collect{|vs| value_colors.values_at(*vs)}).flatten]
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# end
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# end
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#end
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@@ -0,0 +1,22 @@
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require 'scout/work_queue'
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class RbbtProcessQueue < WorkQueue
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self.define_method(:start_process, WorkQueue.instance_method(:process))
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def init(&block)
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@worker_proc = block
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start_process(&@callback)
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end
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def callback(&block)
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@callback = block
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end
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def process(obj)
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self.write(obj)
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end
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alias add_process add_worker
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alias remove_process remove_one_worker
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alias remove_process remove_one_worker
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end
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@@ -199,10 +199,10 @@ class RbbtProcessQueue
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@queue.close_write
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if @callback_queue
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Open.purge_pipes(@callback_queue.swrite)
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@callback_queue.close_read
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else
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Open.purge_pipes
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end
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if respawn
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