rbbt-util 5.21.42 → 5.21.43
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/lib/rbbt/util/R/plot.rb +73 -29
- data/lib/rbbt/workflow/accessor.rb +1 -1
- data/lib/rbbt/workflow/step.rb +5 -1
- metadata +62 -62
checksums.yaml
CHANGED
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---
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SHA1:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 10eea8e63f986c9ce28afb952ca203a7553da870
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data.tar.gz: fb6e78a215cf9763eac45fa1cdaf5dfa6785e7d6
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: ae836057fdbf7f61c5cbfbec7f9138a933193cec13f2f091b956004f84fe8ee119b94958af79b72cb76457fe778851512418f85f74201a46208680083a8e3514
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data.tar.gz: fb166d2973f256978e1e7cc77a611c431a9acd21a4e581acf55de1cd959353724db6a5d414842fd6983ddeac6b743d9c55a42995e833b40af5f287c8af5c8150
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data/lib/rbbt/util/R/plot.rb
CHANGED
@@ -121,49 +121,93 @@ data = NULL
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EOF
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end
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-
def self.plot(filename, data, script = nil, width = nil, height = nil, options = {})
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def self.plot(filename, data = nil, script = nil, width = nil, height = nil, options = {}, &block)
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width ||= 200
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height ||= 200
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values = []
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-
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script ||= ""
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if block_given?
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s = StringIO.new
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class << s
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def method_missing(name, *args)
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name = name.to_s
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if name[-1] == '='
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arg = args.first
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value = if String === arg
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arg
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else
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R.ruby2R arg
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end
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add("" << name[0..-2] << "=" << value)
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else
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args_strs = []
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args.each do |arg|
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value = if String === arg
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arg
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else
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R.ruby2R arg
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end
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args_strs << value
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end
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add("" << name << "(" << args_strs * ", " << ")")
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end
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end
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def add(line)
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self.write line << "\n"
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end
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end
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block.call(s)
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s.rewind
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script << "\n" << s.read
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end
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sources = [:plot, options[:source]].flatten.compact
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if data
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data.each do |k,v|
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v = Array === v ? v : [v]
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next if v == "NA" or v.nil? or v.include? "NA" or v.include? nil
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values = v
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break
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end
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-
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values = [values] unless values.nil? or Array === values
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-
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"'numeric'"
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when String
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if v.strip =~ /^[-+]?[\d\.]+$/
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field_classes = values.collect do |v|
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case v
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when FalseClass, TrueClass
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"'logical'"
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when Fixnum, Float
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"'numeric'"
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when String
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if v.strip =~ /^[-+]?[\d\.]+$/
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"'numeric'"
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else
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"'character'"
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end
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when Symbol
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"'factor'"
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else
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"
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":NA"
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end
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when Symbol
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"'factor'"
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else
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":NA"
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end
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end
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options[:R_open] ||= "colClasses=c('character'," + field_classes * ", " + ')' if field_classes.any?
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-
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png("#{ filename }", #{ width }, #{ height })
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{ #{script} }
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dev.off()
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data = NULL
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-
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data.R <<-EOF, :plot, options
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png("#{ filename }", #{ width }, #{ height })
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{ #{script} }
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dev.off()
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data = NULL
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EOF
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else
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R.run <<-EOF, :plot, options
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png("#{ filename }", #{ width }, #{ height })
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{ #{script} }
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dev.off()
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EOF
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end
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end
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end
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end
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@@ -350,7 +350,7 @@ class Step
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end
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def dirty?
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rec_dependencies.collect{|dependency| dependency.path unless dependency.error? and not dependency.recoverable_error? }.compact.uniq.reject{|path| not Path === path or path.exists?}.any?
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rec_dependencies.collect{|dependency| dependency.path unless dependency.error? and not dependency.recoverable_error? }.compact.uniq.reject{|path| not (Path === path) or path.exists?}.any?
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end
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def done?
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data/lib/rbbt/workflow/step.rb
CHANGED
@@ -221,7 +221,11 @@ class Step
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end
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def clean
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-
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status = " "
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status << "dirty" if dirty?
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status << "not running" if not done? and not running?
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status.strip
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Log.medium "Cleaning step: #{path}#{status}"
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abort if not done? and running?
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Step.clean(path)
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self
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metadata
CHANGED
@@ -1,7 +1,7 @@
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--- !ruby/object:Gem::Specification
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name: rbbt-util
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version: !ruby/object:Gem::Version
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version: 5.21.
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version: 5.21.43
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platform: ruby
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authors:
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- Miguel Vazquez
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@@ -487,82 +487,82 @@ signing_key:
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specification_version: 4
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summary: Utilities for the Ruby Bioinformatics Toolkit (rbbt)
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test_files:
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- test/
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- test/test_helper.rb
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- test/rbbt/resource/test_path.rb
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- test/rbbt/
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- test/rbbt/
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- test/rbbt/
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- test/rbbt/
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- test/rbbt/
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- test/rbbt/util/
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- test/rbbt/association/test_item.rb
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- test/rbbt/association/test_database.rb
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- test/rbbt/association/test_open.rb
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- test/rbbt/association/test_index.rb
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- test/rbbt/association/test_util.rb
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- test/rbbt/util/test_concurrency.rb
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- test/rbbt/util/test_log.rb
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- test/rbbt/util/test_chain_methods.rb
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- test/rbbt/util/test_simpleopt.rb
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- test/rbbt/util/simpleopt/test_parse.rb
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- test/rbbt/util/simpleopt/test_get.rb
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- test/rbbt/util/simpleopt/test_setup.rb
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- test/rbbt/util/test_cmd.rb
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- test/rbbt/util/test_semaphore.rb
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- test/rbbt/util/concurrency/test_threads.rb
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- test/rbbt/util/concurrency/processes/test_socket.rb
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- test/rbbt/util/concurrency/test_processes.rb
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- test/rbbt/util/test_tmpfile.rb
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- test/rbbt/util/test_open.rb
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- test/rbbt/util/test_filecache.rb
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- test/rbbt/util/R/test_eval.rb
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- test/rbbt/util/R/test_model.rb
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- test/rbbt/util/test_simpleDSL.rb
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- test/rbbt/util/log/test_progress.rb
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- test/rbbt/util/test_colorize.rb
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- test/rbbt/util/test_R.rb
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- test/rbbt/util/misc/test_lock.rb
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- test/rbbt/util/misc/test_multipart_payload.rb
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- test/rbbt/util/misc/test_bgzf.rb
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- test/rbbt/util/misc/test_pipes.rb
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- test/rbbt/util/misc/test_bgzf.rb
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- test/rbbt/util/misc/test_omics.rb
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- test/rbbt/util/
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- test/rbbt/util/test_R.rb
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- test/rbbt/util/log/test_progress.rb
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- test/rbbt/util/test_colorize.rb
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- test/rbbt/util/test_simpleopt.rb
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- test/rbbt/util/misc/test_multipart_payload.rb
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- test/rbbt/util/test_excel2tsv.rb
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- test/rbbt/util/test_filecache.rb
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- test/rbbt/util/concurrency/test_processes.rb
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- test/rbbt/util/concurrency/test_threads.rb
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- test/rbbt/util/concurrency/processes/test_socket.rb
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- test/rbbt/util/test_semaphore.rb
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- test/rbbt/util/test_misc.rb
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- test/rbbt/util/test_tmpfile.rb
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- test/rbbt/util/R/test_model.rb
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- test/rbbt/util/R/test_eval.rb
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- test/rbbt/test_packed_index.rb
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- test/rbbt/entity/test_identifiers.rb
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- test/rbbt/test_association.rb
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- test/rbbt/knowledge_base/test_traverse.rb
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- test/rbbt/knowledge_base/test_registry.rb
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- test/rbbt/knowledge_base/test_entity.rb
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- test/rbbt/knowledge_base/test_enrichment.rb
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- test/rbbt/knowledge_base/test_syndicate.rb
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- test/rbbt/knowledge_base/test_query.rb
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- test/rbbt/test_resource.rb
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- test/rbbt/test_entity.rb
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- test/rbbt/test_knowledge_base.rb
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- test/rbbt/annotations/test_util.rb
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- test/rbbt/association/test_index.rb
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- test/rbbt/association/test_item.rb
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- test/rbbt/association/test_open.rb
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- test/rbbt/association/test_util.rb
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- test/rbbt/association/test_database.rb
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- test/rbbt/test_tsv.rb
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- test/rbbt/workflow/step/test_dependencies.rb
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- test/rbbt/workflow/test_task.rb
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- test/rbbt/workflow/test_step.rb
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- test/rbbt/workflow/test_doc.rb
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- test/rbbt/
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- test/rbbt/
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- test/rbbt/
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- test/rbbt/
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- test/rbbt/
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- test/rbbt/
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- test/rbbt/persist/tsv/test_sharder.rb
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- test/rbbt/persist/tsv/test_cdb.rb
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-
- test/rbbt/persist/tsv/test_tokyocabinet.rb
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- test/rbbt/persist/tsv/test_leveldb.rb
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- test/rbbt/tsv/test_field_index.rb
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- test/rbbt/workflow/test_step.rb
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- test/rbbt/workflow/test_task.rb
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- test/rbbt/test_association.rb
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531
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- test/rbbt/test_knowledge_base.rb
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- test/rbbt/tsv/parallel/test_traverse.rb
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- test/rbbt/tsv/parallel/test_through.rb
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- test/rbbt/tsv/test_parallel.rb
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- test/rbbt/tsv/
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- test/rbbt/tsv/test_matrix.rb
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+
- test/rbbt/tsv/test_accessor.rb
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- test/rbbt/tsv/test_change_id.rb
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-
- test/rbbt/tsv/test_parser.rb
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- test/rbbt/tsv/test_stream.rb
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- test/rbbt/tsv/test_util.rb
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- test/rbbt/tsv/test_accessor.rb
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- test/rbbt/tsv/test_filter.rb
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- test/rbbt/tsv/test_matrix.rb
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- test/rbbt/tsv/test_attach.rb
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- test/rbbt/tsv/test_manipulate.rb
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- test/rbbt/tsv/
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- test/rbbt/tsv/
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- test/rbbt/tsv/test_field_index.rb
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- test/rbbt/tsv/test_index.rb
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- test/rbbt/tsv/test_util.rb
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- test/rbbt/tsv/test_parser.rb
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- test/rbbt/test_packed_index.rb
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- test/rbbt/test_persist.rb
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- test/rbbt/test_fix_width_table.rb
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568
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-
- test/
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+
- test/rbbt/knowledge_base/test_traverse.rb
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- test/rbbt/knowledge_base/test_entity.rb
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- test/rbbt/knowledge_base/test_query.rb
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552
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- test/rbbt/knowledge_base/test_enrichment.rb
|
553
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- test/rbbt/knowledge_base/test_syndicate.rb
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554
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- test/rbbt/knowledge_base/test_registry.rb
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- test/rbbt/entity/test_identifiers.rb
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- test/rbbt/test_monitor.rb
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- test/rbbt/test_workflow.rb
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- test/rbbt/test_annotations.rb
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- test/rbbt/annotations/test_util.rb
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- test/rbbt/test_resource.rb
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- test/rbbt/persist/tsv/test_tokyocabinet.rb
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- test/rbbt/persist/tsv/test_kyotocabinet.rb
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- test/rbbt/persist/tsv/test_lmdb.rb
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- test/rbbt/persist/tsv/test_leveldb.rb
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565
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- test/rbbt/persist/tsv/test_cdb.rb
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566
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- test/rbbt/persist/tsv/test_sharder.rb
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567
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- test/rbbt/persist/test_tsv.rb
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568
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- test/rbbt/test_tsv.rb
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