rbbt-util 5.8.4 → 5.8.6

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 4c797873ae505de56e3946d6effdb0cabd417c6a
-  data.tar.gz: f191e7f6bd071f97dd3147d0b7c5b672a708c69d
+  metadata.gz: aea518df37bf55a5cb14bb009dc3c3125807563d
+  data.tar.gz: 3d532e26ea01b630418ab2e004c3d6a516c97643
 SHA512:
-  metadata.gz: da7d7f21f11c5564514be72b81734958f0a46b742f40a50252f62442dd4089a96c41da2b0d714c8d135d3851699d519c1f4b95fd3a2830dd89d452453cc4ca2e
-  data.tar.gz: e38d5a7d439fda5310a8db460337414e808762a5996fbc7f6413da71c7506b57d91f5b4d6fab28d2f774652614848a20d4016a8476f58f72d5e91e648d66d90b
+  metadata.gz: 1959de32e8e47f670369dfc897986b4c0dd47f2be68239e23c9d09e35beb71cf68cf578ffd9bc47c3ad1f81f040097a1d333108c6ad32404cc045df8128cfca7
+  data.tar.gz: faedb2e24d5dc400f57802a1fb2c377f421d1b8e42c820bc8e117e5e7d361787ac0e5a5948f086ac1654ff42c55e782d4d766c2779cd1e50a7105850f4000505

data/lib/rbbt/util/log.rb

@@ -27,6 +27,10 @@ module Log
   SEVERITY_COLOR = [reset, cyan, green, magenta, blue, yellow, red] #.collect{|e| "\033[#{e}"}
   HIGHLIGHT = "\033[1m"
 
+  def self.uncolor(str)
+    Term::ANSIColor.uncolor(str)
+  end
+
   def self.color(severity, str = nil)
     return str || "" if nocolor 
     color = SEVERITY_COLOR[severity] if Fixnum === severity

data/lib/rbbt/util/misc.rb

@@ -31,6 +31,48 @@ end
 Lockfile.refresh = false if ENV["RBBT_NO_LOCKFILE_REFRESH"] == "true"
 module Misc
 
+  def self.format_paragraph(text, size = 80, indent = 0, offset = 0)
+    words = text.gsub(/\s+/, "\s").split(" ")
+    lines = []
+    line = " "*offset
+    word = words.shift
+    while word
+      while word and line.length + word.length < size
+        line << word << " "
+        word = words.shift
+      end
+      lines << ((" " * indent) << line[0..-2])
+      line = ""
+    end
+    (lines * "\n")
+  end
+
+  def self.format_definition_list_item(dt, dd, size = 80, indent = 20, color = :yellow)
+    dt = dt.to_s + ":" unless dd.empty?
+    dt = Log.color color, dt if color
+    len = Log.uncolor(dt).length
+
+    if indent < 0
+      text = format_paragraph(dd, size, indent.abs+1, 0)
+      text = dt << "\n" << text
+    else
+      offset = len - indent
+      offset = 0 if offset < 0
+      text = format_paragraph(dd, size, indent.abs+1, offset)
+      text[0..len-1] = dt
+    end
+    text
+  end
+
+  def self.format_definition_list(defs, size = 80, indent = 20, color = :yellow)
+    entries = []
+    defs.each do |dt,dd|
+      text = format_definition_list_item(dt,dd,size,indent, color)
+      entries << text
+    end
+    entries * "\n\n"
+  end
+
   def self.read_stream(stream, size)
     str = nil
     while not str = stream.read(size)

data/lib/rbbt/util/simpleopt/doc.rb

@@ -26,20 +26,22 @@ module SOPT
   end
 
   def self.input_format(name, type = nil, default = nil, short = nil)
-    input_str = (short.nil? or short.empty?) ? Log.color(:blue,"--#{name}") : Log.color(:blue, "-#{short}") << ", " << Log.color(:blue, "--#{name}")
+    input_str = (short.nil? or short.empty?) ? "--#{name}" : "-#{short},--#{name}"
     input_str = Log.color(:blue, input_str)
-    input_str << case type
+    extra = case type
     when nil
-      "#{default != nil ? " (default '#{default}')" : ""}:"
+      ""
     when :boolean
-      "[=false]#{default != nil ? " (default '#{default}')" : ""}:"
+      "[=false]" 
     when :tsv, :text
-      "=<filename.#{type}|->#{default != nil ? " (default '#{default}')" : ""}; Use '-' for STDIN:"
+      "=<file|->"
     when :array
-      "=<string[,string]*|filename.list|->#{default != nil ? " (default '#{default}')" : ""}; Use '-' for STDIN:"
+      "=<list|file|->"
     else
-      "=<#{ type }>#{default != nil ? " (default '#{default}')" : ""}:"
+      "=<#{ type }>"
     end
+    extra << " (default '#{default}')" if default != nil
+    input_str << Log.color(:green, extra)
   end
 
   def self.input_doc(inputs, input_types = nil, input_descriptions = nil, input_defaults = nil, input_shortcuts = nil)
@@ -65,9 +67,9 @@ module SOPT
       type = :string if type.nil?
       register(shortcut, name, type, description) unless self.inputs.include? name
 
-      str  = "  * " << SOPT.input_format(name, type.to_sym, default, shortcut) 
-      str << "\n     " << description << "\n" if description and not description.empty?
-      str
+      name  = SOPT.input_format(name, type.to_sym, default, shortcut) 
+      description 
+      Misc.format_definition_list_item(name, description, 80, 31, nil)
     end * "\n"
   end
 
@@ -82,7 +84,7 @@ module SOPT
 
 #{ Log.color :magenta, "## DESCRIPTION"}
 
-#{description}
+#{Misc.format_paragraph description}
 
 #{ Log.color :magenta, "## OPTIONS"}
 

data/lib/rbbt/workflow.rb

@@ -2,6 +2,7 @@ require 'rbbt/workflow/definition'
 require 'rbbt/workflow/task'
 require 'rbbt/workflow/step'
 require 'rbbt/workflow/accessor'
+require 'rbbt/workflow/doc'
 
 module Workflow
 
@@ -149,16 +150,6 @@ module Workflow
     @libdir 
   end
   
-  def workflow_description
-    @workflow_description ||= begin
-                       file = @libdir['workflow.md']
-                       if file.exists?
-                         file.read
-                       else
-                         ""
-                       end
-                     end
-  end
 
   def helpers
     @helpers ||= {}

data/lib/rbbt/workflow/doc.rb

@@ -0,0 +1,58 @@
+module Workflow
+
+  def self.doc_parse_first_line(str)
+    if str.match(/^([^\n]*)\n\n(.*)/sm)
+      str.replace $2
+      $1
+    else
+      ""
+    end
+  end
+
+  def self.doc_parse_up_to(str, pattern, keep = false)
+    pre, _pat, _post = str.partition pattern
+    if _pat
+      [pre, (keep ? _pat << _post : _post)]
+    else
+      _post
+    end
+  end
+
+  def self.doc_parse_chunks(str, pattern)
+    parts = str.split(pattern)
+    return {} if parts.length < 2
+    tasks = Hash[*parts[1..-1].collect{|v| v.strip}]
+    tasks.delete_if{|t,d| d.empty?}
+    tasks
+  end
+
+  def self.parse_workflow_doc(doc)
+    title = doc_parse_first_line doc
+    description, task_info = doc_parse_up_to doc, /^# Tasks/i
+    task_description, tasks = doc_parse_up_to task_info, /^##/, true
+    tasks = doc_parse_chunks tasks, /## (.*)/ 
+    {:title => title.strip, :description => description.strip, :task_description => task_description.strip, :tasks => tasks}
+  end
+
+  def documentation_markdown
+    file = @libdir['workflow.md'].find
+    if file.exists?
+      file.read
+    else
+      ""
+    end
+  end
+
+  def load_documentation
+    @documentation = Workflow.parse_workflow_doc documentation_markdown
+    @documentation[:tasks].each do |task, description|
+      tasks[task.to_sym].description = description
+    end
+  end
+
+  attr_accessor :documentation
+  def documentation
+    load_documentation if @documentation.nil?
+    @documentation 
+  end
+end

data/lib/rbbt/workflow/usage.rb

@@ -4,10 +4,26 @@ module Task
   def doc(deps = nil)
     puts Log.color :magenta, "## #{ name }:"
     puts "\n" << description  << "\n" if description and not description.empty?
-    puts "Returns: " << Log.color(:blue, result_type.to_s) << "\n"
+    puts
+
+    case
+    when (input_types.values & [:array]).any?
+      puts Log.color(:green, Misc.format_paragraph("Lists are specified as arguments using ',' or '|'. When specified as files the '\\n'
+      also works in addition to the others. You may use the '--array_separator' option
+      the change this default. Whenever a file is specified it may also accept STDIN using
+      the '-' character."))
+      puts
+
+    when (input_types.values & [:text, :tsv]).any?
+      puts Log.color(:green, Misc.format_paragraph("Whenever a file is specified it may also accept STDIN using the '-' character."))
+      puts
+    end
+
     puts SOPT.input_doc(inputs, input_types, input_descriptions, input_defaults, true)
     puts
 
+    puts "Returns: " << Log.color(:blue, result_type.to_s) << "\n"
+    puts
 
     if deps and deps.any?
       puts "From dependencies:"
@@ -28,17 +44,23 @@ module Workflow
     if task.nil?
       puts Log.color :magenta, self.to_s 
       puts Log.color :magenta, "=" * self.to_s.length
-      puts
-      puts "\n" << workflow_description if workflow_description and not workflow_description.empty?
+      if self.documentation[:description] and not self.documentation[:description].empty?
+        puts
+        puts Misc.format_paragraph self.documentation[:description] 
+      end
       puts
 
       puts Log.color :magenta, "## TASKS"
+      if self.documentation[:task_description] and not self.documentation[:task_description].empty?
+        puts
+        puts Misc.format_paragraph self.documentation[:task_description] 
+      end
       puts
+
       tasks.each do |name,task|
-        puts "  * #{ Log.color :green, name.to_s }:"
-        puts "    " << task.description.split(/\n\s*\n/).first if task.description and not task.description.empty?
-        puts
+        puts Misc.format_definition_list_item(name.to_s, task.description || "", 80, 30, :yellow)
       end
+
     else
 
       if Task === task

data/share/rbbt_commands/workflow/task

@@ -35,7 +35,6 @@ end
 
 def usage(workflow = nil, task = nil, exception=nil)
   puts SOPT.doc
-  puts Log.color :magenta, "## WORKFLOW"
   puts
   if workflow.nil?
     puts "No workflow specified"
@@ -45,11 +44,13 @@ def usage(workflow = nil, task = nil, exception=nil)
   if task.nil?
     workflow.load_tasks if workflow.respond_to? :load_tasks
     workflow.doc
+    puts
+    puts "E.g. rbbt workflow task #{workflow.to_s} #{workflow.tasks.keys.first.to_s} -h"
   else
     puts Log.color :magenta, workflow.to_s
     puts Log.color :magenta, "=" * workflow.to_s.length
     puts
-    puts workflow.workflow_description
+    puts workflow.documentation[:description]
     puts
     workflow.doc(task)
   end

data/test/rbbt/util/test_misc.rb

@@ -6,12 +6,59 @@ require 'rbbt/entity'
 
 class TestMisc < Test::Unit::TestCase
 
-  def test_parse_cmd_params
-    ddd Misc.parse_cmd_params("workflow task Translation translate -f 'Associated Gene Name' -l -")
+  def _test_format_paragraph
+    p = <<-EOF
+
+Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor
+incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis
+nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat.
+Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu
+    fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt
+    in culpa qui officia deserunt mollit anim id est laborum.
+
+
+    EOF
+
+    puts Misc.format_paragraph p, 70, 10, 5
+  end
+
+  def test_format_dl
+    p1 = <<-EOF
+Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor
+incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis
+nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat.
+Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu
+    fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt
+    in culpa qui officia deserunt mollit anim id est laborum.
+    EOF
+
+    p2 = <<-EOF
+
+Sed ut perspiciatis unde omnis iste natus error sit voluptatem accusantium
+doloremque laudantium, totam rem aperiam, eaque ipsa quae ab illo inventore
+veritatis et quasi architecto beatae vitae dicta sunt explicabo. Nemo enim
+ipsam voluptatem quia voluptas sit aspernatur aut odit aut fugit, sed quia
+consequuntur magni dolores eos qui ratione voluptatem sequi nesciunt. Neque
+porro quisquam est, qui dolorem ipsum quia dolor sit amet, consectetur,
+adipisci velit, sed quia non numquam eius modi tempora incidunt ut labore et
+dolore magnam aliquam quaerat voluptatem. Ut enim ad minima veniam, quis
+nostrum exercitationem ullam corporis suscipit laboriosam, nisi ut aliquid ex
+ea commodi consequatur? Quis autem vel eum iure reprehenderit qui in ea
+voluptate velit esse quam nihil molestiae consequatur, vel illum qui dolorem
+eum fugiat quo voluptas nulla pariatur?"
+
+    EOF
+
+    puts Misc.format_definition_list({:paragraph_first => p1, :paragraph_second => p2})
+  end
+
+  def _test_parse_cmd_params
+    assert_equal ["workflow", "task", "Translation", "translate", "-f", "Associated Gene Name", "-l", "-"],
+      Misc.parse_cmd_params("workflow task Translation translate -f 'Associated Gene Name' -l -")
   end
 
 
-  def test_fixutf8
+  def _test_fixutf8
     string = "abc\xffdef"
     string = string.force_encoding("UTF-8") if string.respond_to? :force_encoding
     assert(! string.valid_encoding?) if string.respond_to? :valid_encoding?
@@ -20,37 +67,37 @@ class TestMisc < Test::Unit::TestCase
     assert( Misc.fixutf8(string).valid_encoding) if string.respond_to? :valid_encoding
   end
 
-  def test_colors_for
+  def _test_colors_for
     colors, used = Misc.colors_for([1,2,2,1,2,1,2,2,3,3,2,3,2])
     assert_equal Misc::COLOR_LIST[1], used[2]
   end
 
-  def test_total_length
+  def _test_total_length
     ranges = [(0..100), (50..150), (120..160)]
     ranges = [(0..100), (50..150), (120..160), (51..70)]
     assert_equal 161, Misc.total_length(ranges)
   end
 
-  def test_id_filename?
+  def _test_id_filename?
     TmpFile.with_file("") do |file|
       assert Misc.is_filename?(file)
       assert ! Misc.is_filename?("TEST STRING")
     end
   end
 
-  def test_merge_sorted_arrays
+  def _test_merge_sorted_arrays
     assert_equal [1,2,3,4], Misc.merge_sorted_arrays([1,3], [2,4])
   end
 
-  def test_intersect_sorted_arrays
+  def _test_intersect_sorted_arrays
     assert_equal [2,4], Misc.intersect_sorted_arrays([1,2,3,4], [2,4])
   end
 
-  def test_sorted_array_matches
+  def _test_sorted_array_matches
     assert_equal [1,3], Misc.sorted_array_hits(%w(a b c d e), %w(b d))
   end
 
-  def test_binary_include?
+  def _test_binary_include?
     a = %w(a b c d e).sort
     assert Misc.binary_include?(a, "a")
     assert(!Misc.binary_include?(a, "z"))
@@ -59,24 +106,24 @@ class TestMisc < Test::Unit::TestCase
     assert(Misc.binary_include?(a, "d"))
   end
 
-  def test_process_to_hash
+  def _test_process_to_hash
     list = [1,2,3,4]
     assert_equal 4, Misc.process_to_hash(list){|l| l.collect{|e| e * 2}}[2]
   end
 
-#  def test_pdf2text_example
+#  def _test_pdf2text_example
 #    assert PDF2Text.pdf2text(datafile_test('example.pdf')).read =~ /An Example Paper/i
 #  end
 #
-#  def test_pdf2text_EPAR
+#  def _test_pdf2text_EPAR
 #    assert PDF2Text.pdf2text("http://www.ema.europa.eu/docs/en_GB/document_library/EPAR_-_Scientific_Discussion/human/000402/WC500033103.pdf").read =~ /Tamiflu/i
 #  end
 #
-#  def test_pdf2text_wrong
+#  def _test_pdf2text_wrong
 #    assert_raise CMD::CMDError do PDF2Text.pdf2text("http://www.ema.europa.eu/docs/en_GB#").read end
 #  end
 
-  def test_string2hash
+  def _test_string2hash
     assert(Misc.string2hash("--user-agent=firefox").include? "--user-agent")
     assert_equal(true, Misc.string2hash(":true")[:true])
     assert_equal(true, Misc.string2hash("true")["true"])
@@ -87,12 +134,12 @@ class TestMisc < Test::Unit::TestCase
     assert_equal(:j, Misc.string2hash("a=b#c=d#:h=:j")[:h])
   end
   
-  def test_named_array
+  def _test_named_array
     a = NamedArray.setup([1,2,3,4], %w(a b c d))
     assert_equal(1, a['a'])
   end
 
-  def test_path_relative_to
+  def _test_path_relative_to
     assert_equal "test/foo", Misc.path_relative_to('/test', '/test/test/foo')
 
     Misc.profile do
@@ -102,8 +149,8 @@ class TestMisc < Test::Unit::TestCase
     end
   end
 
-#  def test_chunk
-#    test =<<-EOF
+#  def _test_chunk
+#    _test =<<-EOF
 #This is an example file. Entries are separated by Entry
 #-- Entry
 #1
@@ -118,7 +165,7 @@ class TestMisc < Test::Unit::TestCase
 #    assert_equal "1\n2\n3", Misc.chunk(test, /^-- Entry/).first.strip
 #  end
 
-  def test_hash2string
+  def _test_hash2string
     hash = {}
     assert_equal hash, Misc.string2hash(Misc.hash2string(hash))
 
@@ -136,14 +183,14 @@ class TestMisc < Test::Unit::TestCase
  
   end
 
-  def test_merge
+  def _test_merge
     a = [[1],[2]]
     a = NamedArray.setup a, %w(1 2)
     a.merge [3,4]
     assert_equal [1,3], a[0]
   end
 
-  def test_indiferent_hash
+  def _test_indiferent_hash
     a = {:a => 1, "b" => 2}
     a.extend IndiferentHash
 
@@ -153,7 +200,7 @@ class TestMisc < Test::Unit::TestCase
     assert_equal 2, a[:b]
   end
 
-  def test_lockfile
+  def _test_lockfile
 
     TmpFile.with_file do |tmpfile|
       pids = []
@@ -177,7 +224,7 @@ class TestMisc < Test::Unit::TestCase
     end
   end
 
-  def test_positions2hash
+  def _test_positions2hash
     inputs = Misc.positional2hash([:one, :two, :three], 1, :two => 2, :four => 4)
     assert_equal 1, inputs[:one]
     assert_equal 2, inputs[:two]
@@ -185,18 +232,18 @@ class TestMisc < Test::Unit::TestCase
     assert_equal nil, inputs[:four]
   end
 
-  def test_mean
+  def _test_mean
     assert_equal 2, Misc.mean([1,2,3])
     assert_equal 3, Misc.mean([1,2,3,4,5])
   end
 
-  def test_zip_fields
+  def _test_zip_fields
     current = [[:a,1], [:b,2]]
     assert_equal [[:a, :b],[1,2]], Misc.zip_fields(current)
     assert_equal current, Misc.zip_fields(Misc.zip_fields(current))
   end
 
-  def test_add_zipped
+  def _test_add_zipped
     current = [[:a,1], [:b,2]]
     new = %w(A B)
     Misc.append_zipped current, new
@@ -207,20 +254,20 @@ class TestMisc < Test::Unit::TestCase
     assert_equal Math.sqrt(2), Misc.sd([1,3])
   end
 
-  def test_divide
+  def _test_divide
     assert_equal 2, Misc.divide(%w(1 2 3 4 5 6 7 8 9),2).length
   end
 
-  def test_ordered_divide
+  def _test_ordered_divide
     assert_equal 5, Misc.ordered_divide(%w(1 2 3 4 5 6 7 8 9),2).length
   end
 
-  def test_collapse_ranges
+  def _test_collapse_ranges
     ranges = [(0..100), (50..150), (51..61),(200..250), (300..324),(320..350)]
     assert_equal [(0..150),(200..250), (300..350)], Misc.collapse_ranges(ranges)
   end
 
-  def test_humanize
+  def _test_humanize
     str1 = "test_string"
     str2 = "TEST_string"
     str3 = "test"
@@ -232,22 +279,22 @@ class TestMisc < Test::Unit::TestCase
     assert_equal "mutation_enrichment", Misc.snake_case("MutationEnrichment")
   end
 
-  def test_snake_case
+  def _test_snake_case
     str1 = "ACRONIMTest"
     str2 = "ACRONIM_test"
     assert_equal "ACRONIM_test", Misc.snake_case(str1)
     assert_equal "ACRONIM_test", Misc.snake_case(str2)
   end
 
-  def test_correct_vcf_mutations
+  def _test_correct_vcf_mutations
     assert_equal [737407, ["-----", "-----G", "-----GTTAAT"]], Misc.correct_vcf_mutation(737406, "GTTAAT", "G,GG,GGTTAAT")
   end
 
-  def test_fingerprint
+  def _test_fingerprint
     assert_equal '{a=>1}', Misc.fingerprint({:a => 1})
   end
 
-  def test_tarize
+  def _test_tarize
     path = File.expand_path('/home/mvazquezg/git/rbbt-util/lib')
     stream = Misc.tarize(path)
     TmpFile.with_file do |res|
@@ -257,7 +304,7 @@ class TestMisc < Test::Unit::TestCase
     end
   end
 
-  def test_camel_case
+  def _test_camel_case
     assert_equal "DbSNP", Misc.camel_case("db_SNP")
     assert_equal "D3Js", Misc.camel_case("D3Js")
     assert_equal "Structure", Misc.camel_case("Structure")
@@ -265,7 +312,7 @@ class TestMisc < Test::Unit::TestCase
     assert_equal "COSMIC", Misc.camel_case("COSMIC")
   end
 
-  def test_pipe
+  def _test_pipe
     t = 5
     stream = Misc.open_pipe do |sin|
       t.times do |i|

data/test/rbbt/workflow/test_doc.rb

@@ -0,0 +1,29 @@
+require File.join(File.expand_path(File.dirname(__FILE__)), '../..', 'test_helper.rb')
+require 'rbbt/workflow'
+
+class TestWorkflowDoc < Test::Unit::TestCase
+  TEMPLATE=<<-EOF
+Title of the template
+
+Paragraph1
+
+Paragraph2
+
+# Tasks
+
+Paragraph3
+
+## task1
+
+Task 1
+
+## task2
+
+Task 2
+
+  EOF
+  def test_parse
+    ddd Workflow.parse_workflow_doc(TEMPLATE)
+  end
+end
+

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.8.4
+  version: 5.8.6
 platform: ruby
 authors:
 - Miguel Vazquez
@@ -188,6 +188,7 @@ files:
 - lib/rbbt/workflow/accessor.rb
 - lib/rbbt/workflow/annotate.rb
 - lib/rbbt/workflow/definition.rb
+- lib/rbbt/workflow/doc.rb
 - lib/rbbt/workflow/soap.rb
 - lib/rbbt/workflow/step.rb
 - lib/rbbt/workflow/task.rb
@@ -289,6 +290,7 @@ files:
 - test/rbbt/util/test_simpleDSL.rb
 - test/rbbt/util/test_simpleopt.rb
 - test/rbbt/util/test_tmpfile.rb
+- test/rbbt/workflow/test_doc.rb
 - test/rbbt/workflow/test_step.rb
 - test/rbbt/workflow/test_task.rb
 - test/test_helper.rb
@@ -349,6 +351,7 @@ test_files:
 - test/rbbt/test_tsv.rb
 - test/rbbt/workflow/test_task.rb
 - test/rbbt/workflow/test_step.rb
+- test/rbbt/workflow/test_doc.rb
 - test/rbbt/test_persist.rb
 - test/rbbt/test_annotations.rb
 - test/rbbt/persist/test_tsv.rb