rbbt-util 5.8.0 → 5.8.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: d2929287d81291dd772ab9ee6f415b52bafad0db
-  data.tar.gz: 61ad4ae0dade13e2cbc0e02c39107243d92a52e0
+  metadata.gz: d5612376bb0b3bc5345a607fd72cfb4f744eeba8
+  data.tar.gz: 8d8d53efd7203512d28462d609bf6f52a1c492c0
 SHA512:
-  metadata.gz: 14285e88be1d35d8c23fb77ad038d2818ae1df04245bd2fd48bbab4f72b419eff1042764b8173b33c1d96955dee0df7ecfd27a84efb34171abb10bae05169b79
-  data.tar.gz: d96daf9acd2d79ab8b9425d849fd9442b7fd4ee1d614d364d135b9a601d0b7de1278eba414cb464f92f325cb84ab131311dff1937c1bdc2a99d631e7ea5f146b
+  metadata.gz: f858ffbc83f9a199a22c9c1a49b1d40f0de1f1ea8e9979820901040a23a9eb3c7077f354aac6260876c7f04941bd2a2eea976262f6b73a1a46687421fbc441f7
+  data.tar.gz: 3dd1ed9a2dcf25fa5939935f27ad026df16c10a8e464743122e7f6725f8317db82cdee7c5f01b5c7866a442aee9ac9cfc963eca6e276eba372bacc6749ee84d2

data/lib/rbbt/resource/path.rb

@@ -196,6 +196,10 @@ module Path
     TSV.open(self.produce, *args)
   end
 
+  def traverse(options = {}, &block)
+    TSV::Parser.traverse(self.open, options, &block)
+  end
+
   def list
     Open.read(self.produce.find).split "\n"
   end

data/lib/rbbt/tsv.rb

@@ -110,20 +110,11 @@ module TSV
       Parser.new stream, options
     end
   end
-
   def self.parse(stream, data, options = {})
-    monitor, grep, invert_grep, head = Misc.process_options options, :monitor, :grep, :invert_grep, :head
-
-    parser = Parser.new stream, options
 
-    if grep
-      stream.rewind
-      stream = Open.grep(stream, grep, invert_grep)
-      parser.first_line = stream.gets
-    end
-
-    line = parser.rescue_first_line
+    parser = TSV::Parser.new stream, options
 
+    # dump with tchmgr
     if defined? TokyoCabinet and TokyoCabinet::HDB === data and parser.straight and
       data.close
       begin
@@ -137,9 +128,11 @@ module TSV
       data.write
     end
 
+    # make TSV
     data.extend TSV unless TSV === data
     data.unnamed = true
 
+    # choose serializer
     if data.serializer == :type
       data.serializer = case
                         when parser.cast.nil?
@@ -155,59 +148,11 @@ module TSV
                         end
     end
 
-    if monitor and (stream.respond_to?(:size) or (stream.respond_to?(:stat) and stream.stat.respond_to? :size)) and stream.respond_to?(:pos)
-      size = case
-             when stream.respond_to?(:size)
-               stream.size
-             else
-               stream.stat.size
-             end
-      desc = "Parsing Stream"
-      step = 100
-      if Hash === monitor
-        desc = monitor[:desc] if monitor.include? :desc 
-        step = monitor[:step] if monitor.include? :step 
-      end
-      progress_monitor = Progress::Bar.new(size, 0, step, desc)
-    else
-      progress_monitor = nil
-    end
-
-    line_num = 1
-    begin
-      while not line.nil? 
-        begin
-          progress_monitor.tick(stream.pos) if progress_monitor 
-
-          raise Parser::SKIP_LINE if line.empty?
-
-          line = Misc.fixutf8(line)
-          line = parser.process line
-          parts = parser.chop_line line
-          key, values = parser.get_values parts
-          values = parser.cast_values values if parser.cast?
-          parser.add_to_data data, key, values
-          line = stream.gets
-          line_num += 1
-          raise Parser::END_PARSING if head and line_num > head.to_i
-        rescue Parser::SKIP_LINE
-          begin
-            line = stream.gets
-            next
-          rescue IOError
-            break
-          end
-        rescue Parser::END_PARSING
-          break
-        rescue IOError
-          Log.exception $!
-          break
-        end
-      end
-    ensure
-      stream.close unless stream.closed?
+    parser.traverse(options) do |key,values|
+      parser.add_to_data data, key, values
     end
 
+    # setup the TSV
     parser.setup data
 
     data.unnamed = false

data/lib/rbbt/tsv/change_id.rb

@@ -1,7 +1,7 @@
 require 'rbbt/tsv'
 
 module TSV
-  def self.change_key(tsv, format, options = {})
+  def self.change_key(tsv, format, options = {}, &block)
     options = Misc.add_defaults options, :persist => false, :identifiers => tsv.identifiers
 
     identifiers, persist_input = Misc.process_options options, :identifiers, :persist_input
@@ -21,18 +21,20 @@ module TSV
 
       tsv = tsv.to_flat  if orig_type == :flat
 
+      tsv = tsv.to_list(&block)  if orig_type == :list
+
       tsv
     else
       tsv.reorder(format)
     end
   end
 
-  def change_key(format, options = {})
+  def change_key(format, options = {}, &block)
     options = Misc.add_defaults options, :identifiers => self.identifiers
-    TSV.change_key(self, format, options)
+    TSV.change_key(self, format, options, &block)
   end
 
-  def self.swap_id(tsv, field, format, options = {})
+  def self.swap_id(tsv, field, format, options = {}, &block)
     options = Misc.add_defaults options, :persist => false, :identifiers => tsv.identifiers
 
     identifiers, persist_input = Misc.process_options options, :identifiers, :persist
@@ -62,6 +64,8 @@ module TSV
 
     tsv = tsv.to_flat  if orig_type == :flat
 
+    tsv = tsv.to_list(&block)  if orig_type == :list
+
     tsv
   end
 

data/lib/rbbt/tsv/parser.rb

@@ -1,7 +1,7 @@
 require 'rbbt/util/cmd'
 module TSV
   class Parser
-    attr_accessor :header_hash, :sep, :sep2, :type, :key_position, :field_positions, :cast, :key_field, :fields, :fix, :select, :serializer, :straight, :take_all, :zipped, :namespace, :first_line
+    attr_accessor :stream, :header_hash, :sep, :sep2, :type, :key_position, :field_positions, :cast, :key_field, :fields, :fix, :select, :serializer, :straight, :take_all, :zipped, :namespace, :first_line, :stream
 
     class SKIP_LINE < Exception; end
     class END_PARSING < Exception; end
@@ -52,9 +52,9 @@ module TSV
 
     def process(line)
       l = line.chomp
-      raise Parser::SKIP_LINE if l[0] == "#"[0] or (Proc === @select and not @select.call l)
+      raise SKIP_LINE if l[0] == "#"[0] or (Proc === @select and not @select.call l)
       l = @fix.call l if Proc === @fix
-      raise Parser::END_PARSING unless l
+      raise END_PARSING unless l
       l
     end
 
@@ -123,46 +123,66 @@ module TSV
     def get_values_flat(parts)
       if key_position and key_position != 0 and field_positions.nil?
         value = parts.shift
-        keys = parts
+        keys = parts.dup
         return [keys, [value]]
       end
 
-      return parts.shift.split(@sep2, -1), parts.collect{|value| value.split(@sep2, -1)} if 
+      return parts.shift.split(@sep2, -1).first, parts.collect{|value| value.split(@sep2, -1)}.flatten if 
         field_positions.nil? and (key_position.nil? or key_position == 0)
 
       keys = parts[key_position].split(@sep2, -1)
 
       if @take_all
-        values = parts.collect{|value| value.split(@sep2, -1)}
+        values = parts.collect{|e| e.split(@sep2, -1) }.flatten
       else
+        if field_positions.nil?
+          parts.delete_at key_position
+          values = parts.first
+        else
+          values = parts[field_positions.first]
+        end
 
-        values = if field_positions.nil?
-                   parts.tap{|o| o.delete_at key_position}
-                 else
-                   parts.values_at *field_positions
-                 end.collect{|value| value.split(@sep2, -1)}
+        values = values.split(@sep2, -1)
       end
-      [keys, values]
+
+      [keys.first, values]
     end
 
     def add_to_data_no_merge_list(data, key, values)
       data[key] = values unless data.include? key
+      nil
     end
 
-    def add_to_data_flat(data, keys, values)
+    def add_to_data_flat_keys(data, keys, values)
       keys.each do |key|
-        data[key] = values.flatten unless data.include? key
+        data[key] = values unless data.include? key
       end
+      nil
+    end
+
+    def add_to_data_flat(data, key, values)
+      data[key] = values unless data.include? key
+      nil
     end
 
-    def add_to_data_flat_merge(data, keys, values)
+    def add_to_data_flat_merge(data, key, values)
+      if data.include? key
+        data[key] = data[key].concat values
+      else
+        data[key] = values
+      end
+      nil
+    end
+
+    def add_to_data_flat_merge_keys(data, keys, values)
       keys.each do |key|
         if data.include? key
-          data[key] = data[key].concat values.flatten 
+          data[key] = data[key].concat values
         else
-          data[key] = values.flatten
+          data[key] = values.dup
         end
       end
+      nil
     end
 
     def add_to_data_no_merge_double(data, keys, values)
@@ -170,6 +190,7 @@ module TSV
         next if data.include? key
         data[key] = values 
       end
+      nil
     end
 
     def add_to_data_merge(data, keys, values)
@@ -184,6 +205,7 @@ module TSV
           data[key] = values
         end
       end
+      nil
     end
 
     def add_to_data_merge_zipped(data, keys, values)
@@ -207,6 +229,7 @@ module TSV
           data[key] = values.collect{|v| [v]}
         end
       end
+      nil
     end
 
     def add_to_data_zipped(data, keys, values)
@@ -224,6 +247,7 @@ module TSV
         next if data.include? key
         data[key] = values.collect{|v| [v]}
       end
+      nil
     end
 
 
@@ -317,6 +341,7 @@ module TSV
     def initialize(stream = nil, options = {})
       @header_hash = Misc.process_options(options, :header_hash) || "#"
       @sep = Misc.process_options(options, :sep) || "\t"
+      @stream = stream
 
       header_options = parse_header(stream)
       options = header_options.merge options
@@ -334,6 +359,9 @@ module TSV
       merge = @zipped if merge.nil?
       merge = false if merge.nil?
 
+      fields = options[:fields]
+      fix_fields(options)
+
       case @type
       when :double 
         self.instance_eval do alias get_values get_values_double end
@@ -363,18 +391,24 @@ module TSV
         self.instance_eval do alias cast_values cast_values_list end
         self.instance_eval do alias add_to_data add_to_data_no_merge_list end
       when :flat
-        @take_all = true if options[:fields].nil?
+        @take_all = true if field_positions.nil?
         self.instance_eval do alias get_values get_values_flat end
         self.instance_eval do alias cast_values cast_values_double end
         if merge
-          self.instance_eval do alias add_to_data add_to_data_flat_merge end
+          if key_position and key_position != 0 and field_positions.nil?
+            self.instance_eval do alias add_to_data add_to_data_flat_merge_keys end
+          else
+            self.instance_eval do alias add_to_data add_to_data_flat_merge end
+          end
         else
-          self.instance_eval do alias add_to_data add_to_data_flat end
+          if key_position and key_position != 0 and field_positions.nil?
+            self.instance_eval do alias add_to_data add_to_data_flat_keys end
+          else
+            self.instance_eval do alias add_to_data add_to_data_flat end
+          end
         end
       end
 
-      fields = options[:fields]
-      fix_fields(options)
 
       @straight = false if @sep != "\t" or not @cast.nil? or merge or (@type == :flat and fields)
     end
@@ -388,5 +422,87 @@ module TSV
       data.cast = @cast if Symbol === @cast
       data
     end
+
+    def traverse(options = {})
+      monitor, grep, invert_grep, head = Misc.process_options options, :monitor, :grep, :invert_grep, :head
+      raise "No block given in TSV::Parser#traverse" unless block_given?
+
+      stream = @stream
+      # get parser
+
+      # grep
+      if grep
+        stream.rewind
+        stream = Open.grep(stream, grep, invert_grep)
+        self.first_line = stream.gets
+      end
+
+      # first line
+      line = self.rescue_first_line
+
+      # setup monitor
+      if monitor and (stream.respond_to?(:size) or (stream.respond_to?(:stat) and stream.stat.respond_to? :size)) and stream.respond_to?(:pos)
+        size = case
+               when stream.respond_to?(:size)
+                 stream.size
+               else
+                 stream.stat.size
+               end
+        desc = "Parsing Stream"
+        step = 100
+        if Hash === monitor
+          desc = monitor[:desc] if monitor.include? :desc 
+          step = monitor[:step] if monitor.include? :step 
+        end
+        progress_monitor = Progress::Bar.new(size, 0, step, desc)
+      else
+        progress_monitor = nil
+      end
+
+      # parser 
+      line_num = 1
+      begin
+        while not line.nil? 
+          begin
+            progress_monitor.tick(stream.pos) if progress_monitor 
+
+            raise SKIP_LINE if line.empty?
+
+            line = Misc.fixutf8(line)
+            line = self.process line
+            parts = self.chop_line line
+            key, values = self.get_values parts
+            values = self.cast_values values if self.cast?
+            
+            yield key, values, self
+
+            line = stream.gets
+            line_num += 1
+            raise END_PARSING if head and line_num > head.to_i
+          rescue SKIP_LINE
+            begin
+              line = stream.gets
+              next
+            rescue IOError
+              break
+            end
+          rescue END_PARSING
+            break
+          rescue IOError
+            Log.exception $!
+            break
+          end
+        end
+      ensure
+        stream.close unless stream.closed?
+      end
+
+      self
+    end
+
+    def self.traverse(stream, options = {}, &block)
+      parser = Parser.new(stream, options)
+      parser.traverse(options, &block)
+    end
   end
 end

data/lib/rbbt/util/log.rb

@@ -31,10 +31,11 @@ module Log
     return str || "" if nocolor 
     color = SEVERITY_COLOR[severity] if Fixnum === severity
     color = Term::ANSIColor.send(severity) if Symbol === severity and Term::ANSIColor.respond_to? severity 
+    color ||= ""
     if str.nil?
       color
     else
-      color + str + color(0)
+      color + str + self.color(0)
     end
   end
 

data/lib/rbbt/workflow/accessor.rb

@@ -94,29 +94,40 @@ class Step
     set_info(:messages, (messages || []) << message)
   end
 
-  attr_accessor :last_log
-  def last_log
-    @last_log ||= Time.now
-  end
-
-  def log(status, message = nil)
-    if message
+  def self.log(status, message, path, &block)
+    if block_given?
+      start = Time.now
+      Log.medium do 
+        now = Time.now
+        str = "#{ Log.color :cyan, status.to_s }"
+        str << ": #{ message }" if message
+        str << " -- #{Log.color :blue, path.to_s}" if path
+        str
+      end
+      res = yield
+      eend = Time.now
       Log.medium do 
         now = Time.now
-        str = "+#{(now - last_log).to_i} #{ Log.color :cyan, status.to_s }: #{ message } -- #{path}"
-        @last_log = now
+        str = "#{ Log.color :cyan, status.to_s } +#{Log.color :green, "%.1g" % (eend - start)}"
+        str << " -- #{Log.color :blue, path.to_s}" if path
         str
       end
-    else                                                                      
-      Log.medium do
+      res
+    else
+      Log.medium do 
         now = Time.now
-        str = "+#{(now - last_log).to_i} #{ Log.color :cyan, status.to_s } -- #{path}"
-        @last_log = now
+        str = "#{ Log.color :cyan, status.to_s }"
+        str << ": #{ message }" if message
+        str << " -- #{Log.color :blue, path.to_s}" if path
         str
       end
     end
   end
 
+  def log(status, message = nil, &block)
+    Step.log(status, message, path, &block)
+  end
+
   def started?
     Open.exists? info_file
   end
@@ -225,27 +236,8 @@ end
 
 module Workflow
 
-  attr_accessor :last_log
-  def last_log
-    @@last_log ||= Time.now
-  end
-
-  def log(status, message = nil)
-    if message
-      Log.medium do 
-        now = Time.now
-        str = "+#{(now - last_log).to_i} #{ Log.color :cyan, status.to_s }: #{ message }"
-        @@last_log = now
-        str
-      end
-    else                                                                      
-      Log.medium do
-        now = Time.now
-        str = "+#{(now - last_log).to_i} #{ Log.color :cyan, status.to_s }"
-        @@last_log = now
-        str
-      end
-    end
+  def log(status, message = nil, &block)
+    Step.log(status, message, nil, &block)
   end
 
   def task_info(name)

data/lib/rbbt/workflow/step.rb

@@ -41,9 +41,9 @@ class Step
       class << self
         attr_accessor :relay_step
         alias original_log log 
-        def log(status, message = nil, do_log = true)
-          original_log(status, message, do_log)
-          relay_step.log([task.name.to_s, status.to_s] * ">", message.nil? ? nil : [task.name.to_s, message] * ">", false)
+        def log(status, message = nil)
+          original_log(status, message)
+          relay_step.log([task.name.to_s, status.to_s] * ">", message.nil? ? nil : [task.name.to_s, message] * ">")
         end
       end
     end
@@ -117,6 +117,7 @@ class Step
           log(:error, "Exception processing dependency #{dependency.path}")
           log(:error, "#{$!.class}: #{$!.message}")
           log(:error, "backtrace: #{$!.backtrace.first}")
+          Log.exception $!
           raise "Exception processing dependency #{dependency.path}"
         end
       }

data/share/rbbt_commands/benchmark/tsv

@@ -0,0 +1,10 @@
+#!/usr/bin/env ruby
+
+require 'rbbt-util'
+
+require 'rbbt/sources/organism'
+
+Misc.benchmark(10) do
+  Organism.identifiers("Hsa").tsv
+end
+

data/share/rbbt_commands/stat/abs

@@ -0,0 +1,43 @@
+#!/usr/bin/env ruby
+
+require 'rbbt'
+require 'rbbt/util/simpleopt'
+
+require 'rbbt/util/R'
+
+$0 = "rbbt #{$previous_commands*""} #{ File.basename(__FILE__) }" if $previous_commands
+
+options = SOPT.setup <<EOF
+Take absolute value
+
+$ rbbt stat density <file>
+
+Display summary information. Works with Tokyocabinet HDB and DBD as well.
+
+-tch--tokyocabinet File is a TC HDB
+-tcb--tokyocabinet_bd File is a TC BDB
+-t--type* Type of tsv (single, list, double, flat)
+-h--header_hash* Change the character used to mark the header line (defaults to #)
+-f--field Field to change
+-h--help Help
+EOF
+
+SOPT.usage if options[:help]
+
+file = ARGV.shift
+
+if file == '-' or file.nil?
+  file = STDIN 
+else
+  file = Open.open file
+end
+
+parser = TSV::Parser.new file, options
+
+options[:fields] = [options.delete(:field) || 0]
+puts TSV.header_lines(parser.key_field, parser.fields)
+parser.traverse(options.merge(:type => :list)) do |k,v|
+  v = v.first
+  v = Array === v ? v.collect{|e| e.to_f.abs } : [v.to_f.abs]
+  puts [k,v].flatten * "\t"
+end

data/share/rbbt_commands/stat/density

@@ -16,10 +16,6 @@ Display summary information. Works with Tokyocabinet HDB and DBD as well.
 
 -tch--tokyocabinet File is a TC HDB
 -tcb--tokyocabinet_bd File is a TC BDB
--t--type* Type of tsv (single, list, double, flat)
--h--header_hash* Change the character used to mark the header line (defaults to #)
--k--key_field* Change the key field
--f--fields* Change the fields to load
 -h--help Help
 EOF
 
@@ -33,7 +29,6 @@ else
   file = Open.open file
 end
 
-
 values = file.read.split("\n").collect{|v| v.to_f}
 
 res = TmpFile.with_file do |tmp|

data/share/rbbt_commands/stat/log

@@ -0,0 +1,43 @@
+#!/usr/bin/env ruby
+
+require 'rbbt'
+require 'rbbt/util/simpleopt'
+
+require 'rbbt/util/R'
+
+$0 = "rbbt #{$previous_commands*""} #{ File.basename(__FILE__) }" if $previous_commands
+
+options = SOPT.setup <<EOF
+Take logs
+
+$ rbbt stat density <file>
+
+Display summary information. Works with Tokyocabinet HDB and DBD as well.
+
+-tch--tokyocabinet File is a TC HDB
+-tcb--tokyocabinet_bd File is a TC BDB
+-t--type* Type of tsv (single, list, double, flat)
+-h--header_hash* Change the character used to mark the header line (defaults to #)
+-f--field Field to change
+-h--help Help
+EOF
+
+SOPT.usage if options[:help]
+
+file = ARGV.shift
+
+if file == '-' or file.nil?
+  file = STDIN 
+else
+  file = Open.open file
+end
+
+parser = TSV::Parser.new file, options
+
+options[:fields] = [options.delete(:field) || 0]
+puts TSV.header_lines(parser.key_field, parser.fields)
+parser.traverse(options.merge(:type => :list)) do |k,v|
+  v = v.first
+  v = Array === v ? v.collect{|e| Math.log(e.to_f) } : [Math.log(v.to_f)]
+  puts [k,v].flatten * "\t"
+end

data/test/rbbt/test_tsv.rb

@@ -54,21 +54,6 @@ row2    A    B    Id3
     end
   end
 
-  def test_headerless_fields
-    content =<<-EOF
-#Id    ValueA    ValueB    OtherID
-row1    a|aa|aaa    b    Id1|Id2
-row2    A    B    Id3
-    EOF
-
-    TmpFile.with_file(content) do |filename|
-      tsv = TSV.open(filename, :sep => /\s+/, :fields => 1)
-      assert_equal ["a", "aa", "aaa"], tsv["row1"][0]
-      assert_equal :double, tsv.type
-      assert_equal [%w(a aa aaa)], tsv["row1"]
-    end
-  end
-
   def test_headerless_fields
     content =<<-EOF
 row1    a|aa|aaa    b    Id1|Id2

data/test/rbbt/tsv/test_change_id.rb

@@ -33,10 +33,17 @@ aa xx
   def setup
     @f1 = tsv(FILE1)
     @f2 = tsv(FILE2)
+    @f3 = tsv(FILE2, :key_field => "Y")
     @id = tsv(IDENTIFIERS)
   end
 
-  def test_change_id
+  def test_swap_id
+    @f3.identifiers = @id
+    assert_equal "a", @f3.swap_id("X","A")["y"]["A"]
+  end
+
+
+  def test_change_key
     @f1.identifiers = @id
     assert @f1.change_key("X").include? "x"
   end

data/test/rbbt/tsv/test_parser.rb

@@ -0,0 +1,34 @@
+require File.expand_path(File.join(File.dirname(__FILE__), '../..', 'test_helper.rb'))
+require 'rbbt/tsv'
+
+class TestTSVParser < Test::Unit::TestCase
+  def test_traverse
+
+    content =<<-EOF
+row1    a|aa|aaa    b    Id1|Id2
+    EOF
+
+    TmpFile.with_file(content) do |filename|
+      TSV::Parser.traverse(Open.open(filename), :sep => /\s+/, :fields => [1], :type => :double) do |k,v|
+        assert_equal ["row1"], k
+        assert_equal [%w(a aa aaa)], v
+      end
+
+      TSV::Parser.traverse(Open.open(filename), :sep => /\s+/, :fields => [1], :type => :list) do |k,v|
+        assert_equal "row1", k
+        assert_equal ["a|aa|aaa"], v
+      end
+
+      TSV::Parser.traverse(Open.open(filename), :sep => /\s+/, :fields => [1], :type => :single) do |k,v|
+        assert_equal "row1", k
+        assert_equal "a|aa|aaa", v
+      end
+
+      TSV::Parser.traverse(Open.open(filename), :sep => /\s+/, :fields => [1], :type => :flat) do |k,v|
+        assert_equal "row1", k
+        assert_equal %w(a aa aaa), v
+      end
+    end
+  end
+end
+

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.8.0
+  version: 5.8.1
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-03-11 00:00:00.000000000 Z
+date: 2014-03-12 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -200,6 +200,7 @@ files:
 - share/rbbt_commands/app/start
 - share/rbbt_commands/app/template
 - share/rbbt_commands/benchmark/pthrough
+- share/rbbt_commands/benchmark/tsv
 - share/rbbt_commands/color
 - share/rbbt_commands/conf/web_user/add
 - share/rbbt_commands/conf/web_user/list
@@ -211,7 +212,9 @@ files:
 - share/rbbt_commands/resource/find
 - share/rbbt_commands/resource/get
 - share/rbbt_commands/resource/produce
+- share/rbbt_commands/stat/abs
 - share/rbbt_commands/stat/density
+- share/rbbt_commands/stat/log
 - share/rbbt_commands/study/task
 - share/rbbt_commands/system/purge
 - share/rbbt_commands/system/report
@@ -264,6 +267,7 @@ files:
 - test/rbbt/tsv/test_index.rb
 - test/rbbt/tsv/test_manipulate.rb
 - test/rbbt/tsv/test_parallel.rb
+- test/rbbt/tsv/test_parser.rb
 - test/rbbt/tsv/test_util.rb
 - test/rbbt/util/concurrency/processes/test_socket.rb
 - test/rbbt/util/concurrency/test_processes.rb
@@ -357,6 +361,7 @@ test_files:
 - test/rbbt/tsv/test_parallel.rb
 - test/rbbt/tsv/test_index.rb
 - test/rbbt/tsv/test_change_id.rb
+- test/rbbt/tsv/test_parser.rb
 - test/rbbt/tsv/test_util.rb
 - test/rbbt/tsv/test_accessor.rb
 - test/rbbt/tsv/test_filter.rb