rbbt-util 4.0.0 → 4.0.1

data/bin/run_workflow.rb

@@ -115,7 +115,7 @@ else
 
   if remote_workflows.include? workflow
     require 'rbbt/workflow/rest/client'
-    workflow = RbbtRestClient.new remote_workflows[workflow]
+    workflow = RbbtRestClient.new remote_workflows[workflow], workflow
   else
     Workflow.require_workflow workflow
     workflow = Workflow.workflows.last

data/lib/rbbt/annotations.rb

@@ -128,7 +128,12 @@ module Annotation
       base.all_inheritance = []
 
       base.module_eval do
+        class << self
+          alias prev_annotation_extended extended
+        end
+
         def self.extended(object)
+          self.send(:prev_annotation_extended, object)
           object.extend Annotated
           if not object.annotation_types.include? self
             object.annotation_types.concat self.inheritance 
@@ -178,6 +183,7 @@ module Annotation
 
     object
   end
+
 end
 
 module AnnotatedArray
@@ -193,23 +199,28 @@ module AnnotatedArray
   end
 
   def annotated_array_each
-    annotation_array_clean_each do |value|
+    annotated_array_clean_each do |value|
       annotation_types.each do |mod|
-        mod.setup(value, annotation)
+        mod.setup(value, *info.values_at(*mod.annotations))
       end
       yield value
     end
   end
 
   def annotated_array_collect
-    annotation_array_clean_collect do |value|
+    annotated_array_clean_collect do |value|
       annotation_types.each do |mod|
-        mod.setup(value, annotation)
+        mod.setup(value, *info.values_at(*mod.annotations))
       end
       yield value
     end
   end
 
+  def annotated_array_subset(list)
+    value = (self & list)
+    annotation_types.each do |mod|
+      mod.setup(value, *info.values_at(*mod.annotations))
+    end
+    value
+  end
 end
-
-

data/lib/rbbt/persist.rb

@@ -4,6 +4,7 @@ require 'rbbt/util/misc'
 require 'rbbt/util/open'
 
 require 'rbbt/persist/tsv'
+require 'set'
 
 module Persist
   CACHEDIR="/tmp/tsv_persistent_cache"
@@ -67,10 +68,13 @@ module Persist
     File.join(persistence_dir, filename)
   end
 
+  TRUE_STRINGS = Set.new ["true", "True", "TRUE", "t", "T", "1", "yes", "Yes", "YES", "y", "Y", "ON", "on"]
   def self.load_file(path, type)
     case (type || "nil").to_sym
     when :nil
       nil
+    when :boolean
+      TRUE_STRINGS.include? Open.read(path).chomp.strip
     when :tsv
       TSV.open(path)
     when :marshal_tsv
@@ -105,6 +109,8 @@ module Persist
     case (type || "nil").to_sym
     when :nil
       nil
+    when :boolean
+      Open.write(path, content ? "true" : "false")
     when :fwt
       content.file.seek 0
       Open.write(path, content.file.read)
@@ -113,7 +119,7 @@ module Persist
     when :string, :text
       Open.write(path, content)
     when :array
-      Open.write(path, content * "\n" + "\n")
+      Open.write(path, content * "\n")
     when :marshal_tsv
       Open.write(path, Marshal.dump(content.dup))
     when :marshal

data/lib/rbbt/tsv.rb

@@ -86,7 +86,18 @@ module TSV
     data.extend TSV unless TSV === data
     data.unnamed = true
 
-    data.serializer = parser.type if data.serializer == :type
+    if data.serializer == :type
+      data.serializer = case
+                        when parser.cast.nil?
+                          data.serializer = parser.type
+                        when (parser.cast == :to_i and parser.type == :list)
+                          data.serializer = :integer_array
+                        when (parser.cast == :to_i and parser.type == :single)
+                          data.serializer = :integer
+                        when (parser.cast == :to_f and parser.type == :single)
+                          data.serializer = :float
+                        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
@@ -120,6 +131,8 @@ module TSV
       rescue Parser::SKIP_LINE
         line = stream.gets
         next
+      rescue Parser::END_PARSING
+        break
       rescue IOError
         break
       end

data/lib/rbbt/tsv/accessor.rb

@@ -145,8 +145,19 @@ module TSV
       elems = collect
     else
       elems = []
-      through :key, field do |key, fields|
-        elems << [key, fields.first]
+      case type
+      when :single
+        through :key, field do |key, field|
+          elems << [key, field]
+        end
+      when :list, :flat
+        through :key, field do |key, fields|
+          elems << [key, fields.first]
+        end
+      when :double
+        through :key, field do |key, fields|
+          elems << [key, fields.first]
+        end
       end
     end
 

data/lib/rbbt/tsv/attach.rb

@@ -42,6 +42,8 @@ module TSV
         done = is.eof?
       end
 
+      os.puts [current_key, current_parts].flatten * sep unless current_key.nil?
+
     end
   end
 

data/lib/rbbt/tsv/manipulate.rb

@@ -1,6 +1,7 @@
 require 'progress-bar'
 require 'rbbt/persist'
 require 'rbbt/tsv/util'
+require 'set'
 
 module TSV
   
@@ -57,27 +58,27 @@ module TSV
 
       raise "Key field #{ new_key_field } not found" if @new_key_field.nil?
       @new_fields = case
-                   when new_fields.nil?
-                     case 
-                     when @new_key_field == :key
-                       :all
-                     when fields.nil?
-                       - @new_key_field
-                     else 
-                       new = (0..fields.length - 1).to_a
-                       new.delete_at(@new_key_field)
-                       new.unshift :key
-                       new
-                     end
-                   else
-                     if Array === new_fields
-                       new_fields.collect do |field|
-                         TSV.identify_field(key_field, fields, field)
-                       end
-                     else
-                       [TSV.identify_field(key_field, fields, new_fields)]
-                     end
-                   end
+                    when new_fields.nil?
+                      case 
+                      when @new_key_field == :key
+                        :all
+                      when fields.nil?
+                        - @new_key_field
+                      else 
+                        new = (0..fields.length - 1).to_a
+                        new.delete_at(@new_key_field)
+                        new.unshift :key
+                        new
+                      end
+                    when Array === new_fields
+                      new_fields.collect do |field|
+                        TSV.identify_field(key_field, fields, field)
+                      end
+                    when (String === new_fields or Symbol === new_fields)
+                      [TSV.identify_field(key_field, fields, new_fields)]
+                    else
+                      raise "Unknown format for new_fields (should be nil, Array or String): #{new_fields.inspect}"
+                    end
 
       @new_key_field_name = case 
                             when @new_key_field == :key
@@ -235,9 +236,21 @@ module TSV
         new[key] = values if yield key, values
       end
     when Array === method
+      method = Set.new method
       with_unnamed do
-        through do |key, values|
-          new[key] = values if ([key,values].flatten & method).any?
+        case type
+        when :single
+          through do |key, value|
+            new[key] = values if method.include? key or method.include? value
+          end
+        when :list, :flat
+          through do |key, values|
+            new[key] = values if method.include? key or (method & values).any?
+          end
+        else
+          through do |key, values|
+            new[key] = values if method.include? key or (method & values.flatten).any?
+          end
         end
       end
     when Regexp === method
@@ -273,9 +286,24 @@ module TSV
         end
       when Array === method
         with_unnamed do
-          through :key, key do |key, values|
-            values = [values] if type == :single
-            new[key] = self[key] if (values.flatten & method).any?
+          method = Set.new method unless Set === method
+          case type
+          when :single
+            through :key, key do |key, value|
+              new[key] = self[key] if method.include? value
+            end
+          when :list
+            through :key, key do |key, values|
+              new[key] = self[key] if method.include? value.first
+            end
+          when :flat #untested
+            through :key, key do |key, values|
+              new[key] = self[key] if (method & values.flatten).any?
+            end
+          else
+            through :key, key do |key, values|
+              new[key] = self[key] if (method & values.first).any?
+            end
           end
         end
       when Regexp === method

data/lib/rbbt/tsv/parser.rb

@@ -4,6 +4,7 @@ module TSV
     attr_accessor :header_hash, :sep, :sep2, :type, :key_position, :field_positions, :cast, :key_field, :fields, :fix, :select, :serializer, :straight
 
     class SKIP_LINE < Exception; end
+    class END_PARSING < Exception; end
 
     def all_fields
       all = [key_field] + fields
@@ -49,6 +50,7 @@ module TSV
       l = line.chomp
       raise Parser::SKIP_LINE if Proc === @select and not @select.call l
       l = @fix.call l if Proc === @fix
+      raise Parser::END_PARSING unless l
       l
     end
 
@@ -85,6 +87,22 @@ module TSV
       data[key] = values unless data.include? key
     end
 
+    def add_to_data_flat(data, keys, values)
+      keys.each do |key|
+        data[key] = values.flatten unless data.include? key
+      end
+    end
+
+    def add_to_data_flat_merge(data, keys, values)
+      keys.each do |key|
+        if data.include? key
+          data[key] = data[key].concat values.flatten 
+        else
+          data[key] = values.flatten
+        end
+      end
+    end
+
     def add_to_data_no_merge_double(data, keys, values)
       keys.each do |key|
         data[key] = values unless data.include? key
@@ -168,7 +186,9 @@ module TSV
             when Integer === field
               field
             when String === field
-              @fields.dup.unshift(@key_field).index field
+              pos = @fields.dup.unshift(@key_field).index field
+              raise "Field not identified: #{ field }" if pos.nil?
+              pos
             else
               raise "Format of fields not understood: #{fields.inspect}"
             end
@@ -196,7 +216,8 @@ module TSV
       @fix = Misc.process_options(options, :fix) 
       @select= Misc.process_options options, :select
 
-      if @type == :double
+      case @type
+      when :double 
         self.instance_eval do alias get_values get_values_double end
         self.instance_eval do alias cast_values cast_values_double end
         if merge
@@ -204,15 +225,22 @@ module TSV
         else
           self.instance_eval do alias add_to_data add_to_data_no_merge_double end
         end
-      else
-        if @type == :single
-          self.instance_eval do alias get_values get_values_single end
-          self.instance_eval do alias cast_values cast_values_single end
+      when :single
+        self.instance_eval do alias get_values get_values_single end
+        self.instance_eval do alias cast_values cast_values_single end
+        self.instance_eval do alias add_to_data add_to_data_no_merge_list end
+      when :list
+        self.instance_eval do alias get_values get_values_list end
+        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
+        self.instance_eval do alias get_values get_values_double 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
         else
-          self.instance_eval do alias get_values get_values_list end
-          self.instance_eval do alias cast_values cast_values_list end
+          self.instance_eval do alias add_to_data add_to_data_flat end
         end
-        self.instance_eval do alias add_to_data add_to_data_no_merge_list end
       end
 
       fix_fields(options)

data/lib/rbbt/util/chain_methods.rb

@@ -1,7 +1,7 @@
 require 'rbbt/util/log'
 
 module ChainMethods
-  def self.extended(base)
+  def self.chain_methods_extended(base)
     if not base.respond_to? :chain_prefix
       metaclass = class << base
         attr_accessor :chain_prefix, :chained_methods
@@ -52,7 +52,10 @@ module ChainMethods
 
       if not metaclass.respond_to? :extended
         metaclass.module_eval do
+          alias prev_chain_methods_extended extended
+
           def extended(base)
+            prev_chain_methods_extended(base)
             setup_chains(base)
           end
         end
@@ -61,4 +64,11 @@ module ChainMethods
 
     base.chain_prefix = base.to_s.downcase.to_sym
   end
+  
+  def self.extended(base)
+    chain_methods_extended(base)
+  end
+
+
+
 end

data/lib/rbbt/util/cmd.rb

@@ -83,7 +83,7 @@ module CMD
       when TrueClass === value
         string << "#{option} "
       else
-        if option.chars.to_a.last == "="
+        if option.to_s.chars.to_a.last == "="
           string << "#{option}#{value} "
         else
           string << "#{option} #{value} "

data/lib/rbbt/util/misc.rb

@@ -1,10 +1,18 @@
 require 'lockfile'
 require 'rbbt/util/chain_methods'
 require 'rbbt/resource/path'
+require 'rbbt/annotations'
 
 module Misc
   class FieldNotFoundError < StandardError;end
 
+  def self.counts(array)
+    counts = Hash.new 0
+    array.each do |e|
+      counts[e] += 1
+    end
+    counts
+  end
   
   IUPAC2BASE = {
     "A" => ["A"],
@@ -261,7 +269,7 @@ module Misc
     when String === options
       new_options = string2hash options
     else
-      raise "Format of '#{options.inspect}' not understood"
+      raise "Format of '#{options.inspect}' not understood. It should be a hash"
     end
     defaults.each do |key, value|
       next unless new_options[key].nil?
@@ -444,7 +452,41 @@ module NamedArray
   end
 
   def named_array_get_brackets(key)
-    named_array_clean_get_brackets(Misc.field_position(fields, key))
+    if defined? Entity
+      entity = (defined?(Entity) and Entity.respond_to?(:formats)) ? Entity.formats[key] : nil
+      if entity
+        if entity.annotations.first == :format
+          entity.setup(named_array_clean_get_brackets(Misc.field_position(fields, key)), key)
+        else
+          entity.setup(named_array_clean_get_brackets(Misc.field_position(fields, key)))
+        end
+      else
+        named_array_clean_get_brackets(Misc.field_position(fields, key))
+      end
+    else
+      named_array_clean_get_brackets(Misc.field_position(fields, key))
+    end
+  end
+
+  def named_array_each(&block)
+    if defined?(Entity) and not fields.nil? and not fields.empty?
+      fields.zip(self) do |field,elem|
+        entity = (defined?(Entity) and Entity.respond_to?(:formats)) ? Entity.formats[field] : nil
+        if entity
+          elem = elem.dup if elem.frozen?
+          if entity.annotations.first == :format
+            elem = entity.setup(elem, field) 
+          else
+            elem = entity.setup(elem)
+          end
+        else
+        end
+        yield(elem)
+        elem
+      end
+    else
+      named_array_clean_each &block
+    end
   end
 
   def named_array_set_brackets(key,value)

data/lib/rbbt/workflow.rb

@@ -9,7 +9,7 @@ module Workflow
   end
   self.workflows = []
 
-  def self.require_workflow(wf_name, wf_dir = nil)
+  def self.require_local_workflow2(wf_name, wf_dir = nil)
     require 'rbbt/resource/path'
 
     if File.exists?(wf_name) or File.exists?(wf_name + '.rb')
@@ -46,6 +46,103 @@ module Workflow
     require wf_dir["workflow.rb"].find
   end
 
+  def self.require_remote_workflow(wf_name, url)
+    require 'rbbt/workflow/rest/client'
+    eval "Object::#{wf_name} = RbbtRestClient.new '#{ url }', '#{wf_name}'"
+  end
+
+  def self.require_local_workflow(wf_name)
+    if Path === wf_name
+      case
+
+        # Points to workflow file
+      when ((File.exists?(wf_name.find) and not File.directory?(wf_name.find)) or File.exists?(wf_name.find + '.rb')) 
+        $LOAD_PATH.unshift(File.join(File.expand_path(File.dirname(wf_name.find)), 'lib'))
+        require wf_name.find
+        Log.debug "Workflow loaded from file: #{ wf_name }"
+        return true
+
+        # Points to workflow dir
+      when (File.exists?(wf_name.find) and File.directory?(wf_name.find) and File.exists?(File.join(wf_name.find, 'workflow.rb')))
+        $LOAD_PATH.unshift(File.join(File.expand_path(wf_name.find), 'lib'))
+        require File.join(wf_name.find, 'workflow.rb')
+        Log.debug "Workflow loaded from directory: #{ wf_name }"
+        return true
+
+      else
+        raise "Workflow path was not resolved: #{ wf_name } (#{wf_name.find})"
+      end
+
+    else
+      case
+
+        # Points to workflow file
+      when ((File.exists?(wf_name) and not File.directory?(wf_name)) or File.exists?(wf_name + '.rb')) 
+        $LOAD_PATH.unshift(File.join(File.expand_path(File.dirname(wf_name)), 'lib'))
+        require wf_name
+        Log.debug "Workflow loaded from file: #{ wf_name }"
+        return true
+
+      when (defined?(Rbbt) and Rbbt.etc.workflow_dir.exists?)
+        dir = Rbbt.etc.workflow_dir.read.strip
+        dir = File.join(dir, wf_name)
+        $LOAD_PATH.unshift(File.join(File.expand_path(dir), 'lib'))
+        require File.join(dir, 'workflow.rb')
+        Log.debug "Workflow #{wf_name} loaded from workflow_dir: #{ dir }"
+        return true
+
+      when defined?(Rbbt)
+        path = Rbbt.workflows[wf_name].find
+        $LOAD_PATH.unshift(File.join(File.expand_path(path), 'lib'))
+        require File.join(path, 'workflow.rb')
+        Log.debug "Workflow #{wf_name} loaded from Rbbt.workflows: #{ path }"
+        return true
+
+      else
+        path = File.join(ENV['HOME'], '.workflows', wf_name)
+        $LOAD_PATH.unshift(File.join(File.expand_path(path), 'lib'))
+        require File.join(path, 'workflow.rb')
+        Log.debug "Workflow #{wf_name} loaded from .workflows: #{ path }"
+        return true
+      end
+    end
+
+    raise "Workflow not found: #{ wf_name }"
+  end
+
+  def self.require_workflow(wf_name)
+    begin
+      Misc.string2const wf_name
+      Log.debug "Workflow #{ wf_name } already loaded"
+      return true
+    rescue Exception
+    end
+
+    if Rbbt.etc.remote_workflows.exists?
+      remote_workflows = Rbbt.etc.remote_workflows.yaml
+      if remote_workflows.include? wf_name
+        url = remote_workflows[wf_name]
+        require_remote_workflow(wf_name, url)
+        Log.debug "Workflow #{ wf_name } loaded remotely: #{ url }"
+        return
+      end
+    end
+
+    begin
+      require_local_workflow(wf_name) 
+    rescue Exception
+      Log.debug $!.message 
+      raise "Workflow not found: #{ wf_name }" if wf_name == wf_name.downcase
+      Log.debug "Trying with downcase: '#{wf_name.downcase}'"
+      begin
+        require_local_workflow(wf_name.downcase)
+      rescue Exception
+        Log.debug $!.message
+        raise "Workflow not found: #{ wf_name }"
+      end
+    end
+  end
+
   def self.extended(base)
     if not base.respond_to? :workdir
       base.extend AnnotatedModule
@@ -59,7 +156,7 @@ module Workflow
         def task_dependencies
           IndiferentHash.setup(@task_dependencies || {})
         end
- 
+
         def tasks
           IndiferentHash.setup(@tasks || {})
         end
@@ -83,7 +180,7 @@ module Workflow
   end
 
   # {{{ Task definition helpers
-  
+
   def task(name, &block)
     if Hash === name
       result_type = name.first.last
@@ -104,7 +201,8 @@ module Workflow
       :input_types => input_types,
       :result_type => Array == result_type ? result_type.to_sym : result_type,
       :input_defaults => input_defaults,
-      :input_descriptions => input_descriptions
+      :input_descriptions => input_descriptions,
+      :result_description => result_description
     }, &block)
 
     @last_task = task
@@ -125,7 +223,7 @@ module Workflow
   end
 
   # {{{ Job management
-  
+
   def resolve_locals(inputs)
     inputs.each do |name, value|
       if value =~ /^local:(.*?):(.*)/ or 
@@ -172,7 +270,7 @@ module Workflow
     step = Step.new path, tasks[task]
     if step.info.include? :dependencies
       step.dependencies = step.info[:dependencies].collect do |task, job|
-        Step.new File.join(workdir, task.to_s, job), tasks[task]
+        load_id(File.join(task.to_s, job))
       end
     end
     step

data/lib/rbbt/workflow/accessor.rb

@@ -58,7 +58,8 @@ class Step
   end
 
   def done?
-    info[:status] == :done or info[:status] == :error
+    status = info[:status]
+    status == :done or status == :error
   end
 
   def error?
@@ -72,7 +73,10 @@ class Step
   end
 
   def files
-    Dir.glob(File.join(files_dir, '*')).collect do |path| File.basename(path) end
+    files = Dir.glob(File.join(files_dir, '**', '*')).reject{|path| File.directory? path}.collect do |path| 
+      Misc.path_relative_to(files_dir, path) 
+    end
+    files
   end
 
   def file(name)
@@ -139,6 +143,7 @@ module Workflow
   def task_info(name)
     task = tasks[name]
     description = task.description
+    result_description = task.result_description
     result_type = task.result_type
     inputs = rec_inputs(name)
     input_types = rec_input_types(name)
@@ -165,6 +170,7 @@ module Workflow
       :input_descriptions => input_descriptions,
       :input_defaults => input_defaults,
       :result_type => result_type,
+      :result_description => result_description,
       :dependencies => dependencies
     }
   end

data/lib/rbbt/workflow/annotate.rb

@@ -2,7 +2,7 @@ module AnnotatedModule
   def self.extended(base)
     if not base.respond_to? :inputs
       class << base
-        attr_accessor :description, :inputs, :input_types, :input_descriptions, :input_defaults
+        attr_accessor :description, :inputs, :input_types, :input_descriptions, :input_defaults, :result_description
 
         def description
           i = @description; @description = ""; i
@@ -27,6 +27,10 @@ module AnnotatedModule
         def description
           i = @description; @description = ""; i
         end
+
+        def result_description
+          i = @result_description; @result_description = nil; i
+        end
       end
 
       base.description = ""
@@ -38,6 +42,10 @@ module AnnotatedModule
     end
   end
 
+  def returns(text)
+    @result_description = text
+  end
+
   def desc(description)
     @description = description
   end

data/lib/rbbt/workflow/step.rb

@@ -86,11 +86,13 @@ class Step
   def clean
     if File.exists?(path) or File.exists?(info_file)
       begin
-        FileUtils.rm info_file
-        FileUtils.rm path 
-        FileUtils.rm_rf files_dir
+        FileUtils.rm info_file if File.exists? info_file
+        FileUtils.rm path if File.exists? path
+        FileUtils.rm path + '.lock' if File.exists? path + '.lock'
+        FileUtils.rm_rf files_dir if File.exists? files_dir
       end
     end
+    self
   end
 
   def rec_dependencies

data/lib/rbbt/workflow/task.rb

@@ -2,7 +2,7 @@ require 'rbbt/util/misc'
 require 'rbbt/persist'
 
 module Task
-  attr_accessor :inputs, :input_types, :result_type, :input_defaults, :input_descriptions, :description, :name
+  attr_accessor :inputs, :input_types, :result_type, :input_defaults, :input_descriptions, :description, :name, :result_description
 
   def self.setup(options = {}, &block)
     block.extend Task

data/test/rbbt/test_fix_width_table.rb

@@ -99,6 +99,7 @@ g:         ____
         assert_equal %w(), f[(20..100)].sort
         assert_equal %w(a b d), f[3].sort
         assert_equal %w(a b c d e), f[(3..4)].sort
+        assert_equal %w(a c e), f[7].sort
       end
     end
   end

data/test/rbbt/test_tsv.rb

@@ -329,4 +329,35 @@ b 2
  
   end
 
+  def test_flat_no_merge
+    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+/, :type => :flat, :fields => ["ValueA"])
+      assert_equal ["a", "aa", "aaa"], tsv["row1"]
+      assert_equal ["ValueA"], tsv.fields
+      assert_equal :flat, tsv.type
+      assert_equal "Id", tsv.key_field
+    end
+  end
+
+  def test_flat_merge
+    content =<<-EOF
+#Id    ValueA    ValueB    OtherID
+row1    a|aa|aaa    b    Id1|Id2
+row1    aaaa    b    Id1|Id2
+row2    A    B    Id3
+    EOF
+
+    TmpFile.with_file(content) do |filename|
+      tsv = TSV.open(filename, :sep => /\s+/, :merge => true, :type => :flat, :fields => ["ValueA"])
+      assert_equal ["a", "aa", "aaa", "aaaa"], tsv["row1"]
+    end
+  end
+
+
 end

data/test/rbbt/tsv/test_accessor.rb

@@ -5,7 +5,7 @@ require 'test/unit'
 
 class TestTSV < Test::Unit::TestCase
 
-  def _test_tsv
+  def test_tsv
     content =<<-EOF
 #Id    ValueA    ValueB    OtherID
 row1    a|aa|aaa    b    Id1|Id2
@@ -20,7 +20,7 @@ row2    A    B    Id3
     end
   end
 
-  def _test_named_values
+  def test_named_values
     content =<<-EOF
 #Id    ValueA    ValueB    OtherID
 row1    a|aa|aaa    b    Id1|Id2
@@ -33,7 +33,7 @@ row2    A    B    Id3
     end
   end
 
-  def _test_to_s
+  def test_to_s
     content =<<-EOF
 #Id    ValueA    ValueB    OtherID
 row1    a|aa|aaa    b    Id1|Id2
@@ -47,7 +47,7 @@ row2    A    B    Id3
     end
   end
   
-  def _test_entries
+  def test_entries
     content =<<-EOF
 #Id    ValueA    ValueB    OtherID
 row1    a|aa|aaa    b    Id1|Id2
@@ -61,7 +61,7 @@ row2    A    B    Id3
  
   end
 
-  def _test_marshal
+  def test_marshal
     content =<<-EOF
 #Id    ValueA    ValueB    OtherID
 row1    a|aa|aaa    b    Id1|Id2
@@ -74,12 +74,12 @@ row2    A    B    Id3
     end
   end
 
-  def _test_zip_fields
+  def test_zip_fields
     a = [%w(1 2), %w(a b)]
     assert_equal a, TSV.zip_fields(TSV.zip_fields(a))
   end
 
-  def _test_indentify_fields
+  def test_indentify_fields
     content =<<-EOF
 #ID ValueA ValueB Comment
 row1 a b c
@@ -92,7 +92,7 @@ row2 A B C
     end
   end
 
-  def _test_sort
+  def test_sort
     content =<<-EOF
 #ID ValueA ValueB Comment
 row1 a B c
@@ -110,7 +110,7 @@ row2 A b C
     end
   end
 
-  def _test_sort_by
+  def test_sort_by
     content =<<-EOF
 #ID ValueA ValueB Comment
 row1 a B c
@@ -146,7 +146,7 @@ row6 A b a
   end
 
 
-  def _test_sort_by_with_proc
+  def test_sort_by_with_proc
     content =<<-EOF
 #Id    ValueA    ValueB    OtherID    Pos
 row1    a|aa|aaa    b    Id1|Id2    2

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: rbbt-util
 version: !ruby/object:Gem::Version 
-  hash: 63
-  prerelease: false
+  hash: 61
+  prerelease: 
   segments: 
   - 4
   - 0
-  - 0
-  version: 4.0.0
+  - 1
+  version: 4.0.1
 platform: ruby
 authors: 
 - Miguel Vazquez
@@ -15,7 +15,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-09-07 00:00:00 +02:00
+date: 2011-10-03 00:00:00 +02:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -117,7 +117,7 @@ dependencies:
   type: :runtime
   version_requirements: *id007
 description: Utilities for handling tsv files, caches, etc
-email: miguel.vazquez@fdi.ucm.es
+email: miguel.vazquez@cnio.es
 executables: 
 - tsv.rb
 - tchash.rb
@@ -237,7 +237,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
 requirements: []
 
 rubyforge_project: 
-rubygems_version: 1.3.7
+rubygems_version: 1.6.2
 signing_key: 
 specification_version: 3
 summary: Utilities for the Ruby Bioinformatics Toolkit (rbbt)