Class: TSV::Parser

Inherits:
Object
  • Object
show all
Defined in:
lib/rbbt/tsv/parser.rb

Defined Under Namespace

Classes: END_PARSING, SKIP_LINE

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(stream = nil, options = {}) ⇒ Parser

Returns a new instance of Parser.



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# File 'lib/rbbt/tsv/parser.rb', line 383

def initialize(stream = nil, options = {})
  @header_hash = Misc.process_options(options, :header_hash) || "#"
  @sep = Misc.process_options(options, :sep) || "\t"
  stream = TSV.get_stream stream
  @stream = stream


  header_options = parse_header(stream)

  options = header_options.merge options

  @type ||= Misc.process_options(options, :type) || :double
  @type ||= :double

  @identifiers = Misc.process_options(options, :identifiers) 

  @filename = Misc.process_options(options, :filename) 
  @filename ||= stream.filename if stream.respond_to? :filename

  @sep2 = Misc.process_options(options, :sep2) || "|"
  @cast = Misc.process_options options, :cast; @cast = @cast.to_sym if String === @cast
  @type ||= Misc.process_options options, :type
  @fix = Misc.process_options(options, :fix) 
  @select= Misc.process_options options, :select
  @zipped = Misc.process_options options, :zipped
  @namespace = Misc.process_options options, :namespace
  merge = Misc.process_options(options, :merge)
  merge = @zipped if merge.nil?
  merge = false if merge.nil?

  fields = options[:fields]
  fix_fields(options)

  @type = @type.strip.to_sym if String === @type
  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
    case
    when (merge and not zipped)
        self.instance_eval do alias add_to_data add_to_data_merge end
    when (merge and zipped)
        self.instance_eval do alias add_to_data add_to_data_merge_zipped end
    when zipped
        self.instance_eval do alias add_to_data add_to_data_zipped end
    else
      self.instance_eval do alias add_to_data add_to_data_no_merge_double end
    end
  when :single
    if header_options[:type] == :flat
      self.instance_eval do alias get_values get_values_single_from_flat 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_double end
    else
      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
    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
    @take_all = true if field_positions.nil?
    self.instance_eval do alias cast_values cast_values_flat end
    merge = true if key_position and key_position != 0 and field_positions.nil?
    if merge 
      self.instance_eval do alias get_values get_values_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_double end
      end
    else
      self.instance_eval do alias get_values get_values_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
  else
    raise "Unknown TSV type: #{@type.inspect}"
  end


  @straight = false if @sep != "\t" or not @cast.nil? or merge or (@type == :flat and fields)
end

Instance Attribute Details

#cast ⇒ Object

Returns the value of attribute cast.



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# File 'lib/rbbt/tsv/parser.rb', line 4

def cast
  @cast
end

#field_positions ⇒ Object

Returns the value of attribute field_positions.



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# File 'lib/rbbt/tsv/parser.rb', line 4

def field_positions
  @field_positions
end

#fields ⇒ Object

Returns the value of attribute fields.



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# File 'lib/rbbt/tsv/parser.rb', line 4

def fields
  @fields
end

#filename ⇒ Object

Returns the value of attribute filename.



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# File 'lib/rbbt/tsv/parser.rb', line 4

def filename
  @filename
end

#first_line ⇒ Object

Returns the value of attribute first_line.



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# File 'lib/rbbt/tsv/parser.rb', line 4

def first_line
  @first_line
end

#fix ⇒ Object

Returns the value of attribute fix.



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# File 'lib/rbbt/tsv/parser.rb', line 4

def fix
  @fix
end

#header_hash ⇒ Object

Returns the value of attribute header_hash.



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# File 'lib/rbbt/tsv/parser.rb', line 4

def header_hash
  @header_hash
end

#identifiers ⇒ Object

Returns the value of attribute identifiers.



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# File 'lib/rbbt/tsv/parser.rb', line 4

def identifiers
  @identifiers
end

#key_field ⇒ Object

Returns the value of attribute key_field.



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# File 'lib/rbbt/tsv/parser.rb', line 4

def key_field
  @key_field
end

#key_position ⇒ Object

Returns the value of attribute key_position.



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# File 'lib/rbbt/tsv/parser.rb', line 4

def key_position
  @key_position
end

#namespace ⇒ Object

Returns the value of attribute namespace.



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# File 'lib/rbbt/tsv/parser.rb', line 4

def namespace
  @namespace
end

#preamble ⇒ Object

Returns the value of attribute preamble.



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# File 'lib/rbbt/tsv/parser.rb', line 4

def preamble
  @preamble
end

#select ⇒ Object

Returns the value of attribute select.



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# File 'lib/rbbt/tsv/parser.rb', line 4

def select
  @select
end

#sep ⇒ Object

Returns the value of attribute sep.



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# File 'lib/rbbt/tsv/parser.rb', line 4

def sep
  @sep
end

#sep2 ⇒ Object

Returns the value of attribute sep2.



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# File 'lib/rbbt/tsv/parser.rb', line 4

def sep2
  @sep2
end

#serializer ⇒ Object

Returns the value of attribute serializer.



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# File 'lib/rbbt/tsv/parser.rb', line 4

def serializer
  @serializer
end

#straight ⇒ Object

Returns the value of attribute straight.



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# File 'lib/rbbt/tsv/parser.rb', line 4

def straight
  @straight
end

#stream ⇒ Object

Returns the value of attribute stream.



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# File 'lib/rbbt/tsv/parser.rb', line 4

def stream
  @stream
end

#take_all ⇒ Object

Returns the value of attribute take_all.



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# File 'lib/rbbt/tsv/parser.rb', line 4

def take_all
  @take_all
end

#type ⇒ Object

Returns the value of attribute type.



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# File 'lib/rbbt/tsv/parser.rb', line 4

def type
  @type
end

#zipped ⇒ Object

Returns the value of attribute zipped.



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# File 'lib/rbbt/tsv/parser.rb', line 4

def zipped
  @zipped
end

Class Method Details

.traverse(stream, options = {}, &block) ⇒ Object 



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# File 'lib/rbbt/tsv/parser.rb', line 593

def self.traverse(stream, options = {}, &block)
  parser = Parser.new(stream, options)
  parser.traverse(options, &block)
end

Instance Method Details

#add_to_data_flat(data, key, values) ⇒ Object 



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# File 'lib/rbbt/tsv/parser.rb', line 183

def add_to_data_flat(data, key, values)
  data[key] = values unless data.include? key
  nil
end

#add_to_data_flat_keys(data, key, values) ⇒ Object 



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# File 'lib/rbbt/tsv/parser.rb', line 178

def add_to_data_flat_keys(data, key, values)
  data[key] = values unless data.include? key
  nil
end

#add_to_data_flat_merge(data, key, values) ⇒ Object 



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# File 'lib/rbbt/tsv/parser.rb', line 188

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

#add_to_data_flat_merge_double(data, keys, values) ⇒ Object 



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# File 'lib/rbbt/tsv/parser.rb', line 197

def add_to_data_flat_merge_double(data, keys, values)
  keys.each do |key|
    if data.include? key
      data[key] = data[key].concat values
    else
      data[key] = values
    end
  end
  nil
end

#add_to_data_flat_merge_keys(data, keys, values) ⇒ Object 



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# File 'lib/rbbt/tsv/parser.rb', line 208

def add_to_data_flat_merge_keys(data, keys, values)
  keys.each do |key|
    if data.include? key
      data[key] = data[key].concat values
    else
      data[key] = values.dup
    end
  end
  nil
end

#add_to_data_merge(data, keys, values) ⇒ Object 



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# File 'lib/rbbt/tsv/parser.rb', line 227

def add_to_data_merge(data, keys, values)
  keys.uniq.each do |key|
    if data.include? key
      new = data[key]
      new.each_with_index do |old, i|
        old.concat values[i]
      end
      data[key] = new
    else
      data[key] = values
    end
  end
  nil
end

#add_to_data_merge_zipped(data, keys, values) ⇒ Object 



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# File 'lib/rbbt/tsv/parser.rb', line 242

def add_to_data_merge_zipped(data, keys, values)
  num = keys.length

  if values.first.length > 1 and num == 1
    keys = keys * values.first.length
    num = keys.length
  end

  values = values.collect{|v| v.length != num ? [v.first] * num : v}
  all = values.unshift keys
  Misc.zip_fields(all).each do |values|
    key = values.shift
    if data.include? key
      data[key] = data[key].zip(values).collect do |old, new|
        old.push new
        old
      end
    else
      data[key] = values.collect{|v| [v]}
    end
  end
  nil
end

#add_to_data_no_merge_double(data, keys, values) ⇒ Object 



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# File 'lib/rbbt/tsv/parser.rb', line 219

def add_to_data_no_merge_double(data, keys, values)
  keys.each do |key|
    next if data.include? key
    data[key] = values 
  end
  nil
end

#add_to_data_no_merge_list(data, key, values) ⇒ Object 



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# File 'lib/rbbt/tsv/parser.rb', line 173

def add_to_data_no_merge_list(data, key, values)
  data[key] = values unless data.include? key
  nil
end

#add_to_data_zipped(data, keys, values) ⇒ Object 



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# File 'lib/rbbt/tsv/parser.rb', line 266

def add_to_data_zipped(data, keys, values)
  num = keys.length

  if values.first.length > 1 and num == 1
    keys = keys * values.first.length
    num = keys.length
  end

  values = values.collect{|v| v.length != num ? [v.first] * num : v}
  all = values.unshift keys
  Misc.zip_fields(all).each do |values|
    key = values.shift
    next if data.include? key
    data[key] = values.collect{|v| [v]}
  end
  nil
end

#all_fields ⇒ Object 



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# File 'lib/rbbt/tsv/parser.rb', line 9

def all_fields
  all = [key_field] + fields
  NamedArray.setup all, all
end

#annotate(data) ⇒ Object 



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# File 'lib/rbbt/tsv/parser.rb', line 484

def annotate(data)
  setup(data)
end

#cast? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rbbt/tsv/parser.rb', line 69

def cast?
  !! @cast
end

#cast_values_double(values) ⇒ Object 



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# File 'lib/rbbt/tsv/parser.rb', line 312

def cast_values_double(values)
  case
  when Symbol === cast
    values.collect{|list| list.collect{|v| v.send(cast)}}
  when Proc === cast
    values.collect{|list| list.collect{|v| cast.call v }}
  end
end

#cast_values_flat(values) ⇒ Object 



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# File 'lib/rbbt/tsv/parser.rb', line 303

def cast_values_flat(values)
  case
  when Symbol === cast
    values.collect{|v| v.send(cast)}
  when Proc === cast
    values.collect{|v| cast.call v }
  end
end

#cast_values_list(values) ⇒ Object 



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# File 'lib/rbbt/tsv/parser.rb', line 294

def cast_values_list(values)
  case
  when Symbol === cast
    values.collect{|v| v.send(cast)}
  when Proc === cast
    values.collect{|v| cast.call v}
  end
end

#cast_values_single(value) ⇒ Object 



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# File 'lib/rbbt/tsv/parser.rb', line 285

def cast_values_single(value)
  case
  when Symbol === cast
    value.send(cast)
  when Proc === cast
    cast.call value
  end
end

#chop_line(line) ⇒ Object 



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# File 'lib/rbbt/tsv/parser.rb', line 73

def chop_line(line)
  @sep == " " ? line.split(/ /, -1) : line.split(@sep, -1)
end

#fix_fields(options) ⇒ Object 



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# File 'lib/rbbt/tsv/parser.rb', line 325

def fix_fields(options)
  key_field = Misc.process_options options, :key_field
  fields    = Misc.process_options options, :fields


  if (key_field.nil? or key_field == 0 or key_field == :key) and
    (fields.nil? or fields == @fields or (not @fields.nil? and fields == (1..@fields.length).to_a))

    @straight = true
    return
  else
    @straight = false

    case
    when (key_field.nil? or (not Integer === key_field and @key_field.nil?) or key_field == @key_field or key_field == 0)
      @key_position = 0
    when Integer === key_field
      @key_position = key_field
    when String === key_field
      @key_position = @fields.dup.unshift(@key_field).index key_field
      raise "Key field #{ key_field } was not found" if @key_position.nil?
    when :key == key_field
      @key_position = 0
    else
      raise "Format of key_field not understood: #{key_field.inspect}"
    end

    if (fields.nil? or (not (Array === fields and Integer === fields.first) and @fields.nil?) or fields == @fields or (not @fields.nil? and fields == (1..@fields.length).to_a))
      if not @fields.nil? and type != :flat
        @field_positions = (0..@fields.length).to_a
        @field_positions.delete @key_position
      end
    else
      fields = [fields] if not Array === fields
      @field_positions = fields.collect{|field|
        case
        when Integer === field
          field
        when String === 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: #{field.inspect}"
        end
      }
    end

    new_key_field = @fields.dup.unshift(@key_field)[@key_position] if not @fields.nil?
    @fields = @fields.dup.unshift(@key_field).values_at *@field_positions if not @fields.nil? and not @field_positions.nil?
    @fields ||= fields if Array === fields and String === fields.first
    @fields = [@key_field] if new_key_field != @key_field and type == :flat and @field_positions.nil?
    @key_field = new_key_field 
    @key_field ||= key_field if String === key_field

  end
end

#get_values_double(parts) ⇒ Object 



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# File 'lib/rbbt/tsv/parser.rb', line 111

def get_values_double(parts)
  return parts.shift.split(@sep2, -1), parts.collect{|value| value.split(@sep2, -1)} if field_positions.nil? and key_position.nil?
  keys = parts[key_position].split(@sep2, -1)
  values = case
           when field_positions.nil?
            parts.tap{|o| o.delete_at key_position}
           when field_positions.empty?
             []
           else
             parts.values_at *field_positions
           end.collect{|value| value.nil? ? [] : value.split(@sep2, -1) }
  [keys, values]
end

#get_values_flat(parts) ⇒ Object 



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# File 'lib/rbbt/tsv/parser.rb', line 167

def get_values_flat(parts)
  keys, values = get_values_flat_merge(parts)
  [keys.first, values]
end

#get_values_flat_inverse(parts) ⇒ Object 



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# File 'lib/rbbt/tsv/parser.rb', line 125

def get_values_flat_inverse(parts)
  value = parts.shift
  keys = parts
  [keys, [value]]
end

#get_values_flat_merge(parts) ⇒ Object 



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# File 'lib/rbbt/tsv/parser.rb', line 132

def get_values_flat_merge(parts)
  begin
    orig = parts

    if key_position and key_position != 0 and field_positions.nil?
      value = parts.shift.split(@sep2, -1)
      keys = parts.collect{|p| p.split(@sep2, -1) }.flatten
      return [keys, value]
    end

    return parts.shift.split(@sep2, -1), parts.collect{|value| value.split(@sep2, -1)}.flatten if 
    field_positions.nil? and (key_position.nil? or key_position == 0)
  rescue
    raise $!
  end

  str = parts[key_position]
  keys = str.split(@sep2, -1)

  if @take_all
    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 = values.split(@sep2, -1)
  end

  [keys, values]
end

#get_values_list(parts) ⇒ Object 



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# File 'lib/rbbt/tsv/parser.rb', line 95

def get_values_list(parts)
  return parts.shift, parts if field_positions.nil? and key_position.nil?
  key = parts[key_position]

  values = case
           when field_positions.nil?
            parts.tap{|o| o.delete_at key_position}
           when field_positions.empty?
             []
           else
            parts.values_at *field_positions
           end

  [key, values]
end

#get_values_single(parts) ⇒ Object 



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# File 'lib/rbbt/tsv/parser.rb', line 88

def get_values_single(parts)
  return parts.shift, parts.first if field_positions.nil? and key_position.nil?
  key = parts[key_position]
  value = parts[(field_positions.nil? or field_positions.empty?) ? 0 : field_positions.first]
  [key, value]
end

#get_values_single_from_flat(parts) ⇒ Object 



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# File 'lib/rbbt/tsv/parser.rb', line 77

def get_values_single_from_flat(parts)
  return parts.shift, parts.first if field_positions.nil? and key_position.nil?
  if key_position == 0
    [parts.shift, parts.first]
  else
    key = parts.shift
    [parts, key]
  end

end

#identify_field(field) ⇒ Object 



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# File 'lib/rbbt/tsv/parser.rb', line 589

def identify_field(field)
  TSV.identify_field(key_field, fields, field)
end

#options ⇒ Object 



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# File 'lib/rbbt/tsv/parser.rb', line 488

def options
  options = {}
  TSV::ENTRIES.each do |entry|
    if self.respond_to? entry
      value = self.send(entry) 
      options[entry.to_sym] = value unless value.nil?
    end
  end
  options[:sep] = @sep if @sep and @sep != "\t" and @sep != /\t/
  IndiferentHash.setup options
end

#parse_header(stream) ⇒ Object 



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# File 'lib/rbbt/tsv/parser.rb', line 14

def parse_header(stream)
  options = {}
  @preamble = []

  # Get line

  #Thread.pass while IO.select([stream], nil, nil, 1).nil? if IO === stream
  line = stream.gets
  return {} if line.nil?
  #raise "Empty content: #{ stream.inspect }" if line.nil?
  line = Misc.fixutf8 line.chomp

  # Process options line

  if line and line =~ /^#{@header_hash}: (.*)/
    options = Misc.string2hash $1.chomp
    line = stream.gets
    line = Misc.fixutf8 line.chomp if line
  end

  # Determine separator

  @sep = options[:sep] if options[:sep]

  # Process fields line

  preamble << line if line
  while line and Misc.fixutf8(line) =~ /^#{@header_hash}/ 
    @fields = line.split(@sep)
    @key_field = @fields.shift
    @key_field = @key_field[(0 + header_hash.length)..-1] # Remove initial hash character

    #Thread.pass while IO.select([stream], nil, nil, 1).nil? if IO === stream
    line = (@header_hash != "" ?  stream.gets : nil)
    line = Misc.fixutf8 line.chomp if line
    preamble << line if line
  end

  @preamble = preamble[0..-3] * "\n"

  line ||= stream.gets

  @first_line = line

  options
end

#process(line) ⇒ Object

Raises:



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# File 'lib/rbbt/tsv/parser.rb', line 61

def process(line)
  l = line.chomp
  raise SKIP_LINE if l[0] == "#"[0] or (Proc === @select and not @select.call l)
  l = @fix.call l if Proc === @fix
  raise END_PARSING unless l
  l
end

#rescue_first_line ⇒ Object 



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# File 'lib/rbbt/tsv/parser.rb', line 321

def rescue_first_line
  @first_line
end

#setup(data) ⇒ Object 



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# File 'lib/rbbt/tsv/parser.rb', line 472

def setup(data)
  data.extend TSV unless TSV === data
  data.type = @type
  data.key_field = @key_field
  data.fields = @fields
  data.namespace = @namespace
  data.filename = @filename
  data.identifiers = @identifiers
  data.cast = @cast if Symbol === @cast
  data
end

#traverse(options = {}) ⇒ Object 



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# File 'lib/rbbt/tsv/parser.rb', line 500

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 and false
  #  stream.rewind if stream.eof?
  #  stream = Open.grep(stream, grep, invert_grep)
  #  self.first_line = stream.gets
  #end

  # first line
  line = self.rescue_first_line

  progress_monitor, monitor = monitor, nil if Log::ProgressBar === monitor
  # 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
    size = nil if size.to_i == 0
    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 = Log::ProgressBar.new(size, :desc => desc)
  end

  # parser 
  line_num = 1
  begin

    while not line.nil? 
      begin
        #progress_monitor.tick(stream.pos) if progress_monitor 
        progress_monitor.tick if progress_monitor 

        raise SKIP_LINE if line.empty?

        line = Misc.fixutf8(line)
        line = self.process line
        raise SKIP_LINE if line.empty?
        parts = self.chop_line line
        key, values = self.get_values parts
        values = self.cast_values values if self.cast?
        
        yield key, values

        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
        stream.close unless stream.closed?
        begin stream.join; rescue Exception; end if stream.respond_to? :join and not stream.joined?
        break
      rescue Errno::EPIPE
        Log.error "Pipe closed while parsing #{Misc.fingerprint stream}: #{$!.message}"
        stream.abort if stream.respond_to? :abort
        raise $!
      rescue Exception
        Log.error "Exception parsing #{Misc.fingerprint stream}: #{$!.message}"
        stream.abort $! if stream.respond_to? :abort
        raise $!
      end
    end
  ensure
    stream.close unless stream.closed?
    stream.join if stream.respond_to? :join and not stream.joined?
  end

  self
end