Module: Annotated

Defined in:
lib/rbbt/annotations.rb,
lib/rbbt/annotations/util.rb

Overview

{{{ ANNOTATED

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Instance Attribute Details

#container ⇒ Object

Returns the value of attribute container.



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# File 'lib/rbbt/annotations.rb', line 9

def container
  @container
end

#container_index ⇒ Object

Returns the value of attribute container_index.



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# File 'lib/rbbt/annotations.rb', line 9

def container_index
  @container_index
end

Class Method Details

.flatten(array) ⇒ Object 



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# File 'lib/rbbt/annotations/util.rb', line 5

def self.flatten(array)
  return array unless Array === array and not array.empty?
  array.extend AnnotatedArray if Annotated === array
  return array.flatten if AnnotatedArray === array
  begin
    return array if array.compact.collect{|e| e.info }.uniq.length > 1
  rescue
    return array
  end
  array.compact.first.annotate(array.flatten).tap{|a| a.extend AnnotatedArray }
end

.load_entity(object, info) ⇒ Object 



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# File 'lib/rbbt/annotations/util.rb', line 17

def self.load_entity(object, info)
  annotation_types = info.delete(:annotation_types) || info.delete("annotation_types") || []
  annotation_types = annotation_types.split("|") if String === annotation_types

  return object if annotation_types.nil? or annotation_types.empty?

  annotated_array = false
  annotated_array = true if (info.delete(:annotated_array) || info.delete("annotated_array")).to_s == "true"
  entity_id = info.delete(:entity_id) || info.delete("entity_id")

  annotation_types.each do |mod|
    begin
      mod = Misc.string2const(mod) if String === mod
      object.extend mod unless mod === object
    rescue Exception
      Log.warn "Exception loading annotation into object: #{$!.message}"
    end
  end

  object.instance_variable_set(:@annotation_values, info) 

  object.instance_variable_set(:@id, entity_id) if entity_id

  object.extend AnnotatedArray if annotated_array and Array === object

  object
end

.load_hash(hash) ⇒ Object 



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# File 'lib/rbbt/annotations/util.rb', line 239

def self.load_hash(hash)
  if Array === hash
    hash.collect{|h| load_hash(h) }
  else
    literal = hash[:literal]
    info = hash[:info]
    info[:annotation_types].each do |type|
      type = Kernel.const_get(type) if String === type
      type.setup(literal, info) 
    end
    literal
  end
end

.load_info(fields, values) ⇒ Object 



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# File 'lib/rbbt/annotations/util.rb', line 53

def self.load_info(fields, values)
  info = {}
  fields.each_with_index do |field,i|
    next if field == "literal"
    case field
    when "JSON"
      JSON.parse(values[i]).each do |key, value|
        info[key.to_sym] = value
      end
    when nil
      next
    else
      info[field.to_sym] = resolve_array(values[i])
    end
  end
  info
end

.load_tsv(tsv) ⇒ Object 



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# File 'lib/rbbt/annotations/util.rb', line 97

def self.load_tsv(tsv)
  tsv.with_unnamed do
    annotated_entities = tsv.collect do |id, values|
      Annotated.load_tsv_values(id, values, tsv.fields)
    end

    case tsv.key_field 
    when "List"
      annotated_entities.first
    else
      annotated_entities
    end
  end
end

.load_tsv_values(id, values, *fields) ⇒ Object 



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# File 'lib/rbbt/annotations/util.rb', line 71

def self.load_tsv_values(id, values, *fields)
  fields = fields.flatten
  literal_pos = fields.index "literal"

  object = case
           when literal_pos
             values[literal_pos].tap{|o| o.force_encoding(Encoding.default_external)}
           else
             id.dup
           end

  object = resolve_array(object)

  if Array === values.first
    Misc.zip_fields(values).collect do |v|
      info = load_info(fields, v)
    end
  else
    info = load_info(fields, values)
  end

  self.load_entity(object, info)

  object
end

.purge(object) ⇒ Object 



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# File 'lib/rbbt/annotations.rb', line 155

def self.purge(object)
  case object
  when Path
    object
  when String
    object.respond_to?(:clean_annotations) ?
      object.clean_annotations : 
      object
  when Array
    object.respond_to?(:clean_annotations) ?
      object.clean_annotations(true) : 
      object.inject([]){|acc,e| acc << Annotated.purge(e); acc}
  when TSV
    object.unnamed = true
    object
  when Hash
    new = {}
    object.each do |key, value|
      Annotated.purge key
      new[key] = Annotated.purge value
    end
    new
  else
    object
  end
end

.resolve_array(entry) ⇒ Object 



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# File 'lib/rbbt/annotations/util.rb', line 45

def self.resolve_array(entry)
  if String === entry && entry =~ /^Array:/
    entry["Array:".length..-1].split("|")
  else
    entry
  end
end

.to_hash(e) ⇒ Object 



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# File 'lib/rbbt/annotations/util.rb', line 220

def self.to_hash(e)
  hash = {}
  if Array === e && AnnotatedArray === e
    hash[:literal] = Annotated.purge(e)
    hash[:info] = e.info
  elsif Array === e
    hash = e.collect do |_e|
      _hash = {}
      _hash[:literal] = _e.dup
      _hash[:info] = _e.info if _e.respond_to?(:info)
      _hash
    end
  else
    hash[:literal] = e.dup
    hash[:info] = e.info
  end
  hash
end

.tsv(annotations, *fields) ⇒ Object 



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# File 'lib/rbbt/annotations/util.rb', line 113

def self.tsv(annotations, *fields)
  return nil if annotations.nil?

  fields = case

           when ((fields.compact.empty?) && ! annotations.empty?)
             fields = AnnotatedArray === annotations ? annotations.annotations : annotations.compact.first.annotations
             fields << :annotation_types

           when (fields == [:literal] and ! annotations.compact.empty?)
             fields << :literal

           when (fields == [:all] && Annotated === annotations)
             annotation_names = annotations.annotations
             annotation_names += annotations.first.annotations if Annotated === annotations.first
             fields = [:annotation_types] + annotation_names.uniq
             fields << :annotated_array if AnnotatedArray === annotations
             fields << :literal

           when (fields == [:all] && ! annotations.compact.empty?)
             raise "Input array must be annotated or its elements must be" if not Annotated === annotations.compact.first and not Array === annotations.compact.first
             raise "Input array must be annotated or its elements must be. No double arrays of singly annotated entities." if not Annotated === annotations.compact.first and Array === annotations.compact.first
             fields = [:annotation_types] + (Annotated === annotations ? 
                                             annotations.annotations: 
                                             annotations.compact.first.annotations)
             fields << :literal

           when annotations.empty?
             [:annotation_types, :literal]

           else
             fields.flatten

           end

  fields = fields.collect{|f| f.to_s}.uniq

  case
  when (Annotated === annotations and not (AnnotatedArray === annotations and annotations.double_array))
    tsv = TSV.setup({}, :key_field => "List", :fields => fields, :type => :list, :unnamed => true)

    annot_id = annotations.id
    annot_id = annot_id * "," if Array === annot_id
    tsv[annot_id] = annotations.tsv_values(*fields).dup

  when Array === annotations 
    tsv = TSV.setup({}, :key_field => "ID", :fields => fields, :type => :list, :unnamed => true)

    annotations.compact.each_with_index do |annotation,i|
      tsv[annotation.id + "#" << i.to_s] = annotation.tsv_values(*fields).dup
    end

  else
    raise "Annotations need to be an Array to create TSV"
  end

  tsv
end

Instance Method Details

#annotate(object) ⇒ Object 



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# File 'lib/rbbt/annotations.rb', line 110

def annotate(object)

  return object unless Array === object or String === object

  annotation_types.each do |annotation|
    object.extend annotation unless annotation === object
  end

  object.instance_variable_set(:@annotation_types, nil)

  if object.instance_variables.include?(:@annotation_values)
    hash = {}
    object.instance_variable_get(:@annotation_values).each{|k,v| hash[k] = v}
    self.annotation_values.each{|k,v| hash[k] = v unless v.nil?}

    object.instance_variable_set(:@annotation_values, hash)
    object.instance_variable_set(:@shared_annotations,  false)
  else
    object.instance_variable_set(:@annotation_values,  self.annotation_values)
    object.instance_variable_set(:@shared_annotations,  true)
    @shared_annotations = true
  end

  object.extend AnnotatedArray if AnnotatedArray === self and Array === object

  object
end

#annotation_md5 ⇒ Object 



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# File 'lib/rbbt/annotations.rb', line 93

def annotation_md5
  if annotation_values.instance_variable_get(:@annotation_md5).nil?
    annotation_values.instance_variable_set(:@annotation_md5, Misc.hash2md5(annotation_values))
  end
  annotation_values.instance_variable_get(:@annotation_md5)
end

#annotation_types ⇒ Object 



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# File 'lib/rbbt/annotations.rb', line 28

def annotation_types

  @annotation_types ||= class << self; self; end.
    included_modules.
    select{|m| 
      Annotation === m
    }
end

#annotation_values ⇒ Object 



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# File 'lib/rbbt/annotations.rb', line 11

def annotation_values
  @annotation_values ||= {}
end

#annotations ⇒ Object 



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# File 'lib/rbbt/annotations.rb', line 37

def annotations
  if @annotations.nil? 
    @annotations = []

    annotation_types.each do |annotation_type|
      @annotations.concat annotation_type.annotations
    end

    @annotations
  else
    @annotations
  end
end

#clean_annotations(recursive = false) ⇒ Object 



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# File 'lib/rbbt/annotations.rb', line 138

def clean_annotations(recursive = false)
  case
  when self.nil?
    nil
  when Array === self
    if recursive
      [].concat self.collect{|e| e.respond_to?(:clean_annotations)? e.clean_annotations : e}
    else
      [].concat self
    end
  when String === self
    "" << self
  else
    self.dup
  end
end

#detach_annotations ⇒ Object 



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# File 'lib/rbbt/annotations.rb', line 15

def detach_annotations
  @annotation_values = @annotation_values.dup
  @annotation_values.instance_variable_set(:@annotation_md5, nil)
  @shared_annotations = false
end

#id ⇒ Object

ToDo This does not make much sense, why not change :id directly



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# File 'lib/rbbt/annotations.rb', line 105

def id
  @id ||= self.respond_to?(:annotation_id) ? 
    annotation_id : self_md5
end

#info(masked = false) ⇒ Object 



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# File 'lib/rbbt/annotations.rb', line 69

def info(masked = false)

  if @info.nil?
    annotation_values = self.annotation_values
    annotation_values = annotation_values.dup unless annotation_values.nil?
    info = annotation_values
    info[:annotation_types] = annotation_types
    info[:annotated_array] = true if AnnotatedArray === self
    @info = info
  end

  if masked 
    if @masked_info.nil?
      @masked_info = @info.dup
      masked_annotations.each do |annotation|
        @masked_info.delete annotation
      end
    end
    @masked_info
  else
    @info
  end
end

#make_list ⇒ Object 



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# File 'lib/rbbt/annotations.rb', line 182

def make_list
  new = [self]
  self.annotate(new)
  new.extend AnnotatedArray
  new
end

#marshal_dump ⇒ Object 



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# File 'lib/rbbt/annotations/util.rb', line 253

def marshal_dump
  Annotated.to_hash(self)
end

#masked_annotations ⇒ Object 



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# File 'lib/rbbt/annotations.rb', line 51

def masked_annotations
  if @masked_annotations.nil? 
    @masked_annotations = []

    annotation_types.each do |annotation_type|
      @masked_annotations.concat annotation_type.masked_annotations
    end

    @masked_annotations
  else
    @masked_annotations
  end
end

#reset ⇒ Object 



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# File 'lib/rbbt/annotations.rb', line 21

def reset
  @info = nil
  @id = nil
  @self_md5 = nil
  annotation_values.instance_variable_set(:@annotation_md5, nil)
end

#self_md5 ⇒ Object 



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# File 'lib/rbbt/annotations.rb', line 100

def self_md5
  @self_md5 ||= Misc.digest(annotation_md5 + self.to_s)
end

#tsv_values(*fields) ⇒ Object 



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# File 'lib/rbbt/annotations/util.rb', line 172

def tsv_values(*fields)
  if Array === self and (not AnnotatedArray === self or self.double_array)
    Misc.zip_fields(self.compact.collect{|e| e.tsv_values(fields)})
  else
    fields = fields.flatten

    info = self.info

    values = []

    fields.each do |field|
      values << case

      when Proc === field
        field.call(self)

      when field == "JSON"
        if AnnotatedArray === self
          info.merge(:annotated_array => true).to_json
        else
          info.to_json
        end

      when field == "annotation_types"
        annotation_types.collect{|t| t.to_s} * "|"

      when field == "annotated_array"
        AnnotatedArray === self

      when field == "literal"
        (Array === self ? "Array:" << self * "|" : self).gsub(/\n|\t/, ' ')

      when info.include?(field.to_sym)
        res = info[field.to_sym]
        Array === res ? "Array:" << res * "|" : res

      when self.respond_to?(field)
        res = self.send(field)
        Array === res ? "Array:"<< res * "|" : res

      end
    end


    values
  end
end

#unmasked_annotations ⇒ Object 



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# File 'lib/rbbt/annotations.rb', line 65

def unmasked_annotations
  @unmasked_annotations ||= annotations - masked_annotations
end