Class: Tools::InteractiveKey

Inherits:
Object
  • Object
show all
Defined in:
lib/tools/interactive_key.rb

Overview

Contains methods used to build an interactive key

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(observation_matrix_id: nil, project_id: nil, language_id: nil, keyword_ids: nil, row_filter: nil, otu_filter: nil, sorting: 'weighted', error_tolerance: 0, identified_to_rank: nil, eliminate_unknown: nil, selected_descriptors: nil) ⇒ InteractiveKey

Returns a new instance of InteractiveKey.



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# File 'lib/tools/interactive_key.rb', line 151

def initialize(
  observation_matrix_id: nil,
  project_id: nil,
  language_id: nil,
  keyword_ids: nil,
  row_filter: nil,
  otu_filter: nil,
  sorting: 'weighted',
  error_tolerance: 0,
  identified_to_rank: nil,
  eliminate_unknown: nil,
  selected_descriptors: nil)

  # raise if observation_matrix_id.blank? || project_id.blank?
  @observation_matrix_id = observation_matrix_id
  @project_id = project_id
  @observation_matrix = ObservationMatrix.where(project_id: project_id).find(observation_matrix_id)
  @observation_matrix_citation = @observation_matrix.source
  @descriptor_available_languages = descriptor_available_languages
  @language_id = language_id
  @language_to_use = language_to_use
  @keyword_ids = keyword_ids
  @descriptor_available_keywords = descriptor_available_keywords
  @descriptors_with_filter = descriptors_with_keywords
  @row_filter = row_filter
  @otu_filter = otu_filter
  @row_id_filter_array = row_filter_array
  @otu_id_filter_array = otu_filter_array
  @rows_with_filter = get_rows_with_filter
  @sorting = sorting
  @error_tolerance = error_tolerance.to_i
  @eliminate_unknown = eliminate_unknown == 'true' ? true : false
  @identified_to_rank = identified_to_rank
  @selected_descriptors = selected_descriptors
  @selected_descriptors_hash = selected_descriptors_hash_initiate

  @row_hash = row_hash_initiate

  @descriptors_hash = descriptors_hash_initiate

  ###main_logic

  @remaining = remaining_taxa
  @eliminated = eliminated_taxa
  @list_of_descriptors = useful_descriptors
  ### delete temporary data
  @row_hash = nil #
  @descriptors_hash = nil
  @rows_with_filter = nil
  @descriptors_with_filter = nil
end

Instance Attribute Details

#descriptor_available_keywords ⇒ Object

Returns the list of all Tags used with the descriptors. Descriptors could be filtered by tag_id



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# File 'lib/tools/interactive_key.rb', line 91

def descriptor_available_keywords
  @descriptor_available_keywords
end

#descriptor_available_languages ⇒ Object

Returns the list of available Languages used as translations for descriptors and character_states (in translations are available)



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# File 'lib/tools/interactive_key.rb', line 81

def descriptor_available_languages
  @descriptor_available_languages
end

#descriptors ⇒ Object

Temporary attribute. Used for validation.



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# File 'lib/tools/interactive_key.rb', line 86

def descriptors
  @descriptors
end

#descriptors_hash ⇒ Object

temporary hash of descriptors; used for calculation of useful and not useful descriptors and their states



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# File 'lib/tools/interactive_key.rb', line 149

def descriptors_hash
  @descriptors_hash
end

#descriptors_with_filter ⇒ Object

Temporary attribute. Used for validation. List of descriptors reduced by keyword_ids



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# File 'lib/tools/interactive_key.rb', line 101

def descriptors_with_filter
  @descriptors_with_filter
end

#eliminate_unknown ⇒ Object

Optional attribute to eliminate taxa with no scores on a used descriptor: ‘false’ - default or ‘true’ If true, the rows without scores will be eliminated



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# File 'lib/tools/interactive_key.rb', line 45

def eliminate_unknown
  @eliminate_unknown
end

#eliminated ⇒ Object

Returns the list of objects eliminated by previously used descriptors. The list may include collection_objects OR otus OR valid taxon_names



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# File 'lib/tools/interactive_key.rb', line 134

def eliminated
  @eliminated
end

#error_tolerance ⇒ Object

Optional attribute. Number of allowed errors during identification



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# File 'lib/tools/interactive_key.rb', line 50

def error_tolerance
  @error_tolerance
end

#identified_to_rank ⇒ Object

Optional attribute to limit identification to OTU or a particular nomenclatural rank. Valid values are ‘otu’, ‘species’, ‘genus’, etc.



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# File 'lib/tools/interactive_key.rb', line 55

def identified_to_rank
  @identified_to_rank
end

#keyword_ids ⇒ Object

Optional attribute to provide a list of tagIDs to limit the set of descriptors to those taged: “keyword_ids=1|5|15”



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# File 'lib/tools/interactive_key.rb', line 24

def keyword_ids
  @keyword_ids
end

#language_id ⇒ Object

Optional attribute to display the descriptors and character_states in a particular language (when translations are available)



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# File 'lib/tools/interactive_key.rb', line 19

def language_id
  @language_id
end

#language_to_use ⇒ Object

Returns Language as an object if the language_id was provided (used to display descriptors in a particular language)



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# File 'lib/tools/interactive_key.rb', line 96

def language_to_use
  @language_to_use
end

#list_of_descriptors ⇒ Object

Return the list of descriptors and their states. Translated (if needed) and Sorted Each descriptor has an attribute :status, which could be ‘used’, ‘useful’, ‘useless’ for further identification



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# File 'lib/tools/interactive_key.rb', line 122

def list_of_descriptors
  @list_of_descriptors
end

#observation_matrix ⇒ Object

Returns observation_matrix as an object



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# File 'lib/tools/interactive_key.rb', line 71

def observation_matrix
  @observation_matrix
end

#observation_matrix_citation ⇒ Object

Returns observation_matrix_citation as an object



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# File 'lib/tools/interactive_key.rb', line 76

def observation_matrix_citation
  @observation_matrix_citation
end

#observation_matrix_id ⇒ Object

Required attribude to build the key



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# File 'lib/tools/interactive_key.rb', line 9

def observation_matrix_id
  @observation_matrix_id
end

#otu_filter ⇒ Object

Optional attribute to provide a list of otuIDs to limit the set “otu_filter=1|5|10”



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# File 'lib/tools/interactive_key.rb', line 34

def otu_filter
  @otu_filter
end

#otu_id_filter_array ⇒ Object

Array of otu_ids in the @otu_filter



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# File 'lib/tools/interactive_key.rb', line 116

def otu_id_filter_array
  @otu_id_filter_array
end

#project_id ⇒ Object

Required attribute to build the key



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# File 'lib/tools/interactive_key.rb', line 14

def project_id
  @project_id
end

#remaining ⇒ Object

Returns the list of objects not eliminated by previously used descriptors. The list may include collection_objects OR otus OR valid taxon_names



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# File 'lib/tools/interactive_key.rb', line 128

def remaining
  @remaining
end

#row_filter ⇒ Object

Optional attribute to provide a list of rowIDs to limit the set “row_filter=1|5|10”



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# File 'lib/tools/interactive_key.rb', line 29

def row_filter
  @row_filter
end

#row_hash ⇒ Object

Temporary hash of rows; used for calculation of remaining and eliminated rows



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# File 'lib/tools/interactive_key.rb', line 144

def row_hash
  @row_hash
end

#row_id_filter_array ⇒ Object

Array of row_ids in the @row_filter



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# File 'lib/tools/interactive_key.rb', line 111

def row_id_filter_array
  @row_id_filter_array
end

#rows_with_filter ⇒ Object

Temporary attribute. Used for validation. list of rows to be included into the matrix



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# File 'lib/tools/interactive_key.rb', line 106

def rows_with_filter
  @rows_with_filter
end

#selected_descriptors ⇒ Object

Optional attribute: descriptors and states selected during identification “123:1|3||125:3|5||135:2||140:3-5” Each used descriptor is separated by ‘||’. States or values are separated from descriptors with ‘:’. Multiple selected character_states for one descriptor are separated by ‘|’. Sample states can use numerical ranges



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# File 'lib/tools/interactive_key.rb', line 64

def selected_descriptors
  @selected_descriptors
end

#selected_descriptors_hash ⇒ Object

selected_descriptors String is converted into Hash



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# File 'lib/tools/interactive_key.rb', line 139

def selected_descriptors_hash
  @selected_descriptors_hash
end

#sorting ⇒ Object

Optional attribute to sort the list of descriptors. Options: ‘ordered’, ‘weighted’, ‘optimized’. Optimized is a default if nothing is provided



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# File 'lib/tools/interactive_key.rb', line 39

def sorting
  @sorting
end

Instance Method Details

#descriptors_hash_initiate ⇒ Object

descriptors_hash: {:descriptor, ### (descriptor)

:observations,         ### (array of observations for )
:state_ids,            ### {hash of state_ids used in the particular matrix
}}



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# File 'lib/tools/interactive_key.rb', line 287

def descriptors_hash_initiate
  h = {}

  descriptors_with_keywords.each do |d|
    h[d.id] = {}
    h[d.id][:descriptor] = d
    h[d.id][:weight_index] = 0
    h[d.id][:state_ids] = {}
    h[d.id][:count] = 0
    h[d.id][:min] = 999999 if d.type == 'Descriptor::Continuous' || d.type == 'Descriptor::Sample' # min value used as continuous or sample
    h[d.id][:max] = -999999 if d.type == 'Descriptor::Continuous' || d.type == 'Descriptor::Sample' # max value used as continuous or sample
    if d.type == 'Descriptor::PresenceAbsence'
      h[d.id][:state_ids]['true'] = {}
      h[d.id][:state_ids]['true'][:rows] = {}
      h[d.id][:state_ids]['true'][:status] = 'useless'
      h[d.id][:state_ids]['false'] = {}
      h[d.id][:state_ids]['false'][:rows] = {}
      h[d.id][:state_ids]['true'][:status] = 'useless'
    end
    h[d.id][:observations] = {} # all observation for a particular
    h[d.id][:observation_hash] = {} ### state_ids, true/false for a particular descriptor/otu_id/catalog_id combination (for PresenceAbsence or Qualitative or Continuous)
    h[d.id][:status] = 'useless' ### 'used', 'useful', 'useless'
    h[d.id][:status] = 'used' if selected_descriptors_hash[d.id]
  end

  t = ['Observation::Continuous', 'Observation::PresenceAbsence', 'Observation::Qualitative', 'Observation::Sample']

  observation_matrix.observations.where('"observations"."type" IN (?)', t).each do |o|
    if h[o.descriptor_id]
      otu_collection_object = o.observation_object_type + o.observation_object_id.to_s # otu_id.to_s + '|' + o.collection_object_id.to_s
      h[o.descriptor_id][:observations][otu_collection_object] = [] if h[o.descriptor_id][:observations][otu_collection_object].nil? #??????
      h[o.descriptor_id][:observations][otu_collection_object] += [o]                                                                #??????
      h[o.descriptor_id][:observation_hash][otu_collection_object] = [] if h[o.descriptor_id][:observation_hash][otu_collection_object].nil?
      h[o.descriptor_id][:observation_hash][otu_collection_object] += [o.character_state_id.to_s] if o.character_state_id
      h[o.descriptor_id][:observation_hash][otu_collection_object] += ["%g" % o.continuous_value] if o.continuous_value
      h[o.descriptor_id][:observation_hash][otu_collection_object] += [o.presence.to_s] unless o.presence.nil?
    end
  end
  h
end

#descriptors_with_keywords ⇒ Object 



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# File 'lib/tools/interactive_key.rb', line 236

def descriptors_with_keywords
  if keyword_ids
    descriptors.joins(:tags).where('tags.keyword_id IN (?)', keyword_ids.to_s.split('|').map(&:to_i) )
  else
    descriptors
  end
end

#eliminated_taxa ⇒ Object 



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# File 'lib/tools/interactive_key.rb', line 420

def eliminated_taxa
  h = {}
  row_hash.each do |r_key, r_value|
    obj = r_value[:object_at_rank].class.to_s + '|' + r_value[:object_at_rank].id.to_s
    if r_value[:status] == 'eliminated' && !remaining.include?(r_value[:object_at_rank].class.to_s + '|' + r_value[:object_at_rank].id.to_s)
      h[obj] =
        {object: r_value[:object_at_rank],
         row_id: r_value[:object].id,
         errors: r_value[:errors],
         error_descriptors: r_value[:error_descriptors]
        } if h[obj].nil?
    end
  end
  return h.values
end

#get_rows_with_filter ⇒ Object 



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# File 'lib/tools/interactive_key.rb', line 252

def get_rows_with_filter
  observation_matrix.observation_matrix_rows.order(:position)
end

#otu_filter_array ⇒ Object 



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# File 'lib/tools/interactive_key.rb', line 248

def otu_filter_array
  otu_filter.blank? ? nil : otu_filter.to_s.split('|').map(&:to_i)
end

#remaining_taxa ⇒ Object

@error_tolerance - integer

@eliminate_unknown  'true' or 'false'
@descriptors_hash



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# File 'lib/tools/interactive_key.rb', line 344

def remaining_taxa
  h = {}
  language = language_id.blank? ? nil : language_id.to_i

  row_hash.each do |r_key, r_value|
    selected_descriptors_hash.each do |d_key, d_value|
      otu_collection_object = r_value[:object].observation_object_type + r_value[:object].observation_object_id.to_s # otu_id.to_s + '|' + r_value[:object].collection_object_id.to_s
      next if descriptors_hash[d_key].blank?
      d_name = descriptors_hash[d_key][:descriptor].target_name(:key, language) + ': '
      if eliminate_unknown && descriptors_hash[d_key][:observation_hash][otu_collection_object].nil?
        r_value[:errors] += 1
        r_value[:error_descriptors] += [d_name + 'unknown']
      elsif descriptors_hash[d_key][:observation_hash][otu_collection_object].nil?
        #character not scored but no error
      else
        case descriptors_hash[d_key][:descriptor].type
        when 'Descriptor::Continuous'
          if (descriptors_hash[d_key][:observation_hash][otu_collection_object] & d_value).empty?
            r_value[:errors] += 1
            str = d_name + descriptors_hash[d_key][:observations][otu_collection_object].collect{|o| "%g" % o.continuous_value}.join(' OR ')
            r_value[:error_descriptors] += [str]
          end
        when 'Descriptor::PresenceAbsence'
          if (descriptors_hash[d_key][:observation_hash][otu_collection_object] & d_value).empty?
            r_value[:errors] += 1
            str = d_name + descriptors_hash[d_key][:observations][otu_collection_object].collect{|o| o.presence}.join(' OR ')
            r_value[:error_descriptors] += [str]
          end
        when 'Descriptor::Qualitative'
          if (descriptors_hash[d_key][:observation_hash][otu_collection_object] & d_value).empty?
            r_value[:errors] += 1
            str = d_name + descriptors_hash[d_key][:observations][otu_collection_object].collect{|o| o.character_state.target_name(:key, language)}.join(' OR ')
            r_value[:error_descriptors] += [str]
          end
        when 'Descriptor::Sample'
          p = false
          a = d_value.first.split('-')
          d_min = a[0].to_f
          d_max = a[1].nil? ? d_min : a[1].to_f
          descriptors_hash[d_key][:observations][otu_collection_object].each do |o|
            s_min = o.sample_min.to_f
            s_max = o.sample_max.nil? ? s_min : o.sample_max.to_f
            p = true if (d_min >= s_min && d_min <= s_max) || (d_max >= s_min && d_max <= s_max) || (d_min <= s_min && d_max >= s_max)
          end
          if p == false
            r_value[:errors] += 1
            str = d_name + descriptors_hash[d_key][:observations][otu_collection_object].collect{|o| o.sample_min.to_s + '–' + o.sample_max.to_s}.join(' OR ')
            r_value[:error_descriptors] += [str]
          end
        end
      end
    end

    obj = r_value[:object_at_rank].class.to_s + '|' + r_value[:object_at_rank].id.to_s

    if (row_id_filter_array && !row_id_filter_array.include?(r_value[:object].id)) ||
        (otu_id_filter_array && !otu_id_filter_array.include?(r_value[:otu_id]))
      r_value[:status] = 'eliminated'
      r_value[:errors] = 'F'
      r_value[:error_descriptors] = ['Filtered out']
    end

    if r_value[:errors] == 'F' || r_value[:errors] > error_tolerance
      r_value[:status] = 'eliminated'
    elsif h[obj].nil?
      h[obj] =
        {object: r_value[:object_at_rank],
         row_id: r_value[:object].id,
         errors: r_value[:errors],
         error_descriptors: r_value[:error_descriptors]
        }
    end
  end
  return h.values
end

#row_filter_array ⇒ Object 



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# File 'lib/tools/interactive_key.rb', line 244

def row_filter_array
  row_filter.blank? ? nil : row_filter.to_s.split('|').map(&:to_i)
end

#row_hash_initiate ⇒ Object

row_hash: {:object, ### (collection_object or OTU)

:object_at_rank,   ### (converted to OTU or TN)
:row_id,
:otu_id,
:errors,           ### (calculated number of errors)
:status }         ### ('remaining', 'eliminated')



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# File 'lib/tools/interactive_key.rb', line 262

def row_hash_initiate
  h = {}
  rows_with_filter.each do |r|
    otu_collection_object = r.observation_object_type + r.observation_object_id.to_s #  r.otu_id.to_s + '|' + r.collection_object_id.to_s
    h[otu_collection_object] = {}
    h[otu_collection_object][:object] = r
    if identified_to_rank == 'otu'
      h[otu_collection_object][:object_at_rank] = r.current_otu || r
    elsif identified_to_rank
      h[otu_collection_object][:object_at_rank] = r&.current_taxon_name&.ancestor_at_rank(identified_to_rank, inlude_self = true) || r
    else
      h[otu_collection_object][:object_at_rank] = r
    end
    h[otu_collection_object][:otu_id] = r.observation_object_type == 'Otu' ? r.observation_object_id : r.current_otu.id
    h[otu_collection_object][:errors] = 0
    h[otu_collection_object][:error_descriptors] = []
    h[otu_collection_object][:status] = 'remaining' ### if number of errors > @error_tolerance, replaced to 'eliminated'
  end
  h
end

#selected_descriptors_hash_initiate ⇒ Object

returns [‘1’, ‘3’], 125: [‘3’, ‘5’], 135: [‘2’], 136: [‘true’], 140: [‘5-10’] “123:1|3||125:3|5||135:2”



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# File 'lib/tools/interactive_key.rb', line 330

def selected_descriptors_hash_initiate
  h = {}
  return h if selected_descriptors.blank?
  a = selected_descriptors.include?('||') ? selected_descriptors.to_s.split('||') : [selected_descriptors]
  a.each do |i|
    d = i.split(':')
    h[d[0].to_i] = d[1].to_s.include?('|') ? d[1].split('|') : [d[1]]
  end
  h
end

#useful_descriptors ⇒ Object 



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# File 'lib/tools/interactive_key.rb', line 436

def useful_descriptors
  list_of_remaining_taxa = {}
  language = language_id.blank? ? nil : language_id.to_i
  row_hash.each do |r_key, r_value|
    if r_value[:status] != 'eliminated'
      list_of_remaining_taxa[r_value[:object_at_rank] ] = true
    end
  end
  number_of_taxa = list_of_remaining_taxa.count.to_i
  array_of_descriptors = []

  descriptors_hash.each do |d_key, d_value|
    taxa_with_unknown_character_states = {}
    list_of_remaining_taxa.each do |key, value|
      taxa_with_unknown_character_states[key] = value
    end
    # taxa_with_unknown_character_states = list_of_remaining_taxa if @eliminate_unknown == false
    d_value[:observations].each do |otu_key, otu_value|
      otu_collection_object = otu_key
      if true #@row_hash[otu_collection_object]
        otu_value.each do |o|
          if o.character_state_id
            d_value[:state_ids][o.character_state_id.to_s] = {} if d_value[:state_ids][o.character_state_id.to_s].nil?
            d_value[:state_ids][o.character_state_id.to_s][:rows] = {} if d_value[:state_ids][o.character_state_id.to_s][:rows].nil? ## rows which this state identifies
            d_value[:state_ids][o.character_state_id.to_s][:rows][ @row_hash[otu_collection_object][:object_at_rank] ] = true if @row_hash[otu_collection_object][:status] != 'eliminated'
            if selected_descriptors_hash[d_key] && selected_descriptors_hash[d_key].include?(o.character_state_id.to_s)
              d_value[:state_ids][o.character_state_id.to_s][:status] = 'used' ## 'used', 'useful', 'useless'
            else
              d_value[:state_ids][o.character_state_id.to_s][:status] = 'useful' ## 'used', 'useful', 'useless'
            end
          end
          unless o.presence.nil?
            #d_value[:state_ids][o.presence.to_s] = {} if d_value[:state_ids][o.presence.to_s].nil?
            #d_value[:state_ids][o.presence.to_s][:rows] = {} if d_value[:state_ids][o.presence.to_s][:rows].nil? ## rows which this state identifies
            d_value[:state_ids][o.presence.to_s][:rows][ @row_hash[otu_collection_object][:object_at_rank] ] = true if @row_hash[otu_collection_object][:status] != 'eliminated'
            if selected_descriptors_hash[d_key] && selected_descriptors_hash[d_key].include?(o.presence.to_s)
              d_value[:state_ids][o.presence.to_s][:status] = 'used' ## 'used', 'useful', 'useless'
            else
              d_value[:state_ids][o.presence.to_s][:status] = 'useful' ## 'used', 'useful', 'useless'
            end
          end
          unless o.continuous_value.nil?
            d_value[:state_ids][o.id] = true
            if @row_hash[otu_collection_object][:status] != 'eliminated'
              d_value[:count] +=1
              d_value[:min] = o.continuous_value if d_value[:min] > o.continuous_value
              d_value[:max] = o.continuous_value if d_value[:max] < o.continuous_value
            end
          end
          unless o.sample_min.nil?
            d_value[:state_ids][o.id] = {o_min: o.sample_min.to_f, o_max: o.sample_max.to_f}
            if @row_hash[otu_collection_object][:status] != 'eliminated'
              d_value[:count] +=1
              d_value[:min] = o.sample_min if d_value[:min] > o.sample_min
              if o.sample_max
                d_value[:max] = o.sample_max if d_value[:max] < o.sample_max
              else
                d_value[:max] = o.sample_min if d_value[:max] < o.sample_min
              end
            end
          end
          taxa_with_unknown_character_states[ @row_hash[otu_collection_object][:object_at_rank] ] = false if @eliminate_unknown == false
        end
      end
    end
    number_of_taxa_with_unknown_character_states = 0
    number_of_taxa_with_unknown_character_states = taxa_with_unknown_character_states.select{|key, value| value == true}.count if @eliminate_unknown == false

    descriptor = {}
    descriptor[:id] = d_key
    descriptor[:type] = d_value[:descriptor].type
    descriptor[:name] = d_value[:descriptor].target_name(:key, language)
    descriptor[:weight] = d_value[:descriptor].weight
    descriptor[:position] = d_value[:descriptor].position
    descriptor[:usefulness] = 0
    descriptor[:status] = d_value[:status] == 'used' ? 'used' : 'useless'
    descriptor[:description] = d_value[:descriptor].description
    descriptor[:depiction_ids] = d_value[:descriptor].depictions.order(:position).pluck(:id)

    s = 0
    case d_value[:descriptor].type
    when 'Descriptor::Qualitative'
      number_of_states = d_value[:state_ids].count.to_i
      descriptor[:states] = []
      d_value[:state_ids].each do |s_key, s_value|
        c = CharacterState.find(s_key.to_i)
        state = {}
        state[:id] = c.id
        state[:name] = c.target_name(:key, language)
        state[:position] = c.position
        state[:label] = c.label
        state[:number_of_objects] = s_value[:rows].count + number_of_taxa_with_unknown_character_states
        state[:status] = s_value[:status] == 'used' ? 'used' : 'useful'
        n = s_value[:rows].count
        if descriptor[:status] == 'used'
          #do nothing
        elsif n == number_of_taxa || n == 0
          s_value[:status] = 'useless'
          state[:status] = 'useless'
        else
          d_value[:status] = 'useful'
          descriptor[:status] = 'useful'
        end
        state[:depiction_ids] = c.depictions.order(:position).pluck(:id)

        #          weight = rem_taxa/number_of_states + squer (sum (rem_taxa/number_of_states - taxa_in_each_state)^2)
        s += (number_of_taxa / number_of_states - s_value[:rows].count) ** 2
        descriptor[:states] += [state]
      end
      descriptor[:usefulness] = number_of_taxa / number_of_states + Math.sqrt(s) if number_of_states > 0
      descriptor[:states].sort_by!{|i| i[:position]}
    when 'Descriptor::Continuous'
      descriptor[:default_unit] = d_value[:descriptor].default_unit
      descriptor[:min] = d_value[:min]
      descriptor[:max] = d_value[:max]
      number_of_measurements = d_value[:count]
      s = (d_value[:min] - (d_value[:min] / 10)) / (d_value[:max] + 0.0000001 - d_value[:min])
      descriptor[:usefulness] = number_of_taxa * s * (2 - (number_of_measurements / number_of_taxa)) if number_of_taxa > 0
      if descriptor[:status] != 'used' && descriptor[:min] != descriptor[:max]
        d_value[:status] = 'useful'
        descriptor[:status] = 'useful'
      end
    when 'Descriptor::Sample'
      descriptor[:default_unit] = d_value[:descriptor].default_unit
      descriptor[:min] = d_value[:min]
      descriptor[:max] = d_value[:max]
      number_of_measurements = d_value[:count]
      #                               i = max - min ; if 0 then (numMax - numMin / 10)
      #                               sum of all i
      #                               if numMax = numMin then numMax = numMax + 0.00001
      #                               weight = rem_taxa * (sum of i / number of measuments for taxon / (numMax - numMin) ) * (2 - number of measuments for taxon / rem_taxa)
      if d_value[:max] != d_value[:min] && number_of_measurements > 0
        d_value[:state_ids].each do |s_key, s_value|
          if s_value[:o_min] == s_value[:o_max] || s_value[:o_max].blank?
            s += (s_value[:o_min] - (s_value[:o_min] / 10)) / number_of_measurements / (d_value[:max] + 0.0000001 - d_value[:min])
          else
            s += (s_value[:o_max] - s_value[:o_min]) / number_of_measurements / (d_value[:max] + 0.0000001 - d_value[:min])
          end
          if descriptor[:status] != 'used' && (s_value[:o_min] != d_value[:min] || (!s_value[:o_max].blank? && s_value[:o_max] != d_value[:max]))
            d_value[:status] = 'useful'
            descriptor[:status] = 'useful'
          end
        end
      end
      descriptor[:usefulness] = number_of_taxa * s * (2 - (number_of_measurements / number_of_taxa)) if number_of_taxa > 0
    when 'Descriptor::PresenceAbsence'
      number_of_states = 2
      descriptor[:states] = []
      d_value[:state_ids].each do |s_key, s_value|
        state = {}
        state[:name] = s_key
        state[:number_of_objects] = s_value[:rows].count + number_of_taxa_with_unknown_character_states
        state[:status] = s_value[:status] == 'used' ? 'used' : 'useful'
        n = s_value[:rows].count
        if descriptor[:status] == 'used'
          #do nothing
        elsif n == number_of_taxa || n == 0
          s_value[:status] = 'useless'
          state[:status] = 'useless'
        else
          d_value[:status] = 'useful'
          descriptor[:status] = 'useful'
        end
        s += (number_of_taxa / number_of_states - s_value[:rows].count) ** 2
        descriptor[:states] += [state]
      end
      descriptor[:usefulness] = number_of_taxa / number_of_states + Math.sqrt(s) if number_of_states > 0
      descriptor[:states].sort_by!{|i| -i[:name]}
    end
    descriptor[:min] = nil if descriptor[:min] == 999999
    descriptor[:max] = nil if descriptor[:max] == -999999
    descriptor[:min] = "%g" % descriptor[:min] if descriptor[:min]
    descriptor[:max] = "%g" % descriptor[:max] if descriptor[:max]
    array_of_descriptors += [descriptor]
  end
  case sorting
  when 'ordered'
    array_of_descriptors.sort_by!{|i| i[:position]}
  when 'weighted'
    array_of_descriptors.sort_by!{|i| [-i[:weight].to_i, i[:usefulness]] }
  when 'optimized'
    array_of_descriptors.sort_by!{|i| i[:usefulness]}
  end
end