Class: Tools::Description::FromObservationMatrix

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

Overview

localhost:3000/tasks/observation_matrices/description_from_observation_matrix/description?otu_id=45291&observation_matrix_id=24

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(observation_matrix_id: nil, project_id: nil, include_descendants: nil, language_id: nil, keyword_ids: nil, observation_matrix_row_id: nil, otu_id: nil, similar_objects: {}) ⇒ FromObservationMatrix

Returns a new instance of FromObservationMatrix.



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# File 'lib/tools/description/from_observation_matrix.rb', line 108

def initialize( observation_matrix_id: nil,
                project_id: nil,
                include_descendants: nil,
                language_id: nil,
                keyword_ids: nil,
                observation_matrix_row_id: nil,
                otu_id: nil,
                similar_objects: {})

  return false if project_id.blank? || (observation_matrix_id.blank? && observation_matrix_row_id.blank? && otu_id.blank?)

  @project_id = project_id

  @keyword_ids = keyword_ids

  # !! You can skip all this if there are no Observations.
  
  @observation_matrix_id = observation_matrix_id
  @observation_matrix_row_id = observation_matrix_row_id
 
  @include_descendants = include_descendants
  @language_to_use = language_to_use
  @descriptor_available_keywords = descriptor_available_keywords
  @descriptors_with_filter = descriptors_with_keywords
  @descriptor_available_languages = descriptor_available_languages
  @language_id = language_id
  @otu_id = otu_id
  @otu_id_filter_array = otu_id_array
  @collection_object_id_filter_array = collection_object_id_array
  ###main_logic
  @descriptor_hash = get_descriptor_hash

  @generated_description = get_description
  @generated_diagnosis = get_diagnosis

  ###delete temporary data
  # Again, super confusing, these are temporary buffers, so they shouln't be initialized above?
  @descriptors_with_filter = nil
  @descriptor_hash = nil
end

Instance Attribute Details

#collection_object_id_filter_array ⇒ Object

Array of collection_object_ids



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# File 'lib/tools/description/from_observation_matrix.rb', line 79

def collection_object_id_filter_array
  @collection_object_id_filter_array
end

#collection_object_ids_count_hash ⇒ Object

Hash of similar collection_objects



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# File 'lib/tools/description/from_observation_matrix.rb', line 89

def collection_object_ids_count_hash
  @collection_object_ids_count_hash
end

#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/description/from_observation_matrix.rb', line 59

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/description/from_observation_matrix.rb', line 49

def descriptor_available_languages
  @descriptor_available_languages
end

#descriptor_hash ⇒ Object

Temporary attribute. Used to generated description and diagnosis



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# File 'lib/tools/description/from_observation_matrix.rb', line 94

def descriptor_hash
  @descriptor_hash
end

#descriptors ⇒ Object

Temporary attribute. Used for validation.



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# File 'lib/tools/description/from_observation_matrix.rb', line 54

def descriptors
  @descriptors
end

#descriptors_with_filter ⇒ Object

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



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# File 'lib/tools/description/from_observation_matrix.rb', line 69

def descriptors_with_filter
  @descriptors_with_filter
end

#generated_description ⇒ Object

Returns generated description for OTU



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# File 'lib/tools/description/from_observation_matrix.rb', line 99

def generated_description
  @generated_description
end

#generated_diagnosis ⇒ Object

Returns generated diagnosis for OTU



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# File 'lib/tools/description/from_observation_matrix.rb', line 104

def generated_diagnosis
  @generated_diagnosis
end

#include_descendants ⇒ Object

Optional attribude to include descentant otus and collection_objects



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# File 'lib/tools/description/from_observation_matrix.rb', line 17

def include_descendants
  @include_descendants
end

#keyword_ids ⇒ Object

Returns the value of attribute keyword_ids.



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# File 'lib/tools/description/from_observation_matrix.rb', line 106

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/description/from_observation_matrix.rb', line 27

def language_id
  @language_id
end

#language_to_use ⇒ Object 



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# File 'lib/tools/description/from_observation_matrix.rb', line 64

def language_to_use
  @language_to_use
end

#observation_matrix ⇒ Object

Returns observation_matrix as an object



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# File 'lib/tools/description/from_observation_matrix.rb', line 44

def observation_matrix
  @observation_matrix
end

#observation_matrix_id ⇒ Object

Optional attribude to build the description



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# File 'lib/tools/description/from_observation_matrix.rb', line 12

def observation_matrix_id
  @observation_matrix_id
end

#observation_matrix_row_id ⇒ Object

Optional attribute to provide a rowID



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# File 'lib/tools/description/from_observation_matrix.rb', line 32

def observation_matrix_row_id
  @observation_matrix_row_id
end

#otu_id ⇒ Object

Optional attribute to provide a otuID



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# File 'lib/tools/description/from_observation_matrix.rb', line 37

def otu_id
  @otu_id
end

#otu_id_filter_array ⇒ Object

Array of otu_ids in the @otu_filter



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# File 'lib/tools/description/from_observation_matrix.rb', line 74

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/description/from_observation_matrix.rb', line 22

def project_id
  @project_id
end

#similar_objects ⇒ Object

Hash of similar otus_ids and collection_objects_ids



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# File 'lib/tools/description/from_observation_matrix.rb', line 84

def similar_objects
  @similar_objects
end

Instance Method Details

#collection_object_id_array ⇒ Object 



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# File 'lib/tools/description/from_observation_matrix.rb', line 231

def collection_object_id_array
  if include_descendants == 'true' && otu_id_filter_array.present? # Big bug here was = not ==
    CollectionObject.where(project_id:).joins(:taxon_determinations).where(taxon_determinations: {position: 1, otu_id: otu_id_filter_array}).pluck(:id)
  elsif observation_matrix_row_id.present?
    [ObservationMatrixRow.where(project_id:).find(observation_matrix_row_id.to_i)&.observation_object_id.to_i]
  else
    [0]
  end
end

#descriptors_with_keywords ⇒ Object 



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# File 'lib/tools/description/from_observation_matrix.rb', line 206

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

#get_description ⇒ Object 



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# File 'lib/tools/description/from_observation_matrix.rb', line 370

def get_description
  return nil if descriptor_hash.empty?
  or_separator = ' or '
  language = language_id.blank? ? nil : language_id.to_i
  str = ''
  descriptor_name = ''
  state_name = ''
  descriptor_hash.each do |d_key, d_value|
    next if (d_value[:descriptor].type == 'Descriptor::Qualitative' && d_value[:char_states].empty?) ||
      ((d_value[:descriptor].type == 'Descriptor::Continuous' || d_value[:descriptor].type == 'Descriptor::Sample') && d_value[:min] == 999999) ||
      (d_value[:descriptor].type == 'Descriptor::PresenceAbsence' && d_value[:presence].nil?)
    descriptor_name_new = d_value[:descriptor].target_name(:description, language)

    if descriptor_name != descriptor_name_new
      descriptor_name = descriptor_name_new
      str += '. ' if str.present?
      str += descriptor_name + ' '
    else
      str += ', '
    end

    case d_value[:descriptor].type
    when 'Descriptor::Qualitative'
      st_str = []
      d_value[:char_states].each do |cs|
        st_str.append(cs.target_name(:description, language))
      end
      str += st_str.uniq.join(or_separator)
    when 'Descriptor::Continuous'
      if d_value[:min] == d_value[:max]
        str += ['%g' % d_value[:min], d_value[:descriptor].default_unit].compact.join(' ')
      else
        str += ['%g' % d_value[:min] + '–' + '%g' % d_value[:max], d_value[:descriptor].default_unit].compact.join(' ')
      end
    when 'Descriptor::Sample'
      if d_value[:min] == d_value[:max]
        str += ['%g' % d_value[:min], d_value[:descriptor].default_unit].compact.join(' ')
      else
        str += ['%g' % d_value[:min] + '–' + '%g' % d_value[:max], d_value[:descriptor].default_unit].compact.join(' ')
      end
    when 'Descriptor::PresenceAbsence'
      str += d_value[:presence].to_s
    end
  end
  str += '.' if str.present?
  str
end

#get_descriptor_hash ⇒ Object 



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# File 'lib/tools/description/from_observation_matrix.rb', line 241

def get_descriptor_hash
  descriptor_ids = descriptors_with_filter.collect{|i| i.id}
  t = ['Observation::Continuous', 'Observation::PresenceAbsence', 'Observation::Sample']
  otu_ids = otu_id_filter_array.to_a + [0]
  collection_object_ids = collection_object_id_filter_array.to_a + [0]
  descriptor_hash = {}
  @descriptors_with_filter.each do |d|
    descriptor_hash[d.id] = {}
    descriptor_hash[d.id][:descriptor] = d
    descriptor_hash[d.id][:similar_otu_ids] = []
    descriptor_hash[d.id][:similar_collection_object_ids] = []
    descriptor_hash[d.id][:char_states] = [] if d.type == 'Descriptor::Qualitative'
    descriptor_hash[d.id][:char_states_ids] = [] if d.type == 'Descriptor::Qualitative'
    descriptor_hash[d.id][:min] = 999999 if d.type == 'Descriptor::Continuous' || d.type == 'Descriptor::Sample' # min value used as continuous or sample
    descriptor_hash[d.id][:max] = -999999 if d.type == 'Descriptor::Continuous' || d.type == 'Descriptor::Sample' # max value used as continuous or sample
    descriptor_hash[d.id][:presence] = nil if d.type == 'Descriptor::PresenceAbsence'
  end

  char_states = CharacterState.where(project_id:).joins(:observations)
    .where(character_states: {descriptor_id: descriptor_ids})
    .where("( (observations.observation_object_type = 'Otu' and observations.observation_object_id IN (?)) OR (observations.observation_object_type = 'CollectionObject' and observations.observation_object_id IN (?)) )", otu_ids, collection_object_ids)
    .distinct # uniq
  char_states.each do |cs|
    descriptor_hash[cs.descriptor_id][:char_states].append(cs)
    descriptor_hash[cs.descriptor_id][:char_states_ids].append(cs.id)
  end

  observations = Observation.where(project_id:).where(type: t, descriptor_id: descriptor_ids)
    .where("((observation_object_type = 'Otu' AND observation_object_id IN (?)) OR (observation_object_type = 'CollectionObject' AND observation_object_id IN (?)) )", otu_ids, collection_object_ids)
    .distinct # was uniq

  observations.each do |o|
    if !o.continuous_value.nil?
      descriptor_hash[o.descriptor_id][:min] = o.continuous_value if descriptor_hash[o.descriptor_id][:min] > o.continuous_value
      descriptor_hash[o.descriptor_id][:max] = o.continuous_value if descriptor_hash[o.descriptor_id][:max] < o.continuous_value
    elsif !o.sample_min.nil?
      descriptor_hash[o.descriptor_id][:min] = o.sample_min if descriptor_hash[o.descriptor_id][:min] > o.sample_min
      if o.sample_max
        descriptor_hash[o.descriptor_id][:max] = o.sample_max if descriptor_hash[o.descriptor_id][:max] < o.sample_max
      else
        descriptor_hash[o.descriptor_id][:max] = o.sample_min if descriptor_hash[o.descriptor_id][:max] < o.sample_min
      end
    elsif !o.presence.nil?
      if o.presence == true && descriptor_hash[o.descriptor_id][:presence].nil?
        descriptor_hash[o.descriptor_id][:presence] = 'present'
      elsif o.presence == false && descriptor_hash[o.descriptor_id][:presence].nil?
        descriptor_hash[o.descriptor_id][:presence] = 'absent'
      elsif o.presence == true && descriptor_hash[o.descriptor_id][:presence] == 'absent'
        descriptor_hash[o.descriptor_id][:presence] = 'present or absent'
      elsif o.presence == false && descriptor_hash[o.descriptor_id][:presence] == 'present'
        descriptor_hash[o.descriptor_id][:presence] = 'present or absent'
      end
    end
  end

  otu_ids = otu_id_filter_array.to_a + [0]
  collection_object_ids = collection_object_id_filter_array.to_a + [0] # why zero? - to make non empty array, and get value not matching any id in the db

  unless observation_matrix_id.nil?
    otu_ids_count = {}
    collection_object_ids_count = {}
    t = ['Descriptor::Continuous', 'Descriptor::PresenceAbsence', 'Descriptor::Sample']

    char_states = ObservationMatrix.where(project_id:).
      select('descriptors.id AS d_id, character_states.id AS cs_id, observations.id AS o_id, observations.observation_object_id AS o_obj_id, observations.observation_object_type AS o_obj_type, observation_matrix_rows.observation_object_id AS r_obj_id, observation_matrix_rows.observation_object_type AS r_obj_type, observations.character_state_id AS o_cs_id').
      left_outer_joins(:descriptors).
      left_outer_joins(:observation_matrix_rows).
      joins('LEFT OUTER JOIN observations ON observations.descriptor_id = descriptors.id AND (observations.observation_object_id = observation_matrix_rows.observation_object_id AND observations.observation_object_type = observation_matrix_rows.observation_object_type )').
      joins('LEFT OUTER JOIN character_states ON character_states.id = observations.character_state_id').
      where("descriptors.type = 'Descriptor::Qualitative'").
      where('descriptors.id IN (?)', descriptor_ids).
      where("(observation_matrix_rows.observation_object_id NOT IN (?) AND observation_matrix_rows.observation_object_type = 'Otu') OR (observation_matrix_rows.observation_object_id NOT IN (?) AND observation_matrix_rows.observation_object_type = 'CollectionObject')", otu_ids, collection_object_ids).
      where('observation_matrices.id = ?', observation_matrix_id)

    char_states.each do |cs|
      if (cs.r_obj_type == 'Otu' && !descriptor_hash[cs.d_id][:similar_otu_ids].include?(cs.r_obj_id)) ||
          (cs.r_obj_type == 'CollectionObject' && !descriptor_hash[cs.d_id][:similar_collection_object_ids].include?(cs.r_obj_id))
        if cs.r_obj_type == 'Otu' && (descriptor_hash[cs.d_id][:char_states_ids].include?(cs.cs_id) || cs.o_id.nil?)
          descriptor_hash[cs.d_id][:similar_otu_ids].append(cs.r_obj_id)
          otu_ids_count[cs.r_obj_id] = otu_ids_count[cs.r_obj_id].to_i + 1
        elsif cs.r_obj_type == 'CollectionObject' && (descriptor_hash[cs.d_id][:char_states_ids].include?(cs.cs_id) || cs.o_id.nil?)
          descriptor_hash[cs.d_id][:similar_collection_object_ids].append(cs.r_obj_id)
          collection_object_ids_count[cs.r_obj_id] = collection_object_ids_count[cs.r_obj_id].to_i + 1
        end
      end
    end

    observations = ObservationMatrix.
      where(project_id:).
      select('descriptors.id AS d_id, observations.id AS o_id, observations.observation_object_id AS o_obj_id, observations.observation_object_type AS o_obj_type, observations.type, observations.continuous_value, observations.sample_min, observations.sample_max, observations.presence AS o_presence, observation_matrix_rows.observation_object_id AS r_obj_id, observation_matrix_rows.observation_object_type AS r_obj_type, observations.character_state_id AS o_cs_id').
      left_outer_joins(:descriptors).
      left_outer_joins(:observation_matrix_rows).
      joins('LEFT OUTER JOIN observations ON observations.descriptor_id = descriptors.id AND (observations.observation_object_id = observation_matrix_rows.observation_object_id AND observations.observation_object_type = observation_matrix_rows.observation_object_type )').
      where('descriptors.type IN (?)', t).
      where('descriptors.id IN (?)', descriptor_ids).
      where("(observation_matrix_rows.observation_object_id NOT IN (?) AND observation_matrix_rows.observation_object_type = 'Otu') OR (observation_matrix_rows.observation_object_id NOT IN (?) AND observation_matrix_rows.observation_object_type = 'CollectionObject')", otu_ids, collection_object_ids).
      where('observation_matrices.id = ?', @observation_matrix_id)
    observations.each do |o|
      if (o.r_obj_type == 'Otu' && !descriptor_hash[o.d_id][:similar_otu_ids].include?(o.r_obj_id)) ||
          (o.r_obj_type == 'CollectionObject' && !descriptor_hash[o.d_id][:similar_collection_object_ids].include?(o.r_obj_id))
        yes = false
        if o.continuous_value.nil? && o.sample_min.nil? && o.o_presence.nil?
          yes = true
        elsif !o.continuous_value.nil? && o.continuous_value >= descriptor_hash[o.d_id][:min] && o.continuous_value <= descriptor_hash[o.d_id][:max]
          yes = true
        elsif !o.sample_max.nil? && o.sample_max >= descriptor_hash[o.d_id][:min] && o.sample_max <= descriptor_hash[o.d_id][:max]
          yes = true
        elsif !o.sample_min.nil? && o.sample_min >= descriptor_hash[o.d_id][:min] && o.sample_min <= descriptor_hash[o.d_id][:max]
          yes = true
        elsif !o.o_presence.nil? && o.o_presence == true && descriptor_hash[o.d_id][:presence].to_s.include?('present')
          yes = true
        elsif !o.o_presence.nil? && o.o_presence == false && descriptor_hash[o.d_id][:presence].to_s.include?('absent')
          yes = true
        end
        if o.r_obj_type == 'Otu' && yes
          descriptor_hash[o.d_id][:similar_otu_ids].append(o.r_obj_id)
          otu_ids_count[o.r_obj_id] = otu_ids_count[o.r_obj_id].to_i + 1
        elsif o.r_obj_type == 'CollectionObject' && yes
          descriptor_hash[o.d_id][:similar_collection_object_ids].append(o.r_obj_id)
          collection_object_ids_count[o.r_obj_id] = collection_object_ids_count[o.r_obj_id].to_i + 1
        end
      end
    end
    @similar_objects = (otu_ids_count.to_a.map{|i| {otu_id: i[0], similarities: i[1]}} + collection_object_ids_count.to_a.map{|i| {collection_object_id: i[0], similarities: i[1]}}).sort_by{|j| -j[:similarities]}
  end

  descriptor_hash
end

#get_diagnosis ⇒ Object 



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# File 'lib/tools/description/from_observation_matrix.rb', line 418

def get_diagnosis
  return nil if descriptor_hash.empty?

  descriptor_array = descriptor_hash.values.sort_by{|i| i[:similar_otu_ids].count + i[:similar_collection_object_ids].count}
  i = 2
  i_max = descriptor_array.count
  j = 0

  while j < 3
    while i < i_max && i_max > 2 do
      count1 = (descriptor_array[i][:similar_otu_ids] & descriptor_array[i-1][:similar_otu_ids]).count +
        (descriptor_array[i][:similar_collection_object_ids] & descriptor_array[i-1][:similar_collection_object_ids]).count
      count2 = (descriptor_array[i][:similar_otu_ids] & descriptor_array[i-2][:similar_otu_ids]).count +
        (descriptor_array[i][:similar_collection_object_ids] & descriptor_array[i-2][:similar_collection_object_ids]).count
      if count2 > count1
        temp = descriptor_array[i-2]
        descriptor_array[i-2] = descriptor_array[i-1]
        descriptor_array[i-1] = temp
      end
      i += 1
    end
    j += 1
  end

  or_separator = ' or '
  language = language_id.blank? ? nil : language_id.to_i # TODO: this should be a getter/setter so logic isn't here
  str = ''
  descriptor_name = ''
  state_name = ''
  remaining_otus = descriptor_array.first[:similar_otu_ids].to_a
  remaining_co = descriptor_array.first[:similar_collection_object_ids].to_a
  descriptor_array.each do |d_value|
    remaining_otus = remaining_otus & d_value[:similar_otu_ids].to_a
    remaining_co = remaining_co & d_value[:similar_collection_object_ids].to_a
    next if (d_value[:descriptor].type == 'Descriptor::Qualitative' && d_value[:char_states].empty?) ||
      ((d_value[:descriptor].type == 'Descriptor::Continuous' || d_value[:descriptor].type == 'Descriptor::Sample') && d_value[:min] == 999999) ||
      (d_value[:descriptor].type == 'Descriptor::PresenceAbsence' && d_value[:presence].nil?)
    descriptor_name_new = d_value[:descriptor].target_name(:description, language)
    if descriptor_name != descriptor_name_new
      descriptor_name = descriptor_name_new
      str += '. ' if str.present?
      str += descriptor_name + ' '
    else
      str += ', '
    end
    case d_value[:descriptor].type
    when 'Descriptor::Qualitative'
      st_str = []
      d_value[:char_states].each do |cs|
        st_str.append(cs.target_name(:description, language))
      end
      str += st_str.uniq.join(or_separator)
    when 'Descriptor::Continuous'
      if d_value[:min] == d_value[:max]
        str += ['%g' % d_value[:min], d_value[:descriptor].default_unit].compact.join(' ')
      else
        str += ['%g' % d_value[:min] + '–' + '%g' % d_value[:max], d_value[:descriptor].default_unit].compact.join(' ')
      end
    when 'Descriptor::Sample'
      if d_value[:min] == d_value[:max]
        str += ['%g' % d_value[:min], d_value[:descriptor].default_unit].compact.join(' ')
      else
        str += ['%g' % d_value[:min] + '–' + '%g' % d_value[:max], d_value[:descriptor].default_unit].compact.join(' ')
      end
    when 'Descriptor::PresenceAbsence'
      str += d_value[:presence].to_s
    end
    break if remaining_otus.empty? && remaining_co.empty?
  end
  if remaining_otus.empty? && remaining_co.empty?
    str += '.' if str.present?
  else
    str = 'Cannot be separated from other rows in the matrix!'
  end
  str
end

#observation_matrix_row ⇒ Object 



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# File 'lib/tools/description/from_observation_matrix.rb', line 155

def observation_matrix_row
  return nil if @observation_matrix_row_id.blank?
  ObservationMatrixRow.where(project_id:).find(@observation_matrix_row_id)
end

#otu_id_array ⇒ Object 



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# File 'lib/tools/description/from_observation_matrix.rb', line 214

def otu_id_array
  if observation_matrix_row_id.present?
    a = ObservationMatrixRow.where(project_id:).find(observation_matrix_row_id.to_i)
    if a && a.observation_object_type == 'Otu'
      @otu_id = a.observation_object_id
    end
  end

  if otu_id.blank?
    nil
  elsif include_descendants == 'true' # TODO: logic doesn't follow
    ::Otu.where(project_id:).self_and_descendants_of(otu_id.to_i).pluck(:id)
  else
    [otu_id]
  end
end