Class: ObservationMatrixRow

Inherits:
ApplicationRecord show all
Includes:
Housekeeping, Shared::Citations, Shared::Identifiers, Shared::IsData, Shared::Notes, Shared::Tags, SoftValidation
Defined in:
app/models/observation_matrix_row.rb

Overview

A ObservationMatrixRow is a row in an Observation matrix representing an Otu or a CollectionObject

Defined Under Namespace

Classes: Autocomplete

Constant Summary

Constants included from SoftValidation

SoftValidation::ANCESTORS_WITH_SOFT_VALIDATIONS

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Methods included from Shared::IsData

#errors_excepting, #full_error_messages_excepting, #identical, #is_community?, #is_destroyable?, #is_editable?, #is_in_use?, #is_in_users_projects?, #metamorphosize, #similar

Methods included from SoftValidation

#clear_soft_validations, #fix_for, #fix_soft_validations, #soft_fixed?, #soft_valid?, #soft_validate, #soft_validated?, #soft_validations, #soft_validators

Methods included from Shared::Notes

#concatenated_notes_string, #reject_notes

Methods included from Shared::Tags

#reject_tags, #tag_with, #tagged?, #tagged_with?

Methods included from Shared::Identifiers

#identified?, #next_by_identifier, #previous_by_identifier, #reject_identifiers

Methods included from Shared::Citations

#cited?, #mark_citations_for_destruction, #nomenclature_date, #origin_citation_source_id, #reject_citations, #requires_citation?, #sources_by_topic_id

Methods included from Housekeeping

#has_polymorphic_relationship?

Methods inherited from ApplicationRecord

transaction_with_retry

Instance Attribute Details

#cached_observation_matrix_row_item_id ⇒ Integer

Returns if the column item is derived from a ::Single::<FOO> subclass, the id of that instance.

Returns:

  • (Integer) —

    if the column item is derived from a ::Single::<FOO> subclass, the id of that instance



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# File 'app/models/observation_matrix_row.rb', line 29

class ObservationMatrixRow < ApplicationRecord
  include Housekeeping
  include Shared::Citations
  include Shared::Identifiers
  include Shared::Tags
  include Shared::Notes
  include SoftValidation
  include Shared::IsData

  acts_as_list scope: [:observation_matrix_id, :project_id]

  belongs_to :otu, inverse_of: :observation_matrix_rows
  belongs_to :collection_object, inverse_of: :observation_matrix_rows
  belongs_to :observation_matrix, inverse_of: :observation_matrix_rows

  attr_accessor :row_object_global_id

  #list of rows with otu_ids in format '1|3|5'
  scope :with_otu_ids, -> (otu_ids) { where('(observation_matrix_rows.otu_id IN (?))', otu_ids.to_s.split('|').map(&:to_i)).order(:position) }

  def observation_matrix_columns
    ObservationMatrixColumn.where(observation_matrix_id: observation_matrix_id)
  end

  after_initialize :set_reference_count

  validates_presence_of :observation_matrix
  validate :otu_and_collection_object_blank
  validate :otu_and_collection_object_given
  
  validates_uniqueness_of :otu_id, scope: [:observation_matrix_id], if: -> {!otu_id.nil?}
  validates_uniqueness_of :collection_object_id, scope: [:observation_matrix_id], if: -> {!collection_object_id.nil?}

  soft_validate(:sv_cannot_be_separated,
                set: :cannot_be_separated,
                name: 'Cannot be separated',
                description: 'Observation matrix row cannot be separated from other rows in the matrix' )

  # @param array [Array]
  # @return true
  #   incrementally sort the supplied ids
  def self.sort(array)
    array.each_with_index do |id, index|
      ObservationMatrixRow.where(id: id).update_all(position: index + 1) 
    end
    true
  end

  def set_reference_count
    self.reference_count ||= 0
  end

  def row_object
    # exit as quickly as possible
    if o = otu
      return o
    end
    if c = collection_object
      return c
    end
    nil
  end

  # ! if row_object changes (it never should, just create/destroy) this memoization is bad
  def row_object_global_id
    @row_object_global_id ||= row_object.to_global_id.to_s
    @row_object_global_id 
  end

  def row_object_class_name
    return 'Otu' if otu_id
    return 'CollectionObject' if collection_object_id
    raise
  end

  def current_taxon_name
    case row_object_class_name
    when 'Otu'
      row_object.taxon_name
    when 'CollectionObject'
      row_object.current_taxon_name
    end
  end

  def current_otu
    case row_object_class_name
    when 'Otu'
      row_object
    when 'CollectionObject'
      row_object.current_otu
    end
  end

  # TODO: belong in helpers
  def next_row
    observation_matrix.observation_matrix_rows.where("position > ?", position).order(:position).first 
  end

  def previous_row
    observation_matrix.observation_matrix_rows.where("position < ?", position).order('position DESC').first 
  end

  # @return [Scope]
  #  all the observations in this row, ordered (but not gathered)
  def observations
    t = Observation.arel_table

    a = t.alias
    b = t.project(a[Arel.star]).from(a)

    c = ObservationMatrixColumn.arel_table

    d = Descriptor.arel_table
    f = d.project(d[Arel.star]).from(d)

    # Descriptors in the matrix
    f = f.join(c, Arel::Nodes::InnerJoin)
      .on(
        d[:id].eq(c[:descriptor_id]).
        and( c[:observation_matrix_id].eq(observation_matrix_id) )
    ).order(c[:position]).as('a1')

    # TODO: when polymorphic this whole method will collapse and
    # not require this fork
    x = nil
    case row_object_class_name
    when  'Otu'
      x = a[:otu_id].eq(otu_id)
    when 'CollectionObject'
      x = a[:collection_object_id].eq(collection_object_id)
    else
      raise
    end

    # Observations from those descriptros
    b = b.join(f, Arel::Nodes::InnerJoin)
      .on(
        a[:descriptor_id].eq(f[:id]).
        and(x)
    ).as('a2')

    ::Observation.joins(Arel::Nodes::InnerJoin.new(b, Arel::Nodes::On.new(b['id'].eq(t['id']))))
  end

  private

  def otu_and_collection_object_blank
    if otu_id.nil? && collection_object_id.nil?
      errors.add(:base, 'Specify otu OR collection object!')
    end
  end

  def otu_and_collection_object_given
    if !otu_id.nil? && !collection_object_id.nil?
      errors.add(:base, 'Specify otu OR collection object, not both!')
    end
  end

  def sv_cannot_be_separated
    description = Catalog::DescriptionFromObservationMatrix.new(observation_matrix_row_id: self.id)
    if description && description.generated_description.blank?
      soft_validations.add(:base, 'No observations!')
    elsif description && description.generated_diagnosis == 'Cannot be separated from other rows in the matrix!'
      str = description.generated_diagnosis.to_s + ' Similar rows:'
      s = description.similar_objects.first[:similarities]
      description.similar_objects.each do |i|
        break if i[:similarities] != s
        if i[:otu_id]
          str += ' ' + Otu.find(i[:otu_id]).otu_name + '.'
        else
          str += ' Collection object #' + i[:collection_object_id].to_s + '.'
        end
      end
      soft_validations.add(:base, str)
    end
  end
end

#collection_object_id ⇒ Integer?

Returns id of the collecton_object or nil.

Returns:

  • (Integer, nil) —

    id of the collecton_object or nil



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# File 'app/models/observation_matrix_row.rb', line 29

class ObservationMatrixRow < ApplicationRecord
  include Housekeeping
  include Shared::Citations
  include Shared::Identifiers
  include Shared::Tags
  include Shared::Notes
  include SoftValidation
  include Shared::IsData

  acts_as_list scope: [:observation_matrix_id, :project_id]

  belongs_to :otu, inverse_of: :observation_matrix_rows
  belongs_to :collection_object, inverse_of: :observation_matrix_rows
  belongs_to :observation_matrix, inverse_of: :observation_matrix_rows

  attr_accessor :row_object_global_id

  #list of rows with otu_ids in format '1|3|5'
  scope :with_otu_ids, -> (otu_ids) { where('(observation_matrix_rows.otu_id IN (?))', otu_ids.to_s.split('|').map(&:to_i)).order(:position) }

  def observation_matrix_columns
    ObservationMatrixColumn.where(observation_matrix_id: observation_matrix_id)
  end

  after_initialize :set_reference_count

  validates_presence_of :observation_matrix
  validate :otu_and_collection_object_blank
  validate :otu_and_collection_object_given
  
  validates_uniqueness_of :otu_id, scope: [:observation_matrix_id], if: -> {!otu_id.nil?}
  validates_uniqueness_of :collection_object_id, scope: [:observation_matrix_id], if: -> {!collection_object_id.nil?}

  soft_validate(:sv_cannot_be_separated,
                set: :cannot_be_separated,
                name: 'Cannot be separated',
                description: 'Observation matrix row cannot be separated from other rows in the matrix' )

  # @param array [Array]
  # @return true
  #   incrementally sort the supplied ids
  def self.sort(array)
    array.each_with_index do |id, index|
      ObservationMatrixRow.where(id: id).update_all(position: index + 1) 
    end
    true
  end

  def set_reference_count
    self.reference_count ||= 0
  end

  def row_object
    # exit as quickly as possible
    if o = otu
      return o
    end
    if c = collection_object
      return c
    end
    nil
  end

  # ! if row_object changes (it never should, just create/destroy) this memoization is bad
  def row_object_global_id
    @row_object_global_id ||= row_object.to_global_id.to_s
    @row_object_global_id 
  end

  def row_object_class_name
    return 'Otu' if otu_id
    return 'CollectionObject' if collection_object_id
    raise
  end

  def current_taxon_name
    case row_object_class_name
    when 'Otu'
      row_object.taxon_name
    when 'CollectionObject'
      row_object.current_taxon_name
    end
  end

  def current_otu
    case row_object_class_name
    when 'Otu'
      row_object
    when 'CollectionObject'
      row_object.current_otu
    end
  end

  # TODO: belong in helpers
  def next_row
    observation_matrix.observation_matrix_rows.where("position > ?", position).order(:position).first 
  end

  def previous_row
    observation_matrix.observation_matrix_rows.where("position < ?", position).order('position DESC').first 
  end

  # @return [Scope]
  #  all the observations in this row, ordered (but not gathered)
  def observations
    t = Observation.arel_table

    a = t.alias
    b = t.project(a[Arel.star]).from(a)

    c = ObservationMatrixColumn.arel_table

    d = Descriptor.arel_table
    f = d.project(d[Arel.star]).from(d)

    # Descriptors in the matrix
    f = f.join(c, Arel::Nodes::InnerJoin)
      .on(
        d[:id].eq(c[:descriptor_id]).
        and( c[:observation_matrix_id].eq(observation_matrix_id) )
    ).order(c[:position]).as('a1')

    # TODO: when polymorphic this whole method will collapse and
    # not require this fork
    x = nil
    case row_object_class_name
    when  'Otu'
      x = a[:otu_id].eq(otu_id)
    when 'CollectionObject'
      x = a[:collection_object_id].eq(collection_object_id)
    else
      raise
    end

    # Observations from those descriptros
    b = b.join(f, Arel::Nodes::InnerJoin)
      .on(
        a[:descriptor_id].eq(f[:id]).
        and(x)
    ).as('a2')

    ::Observation.joins(Arel::Nodes::InnerJoin.new(b, Arel::Nodes::On.new(b['id'].eq(t['id']))))
  end

  private

  def otu_and_collection_object_blank
    if otu_id.nil? && collection_object_id.nil?
      errors.add(:base, 'Specify otu OR collection object!')
    end
  end

  def otu_and_collection_object_given
    if !otu_id.nil? && !collection_object_id.nil?
      errors.add(:base, 'Specify otu OR collection object, not both!')
    end
  end

  def sv_cannot_be_separated
    description = Catalog::DescriptionFromObservationMatrix.new(observation_matrix_row_id: self.id)
    if description && description.generated_description.blank?
      soft_validations.add(:base, 'No observations!')
    elsif description && description.generated_diagnosis == 'Cannot be separated from other rows in the matrix!'
      str = description.generated_diagnosis.to_s + ' Similar rows:'
      s = description.similar_objects.first[:similarities]
      description.similar_objects.each do |i|
        break if i[:similarities] != s
        if i[:otu_id]
          str += ' ' + Otu.find(i[:otu_id]).otu_name + '.'
        else
          str += ' Collection object #' + i[:collection_object_id].to_s + '.'
        end
      end
      soft_validations.add(:base, str)
    end
  end
end

#name ⇒ String?

Returns TEMPORARY value. Allows for a temporary generated/custom name for the row, useful for example when generating labels for phylogenetic trees. This value is NOT persisted and NOT intended for provenance purposes, it is strictly utilitarian. Consider using custom OTUs to track provenance.

Returns:

  • (String, nil) —

    TEMPORARY value. Allows for a temporary generated/custom name for the row, useful for example when generating labels for phylogenetic trees. This value is NOT persisted and NOT intended for provenance purposes, it is strictly utilitarian. Consider using custom OTUs to track provenance.



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# File 'app/models/observation_matrix_row.rb', line 29

class ObservationMatrixRow < ApplicationRecord
  include Housekeeping
  include Shared::Citations
  include Shared::Identifiers
  include Shared::Tags
  include Shared::Notes
  include SoftValidation
  include Shared::IsData

  acts_as_list scope: [:observation_matrix_id, :project_id]

  belongs_to :otu, inverse_of: :observation_matrix_rows
  belongs_to :collection_object, inverse_of: :observation_matrix_rows
  belongs_to :observation_matrix, inverse_of: :observation_matrix_rows

  attr_accessor :row_object_global_id

  #list of rows with otu_ids in format '1|3|5'
  scope :with_otu_ids, -> (otu_ids) { where('(observation_matrix_rows.otu_id IN (?))', otu_ids.to_s.split('|').map(&:to_i)).order(:position) }

  def observation_matrix_columns
    ObservationMatrixColumn.where(observation_matrix_id: observation_matrix_id)
  end

  after_initialize :set_reference_count

  validates_presence_of :observation_matrix
  validate :otu_and_collection_object_blank
  validate :otu_and_collection_object_given
  
  validates_uniqueness_of :otu_id, scope: [:observation_matrix_id], if: -> {!otu_id.nil?}
  validates_uniqueness_of :collection_object_id, scope: [:observation_matrix_id], if: -> {!collection_object_id.nil?}

  soft_validate(:sv_cannot_be_separated,
                set: :cannot_be_separated,
                name: 'Cannot be separated',
                description: 'Observation matrix row cannot be separated from other rows in the matrix' )

  # @param array [Array]
  # @return true
  #   incrementally sort the supplied ids
  def self.sort(array)
    array.each_with_index do |id, index|
      ObservationMatrixRow.where(id: id).update_all(position: index + 1) 
    end
    true
  end

  def set_reference_count
    self.reference_count ||= 0
  end

  def row_object
    # exit as quickly as possible
    if o = otu
      return o
    end
    if c = collection_object
      return c
    end
    nil
  end

  # ! if row_object changes (it never should, just create/destroy) this memoization is bad
  def row_object_global_id
    @row_object_global_id ||= row_object.to_global_id.to_s
    @row_object_global_id 
  end

  def row_object_class_name
    return 'Otu' if otu_id
    return 'CollectionObject' if collection_object_id
    raise
  end

  def current_taxon_name
    case row_object_class_name
    when 'Otu'
      row_object.taxon_name
    when 'CollectionObject'
      row_object.current_taxon_name
    end
  end

  def current_otu
    case row_object_class_name
    when 'Otu'
      row_object
    when 'CollectionObject'
      row_object.current_otu
    end
  end

  # TODO: belong in helpers
  def next_row
    observation_matrix.observation_matrix_rows.where("position > ?", position).order(:position).first 
  end

  def previous_row
    observation_matrix.observation_matrix_rows.where("position < ?", position).order('position DESC').first 
  end

  # @return [Scope]
  #  all the observations in this row, ordered (but not gathered)
  def observations
    t = Observation.arel_table

    a = t.alias
    b = t.project(a[Arel.star]).from(a)

    c = ObservationMatrixColumn.arel_table

    d = Descriptor.arel_table
    f = d.project(d[Arel.star]).from(d)

    # Descriptors in the matrix
    f = f.join(c, Arel::Nodes::InnerJoin)
      .on(
        d[:id].eq(c[:descriptor_id]).
        and( c[:observation_matrix_id].eq(observation_matrix_id) )
    ).order(c[:position]).as('a1')

    # TODO: when polymorphic this whole method will collapse and
    # not require this fork
    x = nil
    case row_object_class_name
    when  'Otu'
      x = a[:otu_id].eq(otu_id)
    when 'CollectionObject'
      x = a[:collection_object_id].eq(collection_object_id)
    else
      raise
    end

    # Observations from those descriptros
    b = b.join(f, Arel::Nodes::InnerJoin)
      .on(
        a[:descriptor_id].eq(f[:id]).
        and(x)
    ).as('a2')

    ::Observation.joins(Arel::Nodes::InnerJoin.new(b, Arel::Nodes::On.new(b['id'].eq(t['id']))))
  end

  private

  def otu_and_collection_object_blank
    if otu_id.nil? && collection_object_id.nil?
      errors.add(:base, 'Specify otu OR collection object!')
    end
  end

  def otu_and_collection_object_given
    if !otu_id.nil? && !collection_object_id.nil?
      errors.add(:base, 'Specify otu OR collection object, not both!')
    end
  end

  def sv_cannot_be_separated
    description = Catalog::DescriptionFromObservationMatrix.new(observation_matrix_row_id: self.id)
    if description && description.generated_description.blank?
      soft_validations.add(:base, 'No observations!')
    elsif description && description.generated_diagnosis == 'Cannot be separated from other rows in the matrix!'
      str = description.generated_diagnosis.to_s + ' Similar rows:'
      s = description.similar_objects.first[:similarities]
      description.similar_objects.each do |i|
        break if i[:similarities] != s
        if i[:otu_id]
          str += ' ' + Otu.find(i[:otu_id]).otu_name + '.'
        else
          str += ' Collection object #' + i[:collection_object_id].to_s + '.'
        end
      end
      soft_validations.add(:base, str)
    end
  end
end

#observation_matrix_id ⇒ Integer

Returns id of the matrix the row is in.

Returns:

  • (Integer) —

    id of the matrix the row is in



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# File 'app/models/observation_matrix_row.rb', line 29

class ObservationMatrixRow < ApplicationRecord
  include Housekeeping
  include Shared::Citations
  include Shared::Identifiers
  include Shared::Tags
  include Shared::Notes
  include SoftValidation
  include Shared::IsData

  acts_as_list scope: [:observation_matrix_id, :project_id]

  belongs_to :otu, inverse_of: :observation_matrix_rows
  belongs_to :collection_object, inverse_of: :observation_matrix_rows
  belongs_to :observation_matrix, inverse_of: :observation_matrix_rows

  attr_accessor :row_object_global_id

  #list of rows with otu_ids in format '1|3|5'
  scope :with_otu_ids, -> (otu_ids) { where('(observation_matrix_rows.otu_id IN (?))', otu_ids.to_s.split('|').map(&:to_i)).order(:position) }

  def observation_matrix_columns
    ObservationMatrixColumn.where(observation_matrix_id: observation_matrix_id)
  end

  after_initialize :set_reference_count

  validates_presence_of :observation_matrix
  validate :otu_and_collection_object_blank
  validate :otu_and_collection_object_given
  
  validates_uniqueness_of :otu_id, scope: [:observation_matrix_id], if: -> {!otu_id.nil?}
  validates_uniqueness_of :collection_object_id, scope: [:observation_matrix_id], if: -> {!collection_object_id.nil?}

  soft_validate(:sv_cannot_be_separated,
                set: :cannot_be_separated,
                name: 'Cannot be separated',
                description: 'Observation matrix row cannot be separated from other rows in the matrix' )

  # @param array [Array]
  # @return true
  #   incrementally sort the supplied ids
  def self.sort(array)
    array.each_with_index do |id, index|
      ObservationMatrixRow.where(id: id).update_all(position: index + 1) 
    end
    true
  end

  def set_reference_count
    self.reference_count ||= 0
  end

  def row_object
    # exit as quickly as possible
    if o = otu
      return o
    end
    if c = collection_object
      return c
    end
    nil
  end

  # ! if row_object changes (it never should, just create/destroy) this memoization is bad
  def row_object_global_id
    @row_object_global_id ||= row_object.to_global_id.to_s
    @row_object_global_id 
  end

  def row_object_class_name
    return 'Otu' if otu_id
    return 'CollectionObject' if collection_object_id
    raise
  end

  def current_taxon_name
    case row_object_class_name
    when 'Otu'
      row_object.taxon_name
    when 'CollectionObject'
      row_object.current_taxon_name
    end
  end

  def current_otu
    case row_object_class_name
    when 'Otu'
      row_object
    when 'CollectionObject'
      row_object.current_otu
    end
  end

  # TODO: belong in helpers
  def next_row
    observation_matrix.observation_matrix_rows.where("position > ?", position).order(:position).first 
  end

  def previous_row
    observation_matrix.observation_matrix_rows.where("position < ?", position).order('position DESC').first 
  end

  # @return [Scope]
  #  all the observations in this row, ordered (but not gathered)
  def observations
    t = Observation.arel_table

    a = t.alias
    b = t.project(a[Arel.star]).from(a)

    c = ObservationMatrixColumn.arel_table

    d = Descriptor.arel_table
    f = d.project(d[Arel.star]).from(d)

    # Descriptors in the matrix
    f = f.join(c, Arel::Nodes::InnerJoin)
      .on(
        d[:id].eq(c[:descriptor_id]).
        and( c[:observation_matrix_id].eq(observation_matrix_id) )
    ).order(c[:position]).as('a1')

    # TODO: when polymorphic this whole method will collapse and
    # not require this fork
    x = nil
    case row_object_class_name
    when  'Otu'
      x = a[:otu_id].eq(otu_id)
    when 'CollectionObject'
      x = a[:collection_object_id].eq(collection_object_id)
    else
      raise
    end

    # Observations from those descriptros
    b = b.join(f, Arel::Nodes::InnerJoin)
      .on(
        a[:descriptor_id].eq(f[:id]).
        and(x)
    ).as('a2')

    ::Observation.joins(Arel::Nodes::InnerJoin.new(b, Arel::Nodes::On.new(b['id'].eq(t['id']))))
  end

  private

  def otu_and_collection_object_blank
    if otu_id.nil? && collection_object_id.nil?
      errors.add(:base, 'Specify otu OR collection object!')
    end
  end

  def otu_and_collection_object_given
    if !otu_id.nil? && !collection_object_id.nil?
      errors.add(:base, 'Specify otu OR collection object, not both!')
    end
  end

  def sv_cannot_be_separated
    description = Catalog::DescriptionFromObservationMatrix.new(observation_matrix_row_id: self.id)
    if description && description.generated_description.blank?
      soft_validations.add(:base, 'No observations!')
    elsif description && description.generated_diagnosis == 'Cannot be separated from other rows in the matrix!'
      str = description.generated_diagnosis.to_s + ' Similar rows:'
      s = description.similar_objects.first[:similarities]
      description.similar_objects.each do |i|
        break if i[:similarities] != s
        if i[:otu_id]
          str += ' ' + Otu.find(i[:otu_id]).otu_name + '.'
        else
          str += ' Collection object #' + i[:collection_object_id].to_s + '.'
        end
      end
      soft_validations.add(:base, str)
    end
  end
end

#otu_id ⇒ Integer?

Returns id of the OTU or nil.

Returns:

  • (Integer, nil) —

    id of the OTU or nil



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# File 'app/models/observation_matrix_row.rb', line 29

class ObservationMatrixRow < ApplicationRecord
  include Housekeeping
  include Shared::Citations
  include Shared::Identifiers
  include Shared::Tags
  include Shared::Notes
  include SoftValidation
  include Shared::IsData

  acts_as_list scope: [:observation_matrix_id, :project_id]

  belongs_to :otu, inverse_of: :observation_matrix_rows
  belongs_to :collection_object, inverse_of: :observation_matrix_rows
  belongs_to :observation_matrix, inverse_of: :observation_matrix_rows

  attr_accessor :row_object_global_id

  #list of rows with otu_ids in format '1|3|5'
  scope :with_otu_ids, -> (otu_ids) { where('(observation_matrix_rows.otu_id IN (?))', otu_ids.to_s.split('|').map(&:to_i)).order(:position) }

  def observation_matrix_columns
    ObservationMatrixColumn.where(observation_matrix_id: observation_matrix_id)
  end

  after_initialize :set_reference_count

  validates_presence_of :observation_matrix
  validate :otu_and_collection_object_blank
  validate :otu_and_collection_object_given
  
  validates_uniqueness_of :otu_id, scope: [:observation_matrix_id], if: -> {!otu_id.nil?}
  validates_uniqueness_of :collection_object_id, scope: [:observation_matrix_id], if: -> {!collection_object_id.nil?}

  soft_validate(:sv_cannot_be_separated,
                set: :cannot_be_separated,
                name: 'Cannot be separated',
                description: 'Observation matrix row cannot be separated from other rows in the matrix' )

  # @param array [Array]
  # @return true
  #   incrementally sort the supplied ids
  def self.sort(array)
    array.each_with_index do |id, index|
      ObservationMatrixRow.where(id: id).update_all(position: index + 1) 
    end
    true
  end

  def set_reference_count
    self.reference_count ||= 0
  end

  def row_object
    # exit as quickly as possible
    if o = otu
      return o
    end
    if c = collection_object
      return c
    end
    nil
  end

  # ! if row_object changes (it never should, just create/destroy) this memoization is bad
  def row_object_global_id
    @row_object_global_id ||= row_object.to_global_id.to_s
    @row_object_global_id 
  end

  def row_object_class_name
    return 'Otu' if otu_id
    return 'CollectionObject' if collection_object_id
    raise
  end

  def current_taxon_name
    case row_object_class_name
    when 'Otu'
      row_object.taxon_name
    when 'CollectionObject'
      row_object.current_taxon_name
    end
  end

  def current_otu
    case row_object_class_name
    when 'Otu'
      row_object
    when 'CollectionObject'
      row_object.current_otu
    end
  end

  # TODO: belong in helpers
  def next_row
    observation_matrix.observation_matrix_rows.where("position > ?", position).order(:position).first 
  end

  def previous_row
    observation_matrix.observation_matrix_rows.where("position < ?", position).order('position DESC').first 
  end

  # @return [Scope]
  #  all the observations in this row, ordered (but not gathered)
  def observations
    t = Observation.arel_table

    a = t.alias
    b = t.project(a[Arel.star]).from(a)

    c = ObservationMatrixColumn.arel_table

    d = Descriptor.arel_table
    f = d.project(d[Arel.star]).from(d)

    # Descriptors in the matrix
    f = f.join(c, Arel::Nodes::InnerJoin)
      .on(
        d[:id].eq(c[:descriptor_id]).
        and( c[:observation_matrix_id].eq(observation_matrix_id) )
    ).order(c[:position]).as('a1')

    # TODO: when polymorphic this whole method will collapse and
    # not require this fork
    x = nil
    case row_object_class_name
    when  'Otu'
      x = a[:otu_id].eq(otu_id)
    when 'CollectionObject'
      x = a[:collection_object_id].eq(collection_object_id)
    else
      raise
    end

    # Observations from those descriptros
    b = b.join(f, Arel::Nodes::InnerJoin)
      .on(
        a[:descriptor_id].eq(f[:id]).
        and(x)
    ).as('a2')

    ::Observation.joins(Arel::Nodes::InnerJoin.new(b, Arel::Nodes::On.new(b['id'].eq(t['id']))))
  end

  private

  def otu_and_collection_object_blank
    if otu_id.nil? && collection_object_id.nil?
      errors.add(:base, 'Specify otu OR collection object!')
    end
  end

  def otu_and_collection_object_given
    if !otu_id.nil? && !collection_object_id.nil?
      errors.add(:base, 'Specify otu OR collection object, not both!')
    end
  end

  def sv_cannot_be_separated
    description = Catalog::DescriptionFromObservationMatrix.new(observation_matrix_row_id: self.id)
    if description && description.generated_description.blank?
      soft_validations.add(:base, 'No observations!')
    elsif description && description.generated_diagnosis == 'Cannot be separated from other rows in the matrix!'
      str = description.generated_diagnosis.to_s + ' Similar rows:'
      s = description.similar_objects.first[:similarities]
      description.similar_objects.each do |i|
        break if i[:similarities] != s
        if i[:otu_id]
          str += ' ' + Otu.find(i[:otu_id]).otu_name + '.'
        else
          str += ' Collection object #' + i[:collection_object_id].to_s + '.'
        end
      end
      soft_validations.add(:base, str)
    end
  end
end

#position ⇒ Integer

Returns from acts as list.

Returns:

  • (Integer) —

    from acts as list



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# File 'app/models/observation_matrix_row.rb', line 29

class ObservationMatrixRow < ApplicationRecord
  include Housekeeping
  include Shared::Citations
  include Shared::Identifiers
  include Shared::Tags
  include Shared::Notes
  include SoftValidation
  include Shared::IsData

  acts_as_list scope: [:observation_matrix_id, :project_id]

  belongs_to :otu, inverse_of: :observation_matrix_rows
  belongs_to :collection_object, inverse_of: :observation_matrix_rows
  belongs_to :observation_matrix, inverse_of: :observation_matrix_rows

  attr_accessor :row_object_global_id

  #list of rows with otu_ids in format '1|3|5'
  scope :with_otu_ids, -> (otu_ids) { where('(observation_matrix_rows.otu_id IN (?))', otu_ids.to_s.split('|').map(&:to_i)).order(:position) }

  def observation_matrix_columns
    ObservationMatrixColumn.where(observation_matrix_id: observation_matrix_id)
  end

  after_initialize :set_reference_count

  validates_presence_of :observation_matrix
  validate :otu_and_collection_object_blank
  validate :otu_and_collection_object_given
  
  validates_uniqueness_of :otu_id, scope: [:observation_matrix_id], if: -> {!otu_id.nil?}
  validates_uniqueness_of :collection_object_id, scope: [:observation_matrix_id], if: -> {!collection_object_id.nil?}

  soft_validate(:sv_cannot_be_separated,
                set: :cannot_be_separated,
                name: 'Cannot be separated',
                description: 'Observation matrix row cannot be separated from other rows in the matrix' )

  # @param array [Array]
  # @return true
  #   incrementally sort the supplied ids
  def self.sort(array)
    array.each_with_index do |id, index|
      ObservationMatrixRow.where(id: id).update_all(position: index + 1) 
    end
    true
  end

  def set_reference_count
    self.reference_count ||= 0
  end

  def row_object
    # exit as quickly as possible
    if o = otu
      return o
    end
    if c = collection_object
      return c
    end
    nil
  end

  # ! if row_object changes (it never should, just create/destroy) this memoization is bad
  def row_object_global_id
    @row_object_global_id ||= row_object.to_global_id.to_s
    @row_object_global_id 
  end

  def row_object_class_name
    return 'Otu' if otu_id
    return 'CollectionObject' if collection_object_id
    raise
  end

  def current_taxon_name
    case row_object_class_name
    when 'Otu'
      row_object.taxon_name
    when 'CollectionObject'
      row_object.current_taxon_name
    end
  end

  def current_otu
    case row_object_class_name
    when 'Otu'
      row_object
    when 'CollectionObject'
      row_object.current_otu
    end
  end

  # TODO: belong in helpers
  def next_row
    observation_matrix.observation_matrix_rows.where("position > ?", position).order(:position).first 
  end

  def previous_row
    observation_matrix.observation_matrix_rows.where("position < ?", position).order('position DESC').first 
  end

  # @return [Scope]
  #  all the observations in this row, ordered (but not gathered)
  def observations
    t = Observation.arel_table

    a = t.alias
    b = t.project(a[Arel.star]).from(a)

    c = ObservationMatrixColumn.arel_table

    d = Descriptor.arel_table
    f = d.project(d[Arel.star]).from(d)

    # Descriptors in the matrix
    f = f.join(c, Arel::Nodes::InnerJoin)
      .on(
        d[:id].eq(c[:descriptor_id]).
        and( c[:observation_matrix_id].eq(observation_matrix_id) )
    ).order(c[:position]).as('a1')

    # TODO: when polymorphic this whole method will collapse and
    # not require this fork
    x = nil
    case row_object_class_name
    when  'Otu'
      x = a[:otu_id].eq(otu_id)
    when 'CollectionObject'
      x = a[:collection_object_id].eq(collection_object_id)
    else
      raise
    end

    # Observations from those descriptros
    b = b.join(f, Arel::Nodes::InnerJoin)
      .on(
        a[:descriptor_id].eq(f[:id]).
        and(x)
    ).as('a2')

    ::Observation.joins(Arel::Nodes::InnerJoin.new(b, Arel::Nodes::On.new(b['id'].eq(t['id']))))
  end

  private

  def otu_and_collection_object_blank
    if otu_id.nil? && collection_object_id.nil?
      errors.add(:base, 'Specify otu OR collection object!')
    end
  end

  def otu_and_collection_object_given
    if !otu_id.nil? && !collection_object_id.nil?
      errors.add(:base, 'Specify otu OR collection object, not both!')
    end
  end

  def sv_cannot_be_separated
    description = Catalog::DescriptionFromObservationMatrix.new(observation_matrix_row_id: self.id)
    if description && description.generated_description.blank?
      soft_validations.add(:base, 'No observations!')
    elsif description && description.generated_diagnosis == 'Cannot be separated from other rows in the matrix!'
      str = description.generated_diagnosis.to_s + ' Similar rows:'
      s = description.similar_objects.first[:similarities]
      description.similar_objects.each do |i|
        break if i[:similarities] != s
        if i[:otu_id]
          str += ' ' + Otu.find(i[:otu_id]).otu_name + '.'
        else
          str += ' Collection object #' + i[:collection_object_id].to_s + '.'
        end
      end
      soft_validations.add(:base, str)
    end
  end
end

#reference_count ⇒ Integer

Indicates the total number of times this row is referened via some row_item

Returns:

  • (Integer) 


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# File 'app/models/observation_matrix_row.rb', line 29

class ObservationMatrixRow < ApplicationRecord
  include Housekeeping
  include Shared::Citations
  include Shared::Identifiers
  include Shared::Tags
  include Shared::Notes
  include SoftValidation
  include Shared::IsData

  acts_as_list scope: [:observation_matrix_id, :project_id]

  belongs_to :otu, inverse_of: :observation_matrix_rows
  belongs_to :collection_object, inverse_of: :observation_matrix_rows
  belongs_to :observation_matrix, inverse_of: :observation_matrix_rows

  attr_accessor :row_object_global_id

  #list of rows with otu_ids in format '1|3|5'
  scope :with_otu_ids, -> (otu_ids) { where('(observation_matrix_rows.otu_id IN (?))', otu_ids.to_s.split('|').map(&:to_i)).order(:position) }

  def observation_matrix_columns
    ObservationMatrixColumn.where(observation_matrix_id: observation_matrix_id)
  end

  after_initialize :set_reference_count

  validates_presence_of :observation_matrix
  validate :otu_and_collection_object_blank
  validate :otu_and_collection_object_given
  
  validates_uniqueness_of :otu_id, scope: [:observation_matrix_id], if: -> {!otu_id.nil?}
  validates_uniqueness_of :collection_object_id, scope: [:observation_matrix_id], if: -> {!collection_object_id.nil?}

  soft_validate(:sv_cannot_be_separated,
                set: :cannot_be_separated,
                name: 'Cannot be separated',
                description: 'Observation matrix row cannot be separated from other rows in the matrix' )

  # @param array [Array]
  # @return true
  #   incrementally sort the supplied ids
  def self.sort(array)
    array.each_with_index do |id, index|
      ObservationMatrixRow.where(id: id).update_all(position: index + 1) 
    end
    true
  end

  def set_reference_count
    self.reference_count ||= 0
  end

  def row_object
    # exit as quickly as possible
    if o = otu
      return o
    end
    if c = collection_object
      return c
    end
    nil
  end

  # ! if row_object changes (it never should, just create/destroy) this memoization is bad
  def row_object_global_id
    @row_object_global_id ||= row_object.to_global_id.to_s
    @row_object_global_id 
  end

  def row_object_class_name
    return 'Otu' if otu_id
    return 'CollectionObject' if collection_object_id
    raise
  end

  def current_taxon_name
    case row_object_class_name
    when 'Otu'
      row_object.taxon_name
    when 'CollectionObject'
      row_object.current_taxon_name
    end
  end

  def current_otu
    case row_object_class_name
    when 'Otu'
      row_object
    when 'CollectionObject'
      row_object.current_otu
    end
  end

  # TODO: belong in helpers
  def next_row
    observation_matrix.observation_matrix_rows.where("position > ?", position).order(:position).first 
  end

  def previous_row
    observation_matrix.observation_matrix_rows.where("position < ?", position).order('position DESC').first 
  end

  # @return [Scope]
  #  all the observations in this row, ordered (but not gathered)
  def observations
    t = Observation.arel_table

    a = t.alias
    b = t.project(a[Arel.star]).from(a)

    c = ObservationMatrixColumn.arel_table

    d = Descriptor.arel_table
    f = d.project(d[Arel.star]).from(d)

    # Descriptors in the matrix
    f = f.join(c, Arel::Nodes::InnerJoin)
      .on(
        d[:id].eq(c[:descriptor_id]).
        and( c[:observation_matrix_id].eq(observation_matrix_id) )
    ).order(c[:position]).as('a1')

    # TODO: when polymorphic this whole method will collapse and
    # not require this fork
    x = nil
    case row_object_class_name
    when  'Otu'
      x = a[:otu_id].eq(otu_id)
    when 'CollectionObject'
      x = a[:collection_object_id].eq(collection_object_id)
    else
      raise
    end

    # Observations from those descriptros
    b = b.join(f, Arel::Nodes::InnerJoin)
      .on(
        a[:descriptor_id].eq(f[:id]).
        and(x)
    ).as('a2')

    ::Observation.joins(Arel::Nodes::InnerJoin.new(b, Arel::Nodes::On.new(b['id'].eq(t['id']))))
  end

  private

  def otu_and_collection_object_blank
    if otu_id.nil? && collection_object_id.nil?
      errors.add(:base, 'Specify otu OR collection object!')
    end
  end

  def otu_and_collection_object_given
    if !otu_id.nil? && !collection_object_id.nil?
      errors.add(:base, 'Specify otu OR collection object, not both!')
    end
  end

  def sv_cannot_be_separated
    description = Catalog::DescriptionFromObservationMatrix.new(observation_matrix_row_id: self.id)
    if description && description.generated_description.blank?
      soft_validations.add(:base, 'No observations!')
    elsif description && description.generated_diagnosis == 'Cannot be separated from other rows in the matrix!'
      str = description.generated_diagnosis.to_s + ' Similar rows:'
      s = description.similar_objects.first[:similarities]
      description.similar_objects.each do |i|
        break if i[:similarities] != s
        if i[:otu_id]
          str += ' ' + Otu.find(i[:otu_id]).otu_name + '.'
        else
          str += ' Collection object #' + i[:collection_object_id].to_s + '.'
        end
      end
      soft_validations.add(:base, str)
    end
  end
end

#row_object_global_id ⇒ Object

! if row_object changes (it never should, just create/destroy) this memoization is bad



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# File 'app/models/observation_matrix_row.rb', line 93

def row_object_global_id
  @row_object_global_id
end

Class Method Details

.sort(array) ⇒ Object

Returns true incrementally sort the supplied ids.

Parameters:

  • array (Array)

Returns:

  • true incrementally sort the supplied ids



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# File 'app/models/observation_matrix_row.rb', line 70

def self.sort(array)
  array.each_with_index do |id, index|
    ObservationMatrixRow.where(id: id).update_all(position: index + 1) 
  end
  true
end

Instance Method Details

#current_otu ⇒ Object 



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# File 'app/models/observation_matrix_row.rb', line 113

def current_otu
  case row_object_class_name
  when 'Otu'
    row_object
  when 'CollectionObject'
    row_object.current_otu
  end
end

#current_taxon_name ⇒ Object 



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# File 'app/models/observation_matrix_row.rb', line 104

def current_taxon_name
  case row_object_class_name
  when 'Otu'
    row_object.taxon_name
  when 'CollectionObject'
    row_object.current_taxon_name
  end
end

#next_row ⇒ Object

TODO: belong in helpers



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# File 'app/models/observation_matrix_row.rb', line 123

def next_row
  observation_matrix.observation_matrix_rows.where("position > ?", position).order(:position).first 
end

#observation_matrix_columns ⇒ Object 



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# File 'app/models/observation_matrix_row.rb', line 49

def observation_matrix_columns
  ObservationMatrixColumn.where(observation_matrix_id: observation_matrix_id)
end

#observations ⇒ Scope

Returns all the observations in this row, ordered (but not gathered).

Returns:

  • (Scope) —

    all the observations in this row, ordered (but not gathered)



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# File 'app/models/observation_matrix_row.rb', line 133

def observations
  t = Observation.arel_table

  a = t.alias
  b = t.project(a[Arel.star]).from(a)

  c = ObservationMatrixColumn.arel_table

  d = Descriptor.arel_table
  f = d.project(d[Arel.star]).from(d)

  # Descriptors in the matrix
  f = f.join(c, Arel::Nodes::InnerJoin)
    .on(
      d[:id].eq(c[:descriptor_id]).
      and( c[:observation_matrix_id].eq(observation_matrix_id) )
  ).order(c[:position]).as('a1')

  # TODO: when polymorphic this whole method will collapse and
  # not require this fork
  x = nil
  case row_object_class_name
  when  'Otu'
    x = a[:otu_id].eq(otu_id)
  when 'CollectionObject'
    x = a[:collection_object_id].eq(collection_object_id)
  else
    raise
  end

  # Observations from those descriptros
  b = b.join(f, Arel::Nodes::InnerJoin)
    .on(
      a[:descriptor_id].eq(f[:id]).
      and(x)
  ).as('a2')

  ::Observation.joins(Arel::Nodes::InnerJoin.new(b, Arel::Nodes::On.new(b['id'].eq(t['id']))))
end

#otu_and_collection_object_blank ⇒ Object (private) 



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# File 'app/models/observation_matrix_row.rb', line 175

def otu_and_collection_object_blank
  if otu_id.nil? && collection_object_id.nil?
    errors.add(:base, 'Specify otu OR collection object!')
  end
end

#otu_and_collection_object_given ⇒ Object (private) 



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# File 'app/models/observation_matrix_row.rb', line 181

def otu_and_collection_object_given
  if !otu_id.nil? && !collection_object_id.nil?
    errors.add(:base, 'Specify otu OR collection object, not both!')
  end
end

#previous_row ⇒ Object 



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# File 'app/models/observation_matrix_row.rb', line 127

def previous_row
  observation_matrix.observation_matrix_rows.where("position < ?", position).order('position DESC').first 
end

#row_object ⇒ Object 



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# File 'app/models/observation_matrix_row.rb', line 81

def row_object
  # exit as quickly as possible
  if o = otu
    return o
  end
  if c = collection_object
    return c
  end
  nil
end

#row_object_class_name ⇒ Object 



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# File 'app/models/observation_matrix_row.rb', line 98

def row_object_class_name
  return 'Otu' if otu_id
  return 'CollectionObject' if collection_object_id
  raise
end

#set_reference_count ⇒ Object 



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# File 'app/models/observation_matrix_row.rb', line 77

def set_reference_count
  self.reference_count ||= 0
end

#sv_cannot_be_separated ⇒ Object (private) 



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# File 'app/models/observation_matrix_row.rb', line 187

def sv_cannot_be_separated
  description = Catalog::DescriptionFromObservationMatrix.new(observation_matrix_row_id: self.id)
  if description && description.generated_description.blank?
    soft_validations.add(:base, 'No observations!')
  elsif description && description.generated_diagnosis == 'Cannot be separated from other rows in the matrix!'
    str = description.generated_diagnosis.to_s + ' Similar rows:'
    s = description.similar_objects.first[:similarities]
    description.similar_objects.each do |i|
      break if i[:similarities] != s
      if i[:otu_id]
        str += ' ' + Otu.find(i[:otu_id]).otu_name + '.'
      else
        str += ' Collection object #' + i[:collection_object_id].to_s + '.'
      end
    end
    soft_validations.add(:base, str)
  end
end