Class: AnatomicalPart

Inherits:
ApplicationRecord show all
Includes:
Housekeeping, Shared::AutoUuid, Shared::BiologicalAssociations, Shared::Citations, Shared::Confidences, Shared::Containable, Shared::Conveyances, Shared::DataAttributes, Shared::Depictions, Shared::HasPapertrail, Shared::Identifiers, Shared::IsData, Shared::Loanable, Shared::Notes, Shared::Observations, Shared::OriginRelationship, Shared::ProtocolRelationships, Shared::PurlDeprecation, Shared::Tags, Shared::Taxonomy, Shared::Uri
Defined in:
app/models/anatomical_part.rb

Overview

A lightweight but extensible reference to anatomy. It refers to physical objects as instances or concepts (see is_material) The concept is a data node, with inference happening if/when linkages to an Ontology exist. I.e. we are storing only very light-weight data. Use cases:

* Collector goes to field, takes a punch of a fish fin, and returns it ->
  AnatomicalPart has_origin FieldOccurrence
* A wing is dissected from a specimen -> AnatomicalPart has_origin Specimen
* A feather is removed from a bird, and a punch from the feather ->
  AnatomicalPart has_origin AnatomicalPart has_origin FieldOccurrence
* A louse is collected from the Ear of a bat, the louse is collected, the
  Bat is not - AnatomicalPart (ear) has_origin FieldOCcurrence (bat) ->
  BiologicalAssociation <- CollectionObject (louse)

Constant Summary collapse

GRAPH_ENTRY_POINTS = 
[:biological_associations, :origin_relationships]

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 Shared::PurlDeprecation

#head_follow, #looks_obsolete_landing?, #purl_value, #sv_purl_not_deprecated

Methods included from Shared::Tags

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

Methods included from Shared::ProtocolRelationships

#machine_output?, #protocolled?, #reject_protocols

Methods included from Shared::OriginRelationship

#new_objects, #old_objects, #reject_origin_relationships, #set_origin

Methods included from Shared::Containable

#contain, containable_types, #contained?, #contained_by?, #contained_siblings, #enclosing_containers, #put_in_container

Methods included from Shared::Notes

#concatenated_notes_string, #reject_notes

Methods included from Shared::Taxonomy

#taxonomy_for_object

Methods included from Shared::BiologicalAssociations

#all_biological_associations

Methods included from Shared::Loanable

#all_loan_items, #all_loans, #container_loan_items, #container_loaned?, #container_loans, #container_times_loaned, #current_loan, #current_loan_item, #has_been_loaned?, #is_loanable?, #loan_return_date, #loaned_in_container, #on_loan?, #times_loaned

Methods included from Shared::AutoUuid

#create_object_uuid, #generate_uuid_if_required

Methods included from Shared::Identifiers

#dwc_occurrence_id, #identified?, #next_by_identifier, #previous_by_identifier, #reject_identifiers, #uuid

Methods included from Shared::HasPapertrail

#attribute_updated, #attribute_updater, #detect_version

Methods included from Shared::Conveyances

#has_conveyances?, #reject_conveyances, #reject_sounds, #sound_array=

Methods included from Shared::Depictions

#has_depictions?, #image_array=, #reject_depictions, #reject_images

Methods included from Shared::DataAttributes

#import_attributes, #internal_attributes, #keyword_value_hash, #reject_data_attributes

Methods included from Shared::Confidences

#reject_confidences

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 Shared::Uri

#uri_attribute, #valid_uri

Methods included from Housekeeping

#has_polymorphic_relationship?

Methods inherited from ApplicationRecord

transaction_with_retry

Instance Attribute Details

#is_material ⇒ Boolean

Whether or not the anatomical part is based on a physical object - a head vs. some head.

Returns:

  • (Boolean) 


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# File 'app/models/anatomical_part.rb', line 45

class AnatomicalPart < ApplicationRecord
  include Housekeeping
  include Shared::Uri
  include Shared::Citations
  include Shared::Confidences
  include Shared::DataAttributes
  include Shared::Depictions
  include Shared::Conveyances
  include Shared::HasPapertrail
  include Shared::Identifiers
  include Shared::AutoUuid
  # Override the :uri defined by Identifiers. Bad.
  def uri
    self[:uri]
  end
  include Shared::Loanable
  include Shared::BiologicalAssociations
  include Shared::Taxonomy
  include Shared::Notes
  include Shared::Observations
  include Shared::Containable
  include Shared::OriginRelationship
  include Shared::ProtocolRelationships
  include Shared::Tags
  include Shared::PurlDeprecation
  include Shared::IsData

  is_origin_for 'AnatomicalPart', 'Extract', 'Sequence', 'Sound'
  originates_from 'Otu', 'Specimen', 'Lot', 'CollectionObject', 'AnatomicalPart', 'FieldOccurrence'

  GRAPH_ENTRY_POINTS = [:biological_associations, :origin_relationships]

  attr_accessor :origin_object # origin of this part, only used on create
  attr_accessor :no_cached

  belongs_to :origin_otu, class_name: 'Otu', foreign_key: :cached_otu_id, inverse_of: :anatomical_parts
  belongs_to :preparation_type, inverse_of: :anatomical_parts

  # Needed so we can build the origin chain at the same time we're using it to
  # verify that a new AnitomicalPart has an OTU ancestor.
  # Probably not needed outside of creation.
  has_one :inbound_origin_relationship,
    -> { where(new_object_type: 'AnatomicalPart') },
    as: :new_object,
    class_name: 'OriginRelationship',
    inverse_of: :new_object

  accepts_nested_attributes_for :inbound_origin_relationship

  # Must run before associated origin_relationships are destroyed.
  before_destroy :abort_if_has_descendant_anatomical_part, prepend: true
  around_destroy :setOriginRelationshipDestroyContext, prepend: true

  after_save :set_cached, unless: -> { self.no_cached }
  # Runs in the update transaction, so any errors will abort the udpate.
  after_update :propagate_change_to_is_material!, if: :saved_change_to_is_material?

  validates :inbound_origin_relationship, presence: true, on: :create
  validate :name_or_uri_not_both
  validate :top_origin_is_valid_origin
  validate :is_material_matches_origin
  validate :is_material_matches_parent_anatomical_part

  def uuid_required
    is_material
  end

  # Callback on OriginRelationship#create
  def allow_origin_relationship_create?(origin_relationship)
    # Disallow if we already have a parent.
    return false if origin_relationship.new_object == self &&
      OriginRelationship.where(new_object: self).exists?

    true
  end

  # Callback on OriginRelationship#destroy
  def allow_origin_relationship_destroy?(origin_relationship)
    # Allow if we originated the destroy because we're being destroyed (relies
    # on abort_if_has_descendant_anatomical_part to catch cases where that
    # shouldn't be allowed).
    return true if OriginRelationshipDestroyContext.objects_in_destroy&.include?({
      id:, type: 'AnatomicalPart'
    })

    # Disallow if origin_relationship is part of our required ancestry chain.
    return false if origin_relationship.new_object == self

    true
  end

  # @return [Scope]
  #    the max 10 most recently used anatomical_parts
  def self.used_recently(user_id, project_id, used_on = '')
    old_types = valid_old_object_classes
    new_types = valid_new_object_classes
    return [] if !old_types.include?(used_on) && !new_types.include?(used_on)

    t = used_on.constantize.arel_table
    i = t[:updated_at].gt(1.week.ago)
      .and(t[:updated_by_id].eq(user_id))
      .and(t[:project_id].eq(project_id))

    p = AnatomicalPart.arel_table
    o = OriginRelationship.arel_table

    related = used_on.tableize
    related_klass = used_on
    if old_types.include?(used_on) && new_types.include?(used_on)
      a = AnatomicalPart.joins(:related_origin_relationships).joins("JOIN #{related} AS t1 ON t1.id = origin_relationships.old_object_id AND origin_relationships.old_object_type = '#{related_klass}'").where(i)

      b = AnatomicalPart.joins(:origin_relationships).joins("JOIN #{related} AS t2 ON t2.id = origin_relationships.new_object_id AND origin_relationships.new_object_type = '#{related_klass}'").where(i)

      ::Queries.union(AnatomicalPart, [a,b]).pluck(:id).uniq
    elsif old_types.include?(used_on)
      AnatomicalPart.joins(:related_origin_relationships).joins("JOIN #{related} ON #{related}.id = origin_relationships.old_object_id AND origin_relationships.old_object_type = '#{related_klass}'").where(i).pluck(:id).uniq
    else
      AnatomicalPart.joins(:origin_relationships).joins("JOIN #{related} ON #{related}.id = origin_relationships.new_object_id AND origin_relationships.new_object_type = '#{related_klass}'").where(i).pluck(:id).uniq
    end
  end

  # @return [Hash] anatomical_parts optimized for user selection
  def self.select_optimized(user_id, project_id, target = nil)
    r = used_recently(user_id, project_id, target)
    h = {
      quick: [],
      pinboard: AnatomicalPart.pinned_by(user_id).where(project_id:).to_a,
      recent: []
    }

    if target && !r.empty?
      n = target.tableize.to_sym
      h[:recent] = AnatomicalPart.where('"anatomical_parts"."id" IN (?)', r.first(10) ).to_a
      h[:quick] = (AnatomicalPart.pinned_by(user_id).pinboard_inserted.where(project_id:).to_a  +
        AnatomicalPart.where('"anatomical_parts"."id" IN (?)', r.first(4) ).to_a).uniq
    else
      h[:recent] = AnatomicalPart.where(project_id:, updated_by_id: user_id).order('updated_at DESC').limit(10).to_a
      h[:quick] = AnatomicalPart.pinned_by(user_id).pinboard_inserted.where(project_id:).to_a
    end

    h
  end

  # @return [Array[Array, Array]] where the first component is nodes, the second
  # component is edges, i.e. originRelationships.
  def self.graph(id, type)
    case type
    when *(AnatomicalPart.valid_old_object_classes - ['AnatomicalPart'])
      construct_graph_from_top_node(id, type)
    when *(AnatomicalPart.valid_new_object_classes - ['AnatomicalPart'])
      construct_graph_from_low_node(id, type)
    when 'AnatomicalPart'
      part = AnatomicalPart.find_by(id:)
      return [[], []] if part.nil?

      origin = part.taxonomic_origin_object
      # This constructs the full graph starting from origin - if we decide we
      # only want the chain containing the original input then call
      # graph_from_mid_node instead.
      construct_graph_from_top_node(origin.id, origin.class.base_class.name)
    end
  end

  # The top object in the OriginRelationship chain.
  def taxonomic_origin_object
    return @top_origin_object if @top_origin_object.present?

    origin = inbound_origin_relationship
    return nil if origin.nil? # invalid object

    next_parent = nil
    while (next_parent = OriginRelationship.where(new_object_id: origin.old_object_id, new_object_type: origin.old_object_type).first)
      origin = next_parent
    end

    @top_origin_object = origin.old_object
    @top_origin_object
  end

  def containable?
    is_material
  end

  private

  def set_cached
    update_column(:cached, name || uri_label)

    # cached_otu_id is determined by external objects, so is never changed by an
    # update, only a create.
    return if cached_otu_id

    top_origin = taxonomic_origin_object

    if top_origin.class.name == 'Otu'
      update_column(:cached_otu_id, top_origin.id)
    else
      update_column(:cached_otu_id, top_origin.current_otu.id)
    end
  end

  def name_or_uri_not_both
    has_labelled_uri = uri.present? && uri_label.present?
    return if has_labelled_uri && !name.present?
    return if name.present? && !uri.present? && !uri_label.present?

    errors.add(:base, 'Exactly one of 1) name, or 2) uri *and* uri_label, must be present')
  end

  def top_origin_is_valid_origin
    origin = taxonomic_origin_object

    errors.add(:base, 'Anatomical parts must be endpoints of an OriginRelationship!') && return if origin.nil?

    valid = valid_old_object_classes - ['AnatomicalPart']
    t = origin.class.base_class.name
    errors.add(:base, "Class of original origin must be in [#{valid.join(', ')}], not #{t}") && return if !valid.include?(t)

    return if origin.class.name == 'Otu'

    errors.add(:base, "Original origin must have a taxon determination!") && return if !origin.taxon_determinations.exists?
  end

  def is_material_matches_origin
    origin = taxonomic_origin_object
    return if origin.nil? # invalid

    if origin.class.base_class.name == 'CollectionObject' && is_material != true
      errors.add(:base, 'CollectionObject parts must have is_material true!')
      return
    elsif origin.class.base_class.name == 'Otu' && is_material == true
      errors.add(:base, 'OTU parts must have is_material false!')
      return
    end
  end

  def is_material_matches_parent_anatomical_part
    return if inbound_origin_relationship.nil? # invalid
    parent = inbound_origin_relationship.old_object
    return if parent.class.name != 'AnatomicalPart'

    if parent.is_material != is_material
      errors.add(:base, 'is_material must match parent value!')
    end
  end

  def propagate_change_to_is_material!
    # is_material can only be changed on the top AnatomicalPart, so change the
    # value on all AnatomicalPart descendants.
    new_is_material = is_material
    current = [self]

    while(current.present?)
      nxt = []
      current.each do |o|
        o.update_column(:is_material, new_is_material)
        nxt += o.new_objects
      end

      current = nxt.filter { |x| x.class.name == 'AnatomicalPart' }
    end

  end

  # Construct an AnatomicalPart graph starting from an AnatomicalPart. Going up
  # the graph is a chain ending in the source of the AnatomicalPart, going down
  # we include everything, even after we no longer see AnatomicalParts.
  def self.construct_graph_from_mid_node(anatomical_part_id, forward_only: false)
    nodes = []
    origin_relationships = []

    origin = AnatomicalPart.find(anatomical_part_id)
    current = [origin]

    # Go down the graph: going down we show everything, since it all has origin
    # some anatomical part.
    while(current.present?)
      nxt = []
      current.each do |o|
        nodes << o
        # No restriction on old_object_type.
        r = OriginRelationship.where(old_object: o)
        origin_relationships += r
        nxt += o.new_objects
      end

      current = nxt
    end

    # Go up the graph (chain).
    if !forward_only
      current = origin
      while (current.present? && current.class.name == 'AnatomicalPart')
        r = OriginRelationship.where(new_object_id: current.id, new_object_type: 'AnatomicalPart').first
        if r.present?
          origin_relationships << r
          nodes << current.old_objects.first
        end

        current = current.old_objects.first
      end
    end

    return nodes, origin_relationships
  end

  # Construct anatomical part graph starting at a top node, like
  # CollectionObject, FieldOccurrence, OTU. This returns *all* AnatomicalPart
  # children of the top node.
  def self.construct_graph_from_top_node(node_id, node_type)
    origin = node_type.constantize.find(node_id)
    r = OriginRelationship
      .where(
        old_object_id: node_id,
        old_object_type: node_type,
        new_object_type: 'AnatomicalPart'
      )

    origin_relationships = r
    nodes = [origin]
    r.each do |rln|
      anatomical_part = rln.new_object
      new_nodes, new_origin_relationships = construct_graph_from_mid_node(
        anatomical_part.id, forward_only: true
      )
      nodes += new_nodes
      origin_relationships += new_origin_relationships
    end

  return nodes, origin_relationships
  end

  # Construct an AnatomicalPart graph starting from the direct
  # non-anatomical-part child of an anatomical part, like an Extract or a Sound.
  # @param node_type is *not* AnatomicalPart, but we assume its origin *is*.
  def self.construct_graph_from_low_node(node_id, node_type)
    origin = node_type.constantize.find(node_id)
    r = OriginRelationship
      .where(
        new_object_id: node_id,
        new_object_type: node_type,
        old_object_type: 'AnatomicalPart'
      )

    anatomical_part = r.first&.old_object # reverse paths are always a chain (for anatomical parts)

    nodes = [origin]
    origin_relationships = []
    if anatomical_part
      # This can return more children of anatomical_part than just node.
      nodes, origin_relationships = construct_graph_from_mid_node(
        anatomical_part.id
      )
    end

    return nodes, origin_relationships
  end

  def abort_if_has_descendant_anatomical_part
    if OriginRelationship.where(old_object: self).exists?
      errors.add(:base, "This part can't be deleted because it's not the end of an AnatomicalPart chain.")
      throw(:abort)
    end
  end

  def setOriginRelationshipDestroyContext
    OriginRelationshipDestroyContext.objects_in_destroy ||= Set.new
    OriginRelationshipDestroyContext.objects_in_destroy << {
      id:, type: 'AnatomicalPart'
    }

    yield

  ensure
    OriginRelationshipDestroyContext.objects_in_destroy.delete({
      id:, type: 'AnatomicalPart'
    })
  end
end

#name ⇒ String

Name of the anatomical part.

Returns:

  • (String) 


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# File 'app/models/anatomical_part.rb', line 45

class AnatomicalPart < ApplicationRecord
  include Housekeeping
  include Shared::Uri
  include Shared::Citations
  include Shared::Confidences
  include Shared::DataAttributes
  include Shared::Depictions
  include Shared::Conveyances
  include Shared::HasPapertrail
  include Shared::Identifiers
  include Shared::AutoUuid
  # Override the :uri defined by Identifiers. Bad.
  def uri
    self[:uri]
  end
  include Shared::Loanable
  include Shared::BiologicalAssociations
  include Shared::Taxonomy
  include Shared::Notes
  include Shared::Observations
  include Shared::Containable
  include Shared::OriginRelationship
  include Shared::ProtocolRelationships
  include Shared::Tags
  include Shared::PurlDeprecation
  include Shared::IsData

  is_origin_for 'AnatomicalPart', 'Extract', 'Sequence', 'Sound'
  originates_from 'Otu', 'Specimen', 'Lot', 'CollectionObject', 'AnatomicalPart', 'FieldOccurrence'

  GRAPH_ENTRY_POINTS = [:biological_associations, :origin_relationships]

  attr_accessor :origin_object # origin of this part, only used on create
  attr_accessor :no_cached

  belongs_to :origin_otu, class_name: 'Otu', foreign_key: :cached_otu_id, inverse_of: :anatomical_parts
  belongs_to :preparation_type, inverse_of: :anatomical_parts

  # Needed so we can build the origin chain at the same time we're using it to
  # verify that a new AnitomicalPart has an OTU ancestor.
  # Probably not needed outside of creation.
  has_one :inbound_origin_relationship,
    -> { where(new_object_type: 'AnatomicalPart') },
    as: :new_object,
    class_name: 'OriginRelationship',
    inverse_of: :new_object

  accepts_nested_attributes_for :inbound_origin_relationship

  # Must run before associated origin_relationships are destroyed.
  before_destroy :abort_if_has_descendant_anatomical_part, prepend: true
  around_destroy :setOriginRelationshipDestroyContext, prepend: true

  after_save :set_cached, unless: -> { self.no_cached }
  # Runs in the update transaction, so any errors will abort the udpate.
  after_update :propagate_change_to_is_material!, if: :saved_change_to_is_material?

  validates :inbound_origin_relationship, presence: true, on: :create
  validate :name_or_uri_not_both
  validate :top_origin_is_valid_origin
  validate :is_material_matches_origin
  validate :is_material_matches_parent_anatomical_part

  def uuid_required
    is_material
  end

  # Callback on OriginRelationship#create
  def allow_origin_relationship_create?(origin_relationship)
    # Disallow if we already have a parent.
    return false if origin_relationship.new_object == self &&
      OriginRelationship.where(new_object: self).exists?

    true
  end

  # Callback on OriginRelationship#destroy
  def allow_origin_relationship_destroy?(origin_relationship)
    # Allow if we originated the destroy because we're being destroyed (relies
    # on abort_if_has_descendant_anatomical_part to catch cases where that
    # shouldn't be allowed).
    return true if OriginRelationshipDestroyContext.objects_in_destroy&.include?({
      id:, type: 'AnatomicalPart'
    })

    # Disallow if origin_relationship is part of our required ancestry chain.
    return false if origin_relationship.new_object == self

    true
  end

  # @return [Scope]
  #    the max 10 most recently used anatomical_parts
  def self.used_recently(user_id, project_id, used_on = '')
    old_types = valid_old_object_classes
    new_types = valid_new_object_classes
    return [] if !old_types.include?(used_on) && !new_types.include?(used_on)

    t = used_on.constantize.arel_table
    i = t[:updated_at].gt(1.week.ago)
      .and(t[:updated_by_id].eq(user_id))
      .and(t[:project_id].eq(project_id))

    p = AnatomicalPart.arel_table
    o = OriginRelationship.arel_table

    related = used_on.tableize
    related_klass = used_on
    if old_types.include?(used_on) && new_types.include?(used_on)
      a = AnatomicalPart.joins(:related_origin_relationships).joins("JOIN #{related} AS t1 ON t1.id = origin_relationships.old_object_id AND origin_relationships.old_object_type = '#{related_klass}'").where(i)

      b = AnatomicalPart.joins(:origin_relationships).joins("JOIN #{related} AS t2 ON t2.id = origin_relationships.new_object_id AND origin_relationships.new_object_type = '#{related_klass}'").where(i)

      ::Queries.union(AnatomicalPart, [a,b]).pluck(:id).uniq
    elsif old_types.include?(used_on)
      AnatomicalPart.joins(:related_origin_relationships).joins("JOIN #{related} ON #{related}.id = origin_relationships.old_object_id AND origin_relationships.old_object_type = '#{related_klass}'").where(i).pluck(:id).uniq
    else
      AnatomicalPart.joins(:origin_relationships).joins("JOIN #{related} ON #{related}.id = origin_relationships.new_object_id AND origin_relationships.new_object_type = '#{related_klass}'").where(i).pluck(:id).uniq
    end
  end

  # @return [Hash] anatomical_parts optimized for user selection
  def self.select_optimized(user_id, project_id, target = nil)
    r = used_recently(user_id, project_id, target)
    h = {
      quick: [],
      pinboard: AnatomicalPart.pinned_by(user_id).where(project_id:).to_a,
      recent: []
    }

    if target && !r.empty?
      n = target.tableize.to_sym
      h[:recent] = AnatomicalPart.where('"anatomical_parts"."id" IN (?)', r.first(10) ).to_a
      h[:quick] = (AnatomicalPart.pinned_by(user_id).pinboard_inserted.where(project_id:).to_a  +
        AnatomicalPart.where('"anatomical_parts"."id" IN (?)', r.first(4) ).to_a).uniq
    else
      h[:recent] = AnatomicalPart.where(project_id:, updated_by_id: user_id).order('updated_at DESC').limit(10).to_a
      h[:quick] = AnatomicalPart.pinned_by(user_id).pinboard_inserted.where(project_id:).to_a
    end

    h
  end

  # @return [Array[Array, Array]] where the first component is nodes, the second
  # component is edges, i.e. originRelationships.
  def self.graph(id, type)
    case type
    when *(AnatomicalPart.valid_old_object_classes - ['AnatomicalPart'])
      construct_graph_from_top_node(id, type)
    when *(AnatomicalPart.valid_new_object_classes - ['AnatomicalPart'])
      construct_graph_from_low_node(id, type)
    when 'AnatomicalPart'
      part = AnatomicalPart.find_by(id:)
      return [[], []] if part.nil?

      origin = part.taxonomic_origin_object
      # This constructs the full graph starting from origin - if we decide we
      # only want the chain containing the original input then call
      # graph_from_mid_node instead.
      construct_graph_from_top_node(origin.id, origin.class.base_class.name)
    end
  end

  # The top object in the OriginRelationship chain.
  def taxonomic_origin_object
    return @top_origin_object if @top_origin_object.present?

    origin = inbound_origin_relationship
    return nil if origin.nil? # invalid object

    next_parent = nil
    while (next_parent = OriginRelationship.where(new_object_id: origin.old_object_id, new_object_type: origin.old_object_type).first)
      origin = next_parent
    end

    @top_origin_object = origin.old_object
    @top_origin_object
  end

  def containable?
    is_material
  end

  private

  def set_cached
    update_column(:cached, name || uri_label)

    # cached_otu_id is determined by external objects, so is never changed by an
    # update, only a create.
    return if cached_otu_id

    top_origin = taxonomic_origin_object

    if top_origin.class.name == 'Otu'
      update_column(:cached_otu_id, top_origin.id)
    else
      update_column(:cached_otu_id, top_origin.current_otu.id)
    end
  end

  def name_or_uri_not_both
    has_labelled_uri = uri.present? && uri_label.present?
    return if has_labelled_uri && !name.present?
    return if name.present? && !uri.present? && !uri_label.present?

    errors.add(:base, 'Exactly one of 1) name, or 2) uri *and* uri_label, must be present')
  end

  def top_origin_is_valid_origin
    origin = taxonomic_origin_object

    errors.add(:base, 'Anatomical parts must be endpoints of an OriginRelationship!') && return if origin.nil?

    valid = valid_old_object_classes - ['AnatomicalPart']
    t = origin.class.base_class.name
    errors.add(:base, "Class of original origin must be in [#{valid.join(', ')}], not #{t}") && return if !valid.include?(t)

    return if origin.class.name == 'Otu'

    errors.add(:base, "Original origin must have a taxon determination!") && return if !origin.taxon_determinations.exists?
  end

  def is_material_matches_origin
    origin = taxonomic_origin_object
    return if origin.nil? # invalid

    if origin.class.base_class.name == 'CollectionObject' && is_material != true
      errors.add(:base, 'CollectionObject parts must have is_material true!')
      return
    elsif origin.class.base_class.name == 'Otu' && is_material == true
      errors.add(:base, 'OTU parts must have is_material false!')
      return
    end
  end

  def is_material_matches_parent_anatomical_part
    return if inbound_origin_relationship.nil? # invalid
    parent = inbound_origin_relationship.old_object
    return if parent.class.name != 'AnatomicalPart'

    if parent.is_material != is_material
      errors.add(:base, 'is_material must match parent value!')
    end
  end

  def propagate_change_to_is_material!
    # is_material can only be changed on the top AnatomicalPart, so change the
    # value on all AnatomicalPart descendants.
    new_is_material = is_material
    current = [self]

    while(current.present?)
      nxt = []
      current.each do |o|
        o.update_column(:is_material, new_is_material)
        nxt += o.new_objects
      end

      current = nxt.filter { |x| x.class.name == 'AnatomicalPart' }
    end

  end

  # Construct an AnatomicalPart graph starting from an AnatomicalPart. Going up
  # the graph is a chain ending in the source of the AnatomicalPart, going down
  # we include everything, even after we no longer see AnatomicalParts.
  def self.construct_graph_from_mid_node(anatomical_part_id, forward_only: false)
    nodes = []
    origin_relationships = []

    origin = AnatomicalPart.find(anatomical_part_id)
    current = [origin]

    # Go down the graph: going down we show everything, since it all has origin
    # some anatomical part.
    while(current.present?)
      nxt = []
      current.each do |o|
        nodes << o
        # No restriction on old_object_type.
        r = OriginRelationship.where(old_object: o)
        origin_relationships += r
        nxt += o.new_objects
      end

      current = nxt
    end

    # Go up the graph (chain).
    if !forward_only
      current = origin
      while (current.present? && current.class.name == 'AnatomicalPart')
        r = OriginRelationship.where(new_object_id: current.id, new_object_type: 'AnatomicalPart').first
        if r.present?
          origin_relationships << r
          nodes << current.old_objects.first
        end

        current = current.old_objects.first
      end
    end

    return nodes, origin_relationships
  end

  # Construct anatomical part graph starting at a top node, like
  # CollectionObject, FieldOccurrence, OTU. This returns *all* AnatomicalPart
  # children of the top node.
  def self.construct_graph_from_top_node(node_id, node_type)
    origin = node_type.constantize.find(node_id)
    r = OriginRelationship
      .where(
        old_object_id: node_id,
        old_object_type: node_type,
        new_object_type: 'AnatomicalPart'
      )

    origin_relationships = r
    nodes = [origin]
    r.each do |rln|
      anatomical_part = rln.new_object
      new_nodes, new_origin_relationships = construct_graph_from_mid_node(
        anatomical_part.id, forward_only: true
      )
      nodes += new_nodes
      origin_relationships += new_origin_relationships
    end

  return nodes, origin_relationships
  end

  # Construct an AnatomicalPart graph starting from the direct
  # non-anatomical-part child of an anatomical part, like an Extract or a Sound.
  # @param node_type is *not* AnatomicalPart, but we assume its origin *is*.
  def self.construct_graph_from_low_node(node_id, node_type)
    origin = node_type.constantize.find(node_id)
    r = OriginRelationship
      .where(
        new_object_id: node_id,
        new_object_type: node_type,
        old_object_type: 'AnatomicalPart'
      )

    anatomical_part = r.first&.old_object # reverse paths are always a chain (for anatomical parts)

    nodes = [origin]
    origin_relationships = []
    if anatomical_part
      # This can return more children of anatomical_part than just node.
      nodes, origin_relationships = construct_graph_from_mid_node(
        anatomical_part.id
      )
    end

    return nodes, origin_relationships
  end

  def abort_if_has_descendant_anatomical_part
    if OriginRelationship.where(old_object: self).exists?
      errors.add(:base, "This part can't be deleted because it's not the end of an AnatomicalPart chain.")
      throw(:abort)
    end
  end

  def setOriginRelationshipDestroyContext
    OriginRelationshipDestroyContext.objects_in_destroy ||= Set.new
    OriginRelationshipDestroyContext.objects_in_destroy << {
      id:, type: 'AnatomicalPart'
    }

    yield

  ensure
    OriginRelationshipDestroyContext.objects_in_destroy.delete({
      id:, type: 'AnatomicalPart'
    })
  end
end

#no_cached ⇒ Object

Returns the value of attribute no_cached.



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# File 'app/models/anatomical_part.rb', line 78

def no_cached
  @no_cached
end

#origin_object ⇒ Object

origin of this part, only used on create



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

def origin_object
  @origin_object
end

#preparation_type_id ⇒ Integer

Preparation type of this part.

Returns:

  • (Integer) 


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# File 'app/models/anatomical_part.rb', line 45

class AnatomicalPart < ApplicationRecord
  include Housekeeping
  include Shared::Uri
  include Shared::Citations
  include Shared::Confidences
  include Shared::DataAttributes
  include Shared::Depictions
  include Shared::Conveyances
  include Shared::HasPapertrail
  include Shared::Identifiers
  include Shared::AutoUuid
  # Override the :uri defined by Identifiers. Bad.
  def uri
    self[:uri]
  end
  include Shared::Loanable
  include Shared::BiologicalAssociations
  include Shared::Taxonomy
  include Shared::Notes
  include Shared::Observations
  include Shared::Containable
  include Shared::OriginRelationship
  include Shared::ProtocolRelationships
  include Shared::Tags
  include Shared::PurlDeprecation
  include Shared::IsData

  is_origin_for 'AnatomicalPart', 'Extract', 'Sequence', 'Sound'
  originates_from 'Otu', 'Specimen', 'Lot', 'CollectionObject', 'AnatomicalPart', 'FieldOccurrence'

  GRAPH_ENTRY_POINTS = [:biological_associations, :origin_relationships]

  attr_accessor :origin_object # origin of this part, only used on create
  attr_accessor :no_cached

  belongs_to :origin_otu, class_name: 'Otu', foreign_key: :cached_otu_id, inverse_of: :anatomical_parts
  belongs_to :preparation_type, inverse_of: :anatomical_parts

  # Needed so we can build the origin chain at the same time we're using it to
  # verify that a new AnitomicalPart has an OTU ancestor.
  # Probably not needed outside of creation.
  has_one :inbound_origin_relationship,
    -> { where(new_object_type: 'AnatomicalPart') },
    as: :new_object,
    class_name: 'OriginRelationship',
    inverse_of: :new_object

  accepts_nested_attributes_for :inbound_origin_relationship

  # Must run before associated origin_relationships are destroyed.
  before_destroy :abort_if_has_descendant_anatomical_part, prepend: true
  around_destroy :setOriginRelationshipDestroyContext, prepend: true

  after_save :set_cached, unless: -> { self.no_cached }
  # Runs in the update transaction, so any errors will abort the udpate.
  after_update :propagate_change_to_is_material!, if: :saved_change_to_is_material?

  validates :inbound_origin_relationship, presence: true, on: :create
  validate :name_or_uri_not_both
  validate :top_origin_is_valid_origin
  validate :is_material_matches_origin
  validate :is_material_matches_parent_anatomical_part

  def uuid_required
    is_material
  end

  # Callback on OriginRelationship#create
  def allow_origin_relationship_create?(origin_relationship)
    # Disallow if we already have a parent.
    return false if origin_relationship.new_object == self &&
      OriginRelationship.where(new_object: self).exists?

    true
  end

  # Callback on OriginRelationship#destroy
  def allow_origin_relationship_destroy?(origin_relationship)
    # Allow if we originated the destroy because we're being destroyed (relies
    # on abort_if_has_descendant_anatomical_part to catch cases where that
    # shouldn't be allowed).
    return true if OriginRelationshipDestroyContext.objects_in_destroy&.include?({
      id:, type: 'AnatomicalPart'
    })

    # Disallow if origin_relationship is part of our required ancestry chain.
    return false if origin_relationship.new_object == self

    true
  end

  # @return [Scope]
  #    the max 10 most recently used anatomical_parts
  def self.used_recently(user_id, project_id, used_on = '')
    old_types = valid_old_object_classes
    new_types = valid_new_object_classes
    return [] if !old_types.include?(used_on) && !new_types.include?(used_on)

    t = used_on.constantize.arel_table
    i = t[:updated_at].gt(1.week.ago)
      .and(t[:updated_by_id].eq(user_id))
      .and(t[:project_id].eq(project_id))

    p = AnatomicalPart.arel_table
    o = OriginRelationship.arel_table

    related = used_on.tableize
    related_klass = used_on
    if old_types.include?(used_on) && new_types.include?(used_on)
      a = AnatomicalPart.joins(:related_origin_relationships).joins("JOIN #{related} AS t1 ON t1.id = origin_relationships.old_object_id AND origin_relationships.old_object_type = '#{related_klass}'").where(i)

      b = AnatomicalPart.joins(:origin_relationships).joins("JOIN #{related} AS t2 ON t2.id = origin_relationships.new_object_id AND origin_relationships.new_object_type = '#{related_klass}'").where(i)

      ::Queries.union(AnatomicalPart, [a,b]).pluck(:id).uniq
    elsif old_types.include?(used_on)
      AnatomicalPart.joins(:related_origin_relationships).joins("JOIN #{related} ON #{related}.id = origin_relationships.old_object_id AND origin_relationships.old_object_type = '#{related_klass}'").where(i).pluck(:id).uniq
    else
      AnatomicalPart.joins(:origin_relationships).joins("JOIN #{related} ON #{related}.id = origin_relationships.new_object_id AND origin_relationships.new_object_type = '#{related_klass}'").where(i).pluck(:id).uniq
    end
  end

  # @return [Hash] anatomical_parts optimized for user selection
  def self.select_optimized(user_id, project_id, target = nil)
    r = used_recently(user_id, project_id, target)
    h = {
      quick: [],
      pinboard: AnatomicalPart.pinned_by(user_id).where(project_id:).to_a,
      recent: []
    }

    if target && !r.empty?
      n = target.tableize.to_sym
      h[:recent] = AnatomicalPart.where('"anatomical_parts"."id" IN (?)', r.first(10) ).to_a
      h[:quick] = (AnatomicalPart.pinned_by(user_id).pinboard_inserted.where(project_id:).to_a  +
        AnatomicalPart.where('"anatomical_parts"."id" IN (?)', r.first(4) ).to_a).uniq
    else
      h[:recent] = AnatomicalPart.where(project_id:, updated_by_id: user_id).order('updated_at DESC').limit(10).to_a
      h[:quick] = AnatomicalPart.pinned_by(user_id).pinboard_inserted.where(project_id:).to_a
    end

    h
  end

  # @return [Array[Array, Array]] where the first component is nodes, the second
  # component is edges, i.e. originRelationships.
  def self.graph(id, type)
    case type
    when *(AnatomicalPart.valid_old_object_classes - ['AnatomicalPart'])
      construct_graph_from_top_node(id, type)
    when *(AnatomicalPart.valid_new_object_classes - ['AnatomicalPart'])
      construct_graph_from_low_node(id, type)
    when 'AnatomicalPart'
      part = AnatomicalPart.find_by(id:)
      return [[], []] if part.nil?

      origin = part.taxonomic_origin_object
      # This constructs the full graph starting from origin - if we decide we
      # only want the chain containing the original input then call
      # graph_from_mid_node instead.
      construct_graph_from_top_node(origin.id, origin.class.base_class.name)
    end
  end

  # The top object in the OriginRelationship chain.
  def taxonomic_origin_object
    return @top_origin_object if @top_origin_object.present?

    origin = inbound_origin_relationship
    return nil if origin.nil? # invalid object

    next_parent = nil
    while (next_parent = OriginRelationship.where(new_object_id: origin.old_object_id, new_object_type: origin.old_object_type).first)
      origin = next_parent
    end

    @top_origin_object = origin.old_object
    @top_origin_object
  end

  def containable?
    is_material
  end

  private

  def set_cached
    update_column(:cached, name || uri_label)

    # cached_otu_id is determined by external objects, so is never changed by an
    # update, only a create.
    return if cached_otu_id

    top_origin = taxonomic_origin_object

    if top_origin.class.name == 'Otu'
      update_column(:cached_otu_id, top_origin.id)
    else
      update_column(:cached_otu_id, top_origin.current_otu.id)
    end
  end

  def name_or_uri_not_both
    has_labelled_uri = uri.present? && uri_label.present?
    return if has_labelled_uri && !name.present?
    return if name.present? && !uri.present? && !uri_label.present?

    errors.add(:base, 'Exactly one of 1) name, or 2) uri *and* uri_label, must be present')
  end

  def top_origin_is_valid_origin
    origin = taxonomic_origin_object

    errors.add(:base, 'Anatomical parts must be endpoints of an OriginRelationship!') && return if origin.nil?

    valid = valid_old_object_classes - ['AnatomicalPart']
    t = origin.class.base_class.name
    errors.add(:base, "Class of original origin must be in [#{valid.join(', ')}], not #{t}") && return if !valid.include?(t)

    return if origin.class.name == 'Otu'

    errors.add(:base, "Original origin must have a taxon determination!") && return if !origin.taxon_determinations.exists?
  end

  def is_material_matches_origin
    origin = taxonomic_origin_object
    return if origin.nil? # invalid

    if origin.class.base_class.name == 'CollectionObject' && is_material != true
      errors.add(:base, 'CollectionObject parts must have is_material true!')
      return
    elsif origin.class.base_class.name == 'Otu' && is_material == true
      errors.add(:base, 'OTU parts must have is_material false!')
      return
    end
  end

  def is_material_matches_parent_anatomical_part
    return if inbound_origin_relationship.nil? # invalid
    parent = inbound_origin_relationship.old_object
    return if parent.class.name != 'AnatomicalPart'

    if parent.is_material != is_material
      errors.add(:base, 'is_material must match parent value!')
    end
  end

  def propagate_change_to_is_material!
    # is_material can only be changed on the top AnatomicalPart, so change the
    # value on all AnatomicalPart descendants.
    new_is_material = is_material
    current = [self]

    while(current.present?)
      nxt = []
      current.each do |o|
        o.update_column(:is_material, new_is_material)
        nxt += o.new_objects
      end

      current = nxt.filter { |x| x.class.name == 'AnatomicalPart' }
    end

  end

  # Construct an AnatomicalPart graph starting from an AnatomicalPart. Going up
  # the graph is a chain ending in the source of the AnatomicalPart, going down
  # we include everything, even after we no longer see AnatomicalParts.
  def self.construct_graph_from_mid_node(anatomical_part_id, forward_only: false)
    nodes = []
    origin_relationships = []

    origin = AnatomicalPart.find(anatomical_part_id)
    current = [origin]

    # Go down the graph: going down we show everything, since it all has origin
    # some anatomical part.
    while(current.present?)
      nxt = []
      current.each do |o|
        nodes << o
        # No restriction on old_object_type.
        r = OriginRelationship.where(old_object: o)
        origin_relationships += r
        nxt += o.new_objects
      end

      current = nxt
    end

    # Go up the graph (chain).
    if !forward_only
      current = origin
      while (current.present? && current.class.name == 'AnatomicalPart')
        r = OriginRelationship.where(new_object_id: current.id, new_object_type: 'AnatomicalPart').first
        if r.present?
          origin_relationships << r
          nodes << current.old_objects.first
        end

        current = current.old_objects.first
      end
    end

    return nodes, origin_relationships
  end

  # Construct anatomical part graph starting at a top node, like
  # CollectionObject, FieldOccurrence, OTU. This returns *all* AnatomicalPart
  # children of the top node.
  def self.construct_graph_from_top_node(node_id, node_type)
    origin = node_type.constantize.find(node_id)
    r = OriginRelationship
      .where(
        old_object_id: node_id,
        old_object_type: node_type,
        new_object_type: 'AnatomicalPart'
      )

    origin_relationships = r
    nodes = [origin]
    r.each do |rln|
      anatomical_part = rln.new_object
      new_nodes, new_origin_relationships = construct_graph_from_mid_node(
        anatomical_part.id, forward_only: true
      )
      nodes += new_nodes
      origin_relationships += new_origin_relationships
    end

  return nodes, origin_relationships
  end

  # Construct an AnatomicalPart graph starting from the direct
  # non-anatomical-part child of an anatomical part, like an Extract or a Sound.
  # @param node_type is *not* AnatomicalPart, but we assume its origin *is*.
  def self.construct_graph_from_low_node(node_id, node_type)
    origin = node_type.constantize.find(node_id)
    r = OriginRelationship
      .where(
        new_object_id: node_id,
        new_object_type: node_type,
        old_object_type: 'AnatomicalPart'
      )

    anatomical_part = r.first&.old_object # reverse paths are always a chain (for anatomical parts)

    nodes = [origin]
    origin_relationships = []
    if anatomical_part
      # This can return more children of anatomical_part than just node.
      nodes, origin_relationships = construct_graph_from_mid_node(
        anatomical_part.id
      )
    end

    return nodes, origin_relationships
  end

  def abort_if_has_descendant_anatomical_part
    if OriginRelationship.where(old_object: self).exists?
      errors.add(:base, "This part can't be deleted because it's not the end of an AnatomicalPart chain.")
      throw(:abort)
    end
  end

  def setOriginRelationshipDestroyContext
    OriginRelationshipDestroyContext.objects_in_destroy ||= Set.new
    OriginRelationshipDestroyContext.objects_in_destroy << {
      id:, type: 'AnatomicalPart'
    }

    yield

  ensure
    OriginRelationshipDestroyContext.objects_in_destroy.delete({
      id:, type: 'AnatomicalPart'
    })
  end
end

#project_id ⇒ Integer

the project ID

Returns:

  • (Integer) 


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# File 'app/models/anatomical_part.rb', line 45

class AnatomicalPart < ApplicationRecord
  include Housekeeping
  include Shared::Uri
  include Shared::Citations
  include Shared::Confidences
  include Shared::DataAttributes
  include Shared::Depictions
  include Shared::Conveyances
  include Shared::HasPapertrail
  include Shared::Identifiers
  include Shared::AutoUuid
  # Override the :uri defined by Identifiers. Bad.
  def uri
    self[:uri]
  end
  include Shared::Loanable
  include Shared::BiologicalAssociations
  include Shared::Taxonomy
  include Shared::Notes
  include Shared::Observations
  include Shared::Containable
  include Shared::OriginRelationship
  include Shared::ProtocolRelationships
  include Shared::Tags
  include Shared::PurlDeprecation
  include Shared::IsData

  is_origin_for 'AnatomicalPart', 'Extract', 'Sequence', 'Sound'
  originates_from 'Otu', 'Specimen', 'Lot', 'CollectionObject', 'AnatomicalPart', 'FieldOccurrence'

  GRAPH_ENTRY_POINTS = [:biological_associations, :origin_relationships]

  attr_accessor :origin_object # origin of this part, only used on create
  attr_accessor :no_cached

  belongs_to :origin_otu, class_name: 'Otu', foreign_key: :cached_otu_id, inverse_of: :anatomical_parts
  belongs_to :preparation_type, inverse_of: :anatomical_parts

  # Needed so we can build the origin chain at the same time we're using it to
  # verify that a new AnitomicalPart has an OTU ancestor.
  # Probably not needed outside of creation.
  has_one :inbound_origin_relationship,
    -> { where(new_object_type: 'AnatomicalPart') },
    as: :new_object,
    class_name: 'OriginRelationship',
    inverse_of: :new_object

  accepts_nested_attributes_for :inbound_origin_relationship

  # Must run before associated origin_relationships are destroyed.
  before_destroy :abort_if_has_descendant_anatomical_part, prepend: true
  around_destroy :setOriginRelationshipDestroyContext, prepend: true

  after_save :set_cached, unless: -> { self.no_cached }
  # Runs in the update transaction, so any errors will abort the udpate.
  after_update :propagate_change_to_is_material!, if: :saved_change_to_is_material?

  validates :inbound_origin_relationship, presence: true, on: :create
  validate :name_or_uri_not_both
  validate :top_origin_is_valid_origin
  validate :is_material_matches_origin
  validate :is_material_matches_parent_anatomical_part

  def uuid_required
    is_material
  end

  # Callback on OriginRelationship#create
  def allow_origin_relationship_create?(origin_relationship)
    # Disallow if we already have a parent.
    return false if origin_relationship.new_object == self &&
      OriginRelationship.where(new_object: self).exists?

    true
  end

  # Callback on OriginRelationship#destroy
  def allow_origin_relationship_destroy?(origin_relationship)
    # Allow if we originated the destroy because we're being destroyed (relies
    # on abort_if_has_descendant_anatomical_part to catch cases where that
    # shouldn't be allowed).
    return true if OriginRelationshipDestroyContext.objects_in_destroy&.include?({
      id:, type: 'AnatomicalPart'
    })

    # Disallow if origin_relationship is part of our required ancestry chain.
    return false if origin_relationship.new_object == self

    true
  end

  # @return [Scope]
  #    the max 10 most recently used anatomical_parts
  def self.used_recently(user_id, project_id, used_on = '')
    old_types = valid_old_object_classes
    new_types = valid_new_object_classes
    return [] if !old_types.include?(used_on) && !new_types.include?(used_on)

    t = used_on.constantize.arel_table
    i = t[:updated_at].gt(1.week.ago)
      .and(t[:updated_by_id].eq(user_id))
      .and(t[:project_id].eq(project_id))

    p = AnatomicalPart.arel_table
    o = OriginRelationship.arel_table

    related = used_on.tableize
    related_klass = used_on
    if old_types.include?(used_on) && new_types.include?(used_on)
      a = AnatomicalPart.joins(:related_origin_relationships).joins("JOIN #{related} AS t1 ON t1.id = origin_relationships.old_object_id AND origin_relationships.old_object_type = '#{related_klass}'").where(i)

      b = AnatomicalPart.joins(:origin_relationships).joins("JOIN #{related} AS t2 ON t2.id = origin_relationships.new_object_id AND origin_relationships.new_object_type = '#{related_klass}'").where(i)

      ::Queries.union(AnatomicalPart, [a,b]).pluck(:id).uniq
    elsif old_types.include?(used_on)
      AnatomicalPart.joins(:related_origin_relationships).joins("JOIN #{related} ON #{related}.id = origin_relationships.old_object_id AND origin_relationships.old_object_type = '#{related_klass}'").where(i).pluck(:id).uniq
    else
      AnatomicalPart.joins(:origin_relationships).joins("JOIN #{related} ON #{related}.id = origin_relationships.new_object_id AND origin_relationships.new_object_type = '#{related_klass}'").where(i).pluck(:id).uniq
    end
  end

  # @return [Hash] anatomical_parts optimized for user selection
  def self.select_optimized(user_id, project_id, target = nil)
    r = used_recently(user_id, project_id, target)
    h = {
      quick: [],
      pinboard: AnatomicalPart.pinned_by(user_id).where(project_id:).to_a,
      recent: []
    }

    if target && !r.empty?
      n = target.tableize.to_sym
      h[:recent] = AnatomicalPart.where('"anatomical_parts"."id" IN (?)', r.first(10) ).to_a
      h[:quick] = (AnatomicalPart.pinned_by(user_id).pinboard_inserted.where(project_id:).to_a  +
        AnatomicalPart.where('"anatomical_parts"."id" IN (?)', r.first(4) ).to_a).uniq
    else
      h[:recent] = AnatomicalPart.where(project_id:, updated_by_id: user_id).order('updated_at DESC').limit(10).to_a
      h[:quick] = AnatomicalPart.pinned_by(user_id).pinboard_inserted.where(project_id:).to_a
    end

    h
  end

  # @return [Array[Array, Array]] where the first component is nodes, the second
  # component is edges, i.e. originRelationships.
  def self.graph(id, type)
    case type
    when *(AnatomicalPart.valid_old_object_classes - ['AnatomicalPart'])
      construct_graph_from_top_node(id, type)
    when *(AnatomicalPart.valid_new_object_classes - ['AnatomicalPart'])
      construct_graph_from_low_node(id, type)
    when 'AnatomicalPart'
      part = AnatomicalPart.find_by(id:)
      return [[], []] if part.nil?

      origin = part.taxonomic_origin_object
      # This constructs the full graph starting from origin - if we decide we
      # only want the chain containing the original input then call
      # graph_from_mid_node instead.
      construct_graph_from_top_node(origin.id, origin.class.base_class.name)
    end
  end

  # The top object in the OriginRelationship chain.
  def taxonomic_origin_object
    return @top_origin_object if @top_origin_object.present?

    origin = inbound_origin_relationship
    return nil if origin.nil? # invalid object

    next_parent = nil
    while (next_parent = OriginRelationship.where(new_object_id: origin.old_object_id, new_object_type: origin.old_object_type).first)
      origin = next_parent
    end

    @top_origin_object = origin.old_object
    @top_origin_object
  end

  def containable?
    is_material
  end

  private

  def set_cached
    update_column(:cached, name || uri_label)

    # cached_otu_id is determined by external objects, so is never changed by an
    # update, only a create.
    return if cached_otu_id

    top_origin = taxonomic_origin_object

    if top_origin.class.name == 'Otu'
      update_column(:cached_otu_id, top_origin.id)
    else
      update_column(:cached_otu_id, top_origin.current_otu.id)
    end
  end

  def name_or_uri_not_both
    has_labelled_uri = uri.present? && uri_label.present?
    return if has_labelled_uri && !name.present?
    return if name.present? && !uri.present? && !uri_label.present?

    errors.add(:base, 'Exactly one of 1) name, or 2) uri *and* uri_label, must be present')
  end

  def top_origin_is_valid_origin
    origin = taxonomic_origin_object

    errors.add(:base, 'Anatomical parts must be endpoints of an OriginRelationship!') && return if origin.nil?

    valid = valid_old_object_classes - ['AnatomicalPart']
    t = origin.class.base_class.name
    errors.add(:base, "Class of original origin must be in [#{valid.join(', ')}], not #{t}") && return if !valid.include?(t)

    return if origin.class.name == 'Otu'

    errors.add(:base, "Original origin must have a taxon determination!") && return if !origin.taxon_determinations.exists?
  end

  def is_material_matches_origin
    origin = taxonomic_origin_object
    return if origin.nil? # invalid

    if origin.class.base_class.name == 'CollectionObject' && is_material != true
      errors.add(:base, 'CollectionObject parts must have is_material true!')
      return
    elsif origin.class.base_class.name == 'Otu' && is_material == true
      errors.add(:base, 'OTU parts must have is_material false!')
      return
    end
  end

  def is_material_matches_parent_anatomical_part
    return if inbound_origin_relationship.nil? # invalid
    parent = inbound_origin_relationship.old_object
    return if parent.class.name != 'AnatomicalPart'

    if parent.is_material != is_material
      errors.add(:base, 'is_material must match parent value!')
    end
  end

  def propagate_change_to_is_material!
    # is_material can only be changed on the top AnatomicalPart, so change the
    # value on all AnatomicalPart descendants.
    new_is_material = is_material
    current = [self]

    while(current.present?)
      nxt = []
      current.each do |o|
        o.update_column(:is_material, new_is_material)
        nxt += o.new_objects
      end

      current = nxt.filter { |x| x.class.name == 'AnatomicalPart' }
    end

  end

  # Construct an AnatomicalPart graph starting from an AnatomicalPart. Going up
  # the graph is a chain ending in the source of the AnatomicalPart, going down
  # we include everything, even after we no longer see AnatomicalParts.
  def self.construct_graph_from_mid_node(anatomical_part_id, forward_only: false)
    nodes = []
    origin_relationships = []

    origin = AnatomicalPart.find(anatomical_part_id)
    current = [origin]

    # Go down the graph: going down we show everything, since it all has origin
    # some anatomical part.
    while(current.present?)
      nxt = []
      current.each do |o|
        nodes << o
        # No restriction on old_object_type.
        r = OriginRelationship.where(old_object: o)
        origin_relationships += r
        nxt += o.new_objects
      end

      current = nxt
    end

    # Go up the graph (chain).
    if !forward_only
      current = origin
      while (current.present? && current.class.name == 'AnatomicalPart')
        r = OriginRelationship.where(new_object_id: current.id, new_object_type: 'AnatomicalPart').first
        if r.present?
          origin_relationships << r
          nodes << current.old_objects.first
        end

        current = current.old_objects.first
      end
    end

    return nodes, origin_relationships
  end

  # Construct anatomical part graph starting at a top node, like
  # CollectionObject, FieldOccurrence, OTU. This returns *all* AnatomicalPart
  # children of the top node.
  def self.construct_graph_from_top_node(node_id, node_type)
    origin = node_type.constantize.find(node_id)
    r = OriginRelationship
      .where(
        old_object_id: node_id,
        old_object_type: node_type,
        new_object_type: 'AnatomicalPart'
      )

    origin_relationships = r
    nodes = [origin]
    r.each do |rln|
      anatomical_part = rln.new_object
      new_nodes, new_origin_relationships = construct_graph_from_mid_node(
        anatomical_part.id, forward_only: true
      )
      nodes += new_nodes
      origin_relationships += new_origin_relationships
    end

  return nodes, origin_relationships
  end

  # Construct an AnatomicalPart graph starting from the direct
  # non-anatomical-part child of an anatomical part, like an Extract or a Sound.
  # @param node_type is *not* AnatomicalPart, but we assume its origin *is*.
  def self.construct_graph_from_low_node(node_id, node_type)
    origin = node_type.constantize.find(node_id)
    r = OriginRelationship
      .where(
        new_object_id: node_id,
        new_object_type: node_type,
        old_object_type: 'AnatomicalPart'
      )

    anatomical_part = r.first&.old_object # reverse paths are always a chain (for anatomical parts)

    nodes = [origin]
    origin_relationships = []
    if anatomical_part
      # This can return more children of anatomical_part than just node.
      nodes, origin_relationships = construct_graph_from_mid_node(
        anatomical_part.id
      )
    end

    return nodes, origin_relationships
  end

  def abort_if_has_descendant_anatomical_part
    if OriginRelationship.where(old_object: self).exists?
      errors.add(:base, "This part can't be deleted because it's not the end of an AnatomicalPart chain.")
      throw(:abort)
    end
  end

  def setOriginRelationshipDestroyContext
    OriginRelationshipDestroyContext.objects_in_destroy ||= Set.new
    OriginRelationshipDestroyContext.objects_in_destroy << {
      id:, type: 'AnatomicalPart'
    }

    yield

  ensure
    OriginRelationshipDestroyContext.objects_in_destroy.delete({
      id:, type: 'AnatomicalPart'
    })
  end
end

#uri ⇒ Object

Override the :uri defined by Identifiers. Bad.



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# File 'app/models/anatomical_part.rb', line 45

class AnatomicalPart < ApplicationRecord
  include Housekeeping
  include Shared::Uri
  include Shared::Citations
  include Shared::Confidences
  include Shared::DataAttributes
  include Shared::Depictions
  include Shared::Conveyances
  include Shared::HasPapertrail
  include Shared::Identifiers
  include Shared::AutoUuid
  # Override the :uri defined by Identifiers. Bad.
  def uri
    self[:uri]
  end
  include Shared::Loanable
  include Shared::BiologicalAssociations
  include Shared::Taxonomy
  include Shared::Notes
  include Shared::Observations
  include Shared::Containable
  include Shared::OriginRelationship
  include Shared::ProtocolRelationships
  include Shared::Tags
  include Shared::PurlDeprecation
  include Shared::IsData

  is_origin_for 'AnatomicalPart', 'Extract', 'Sequence', 'Sound'
  originates_from 'Otu', 'Specimen', 'Lot', 'CollectionObject', 'AnatomicalPart', 'FieldOccurrence'

  GRAPH_ENTRY_POINTS = [:biological_associations, :origin_relationships]

  attr_accessor :origin_object # origin of this part, only used on create
  attr_accessor :no_cached

  belongs_to :origin_otu, class_name: 'Otu', foreign_key: :cached_otu_id, inverse_of: :anatomical_parts
  belongs_to :preparation_type, inverse_of: :anatomical_parts

  # Needed so we can build the origin chain at the same time we're using it to
  # verify that a new AnitomicalPart has an OTU ancestor.
  # Probably not needed outside of creation.
  has_one :inbound_origin_relationship,
    -> { where(new_object_type: 'AnatomicalPart') },
    as: :new_object,
    class_name: 'OriginRelationship',
    inverse_of: :new_object

  accepts_nested_attributes_for :inbound_origin_relationship

  # Must run before associated origin_relationships are destroyed.
  before_destroy :abort_if_has_descendant_anatomical_part, prepend: true
  around_destroy :setOriginRelationshipDestroyContext, prepend: true

  after_save :set_cached, unless: -> { self.no_cached }
  # Runs in the update transaction, so any errors will abort the udpate.
  after_update :propagate_change_to_is_material!, if: :saved_change_to_is_material?

  validates :inbound_origin_relationship, presence: true, on: :create
  validate :name_or_uri_not_both
  validate :top_origin_is_valid_origin
  validate :is_material_matches_origin
  validate :is_material_matches_parent_anatomical_part

  def uuid_required
    is_material
  end

  # Callback on OriginRelationship#create
  def allow_origin_relationship_create?(origin_relationship)
    # Disallow if we already have a parent.
    return false if origin_relationship.new_object == self &&
      OriginRelationship.where(new_object: self).exists?

    true
  end

  # Callback on OriginRelationship#destroy
  def allow_origin_relationship_destroy?(origin_relationship)
    # Allow if we originated the destroy because we're being destroyed (relies
    # on abort_if_has_descendant_anatomical_part to catch cases where that
    # shouldn't be allowed).
    return true if OriginRelationshipDestroyContext.objects_in_destroy&.include?({
      id:, type: 'AnatomicalPart'
    })

    # Disallow if origin_relationship is part of our required ancestry chain.
    return false if origin_relationship.new_object == self

    true
  end

  # @return [Scope]
  #    the max 10 most recently used anatomical_parts
  def self.used_recently(user_id, project_id, used_on = '')
    old_types = valid_old_object_classes
    new_types = valid_new_object_classes
    return [] if !old_types.include?(used_on) && !new_types.include?(used_on)

    t = used_on.constantize.arel_table
    i = t[:updated_at].gt(1.week.ago)
      .and(t[:updated_by_id].eq(user_id))
      .and(t[:project_id].eq(project_id))

    p = AnatomicalPart.arel_table
    o = OriginRelationship.arel_table

    related = used_on.tableize
    related_klass = used_on
    if old_types.include?(used_on) && new_types.include?(used_on)
      a = AnatomicalPart.joins(:related_origin_relationships).joins("JOIN #{related} AS t1 ON t1.id = origin_relationships.old_object_id AND origin_relationships.old_object_type = '#{related_klass}'").where(i)

      b = AnatomicalPart.joins(:origin_relationships).joins("JOIN #{related} AS t2 ON t2.id = origin_relationships.new_object_id AND origin_relationships.new_object_type = '#{related_klass}'").where(i)

      ::Queries.union(AnatomicalPart, [a,b]).pluck(:id).uniq
    elsif old_types.include?(used_on)
      AnatomicalPart.joins(:related_origin_relationships).joins("JOIN #{related} ON #{related}.id = origin_relationships.old_object_id AND origin_relationships.old_object_type = '#{related_klass}'").where(i).pluck(:id).uniq
    else
      AnatomicalPart.joins(:origin_relationships).joins("JOIN #{related} ON #{related}.id = origin_relationships.new_object_id AND origin_relationships.new_object_type = '#{related_klass}'").where(i).pluck(:id).uniq
    end
  end

  # @return [Hash] anatomical_parts optimized for user selection
  def self.select_optimized(user_id, project_id, target = nil)
    r = used_recently(user_id, project_id, target)
    h = {
      quick: [],
      pinboard: AnatomicalPart.pinned_by(user_id).where(project_id:).to_a,
      recent: []
    }

    if target && !r.empty?
      n = target.tableize.to_sym
      h[:recent] = AnatomicalPart.where('"anatomical_parts"."id" IN (?)', r.first(10) ).to_a
      h[:quick] = (AnatomicalPart.pinned_by(user_id).pinboard_inserted.where(project_id:).to_a  +
        AnatomicalPart.where('"anatomical_parts"."id" IN (?)', r.first(4) ).to_a).uniq
    else
      h[:recent] = AnatomicalPart.where(project_id:, updated_by_id: user_id).order('updated_at DESC').limit(10).to_a
      h[:quick] = AnatomicalPart.pinned_by(user_id).pinboard_inserted.where(project_id:).to_a
    end

    h
  end

  # @return [Array[Array, Array]] where the first component is nodes, the second
  # component is edges, i.e. originRelationships.
  def self.graph(id, type)
    case type
    when *(AnatomicalPart.valid_old_object_classes - ['AnatomicalPart'])
      construct_graph_from_top_node(id, type)
    when *(AnatomicalPart.valid_new_object_classes - ['AnatomicalPart'])
      construct_graph_from_low_node(id, type)
    when 'AnatomicalPart'
      part = AnatomicalPart.find_by(id:)
      return [[], []] if part.nil?

      origin = part.taxonomic_origin_object
      # This constructs the full graph starting from origin - if we decide we
      # only want the chain containing the original input then call
      # graph_from_mid_node instead.
      construct_graph_from_top_node(origin.id, origin.class.base_class.name)
    end
  end

  # The top object in the OriginRelationship chain.
  def taxonomic_origin_object
    return @top_origin_object if @top_origin_object.present?

    origin = inbound_origin_relationship
    return nil if origin.nil? # invalid object

    next_parent = nil
    while (next_parent = OriginRelationship.where(new_object_id: origin.old_object_id, new_object_type: origin.old_object_type).first)
      origin = next_parent
    end

    @top_origin_object = origin.old_object
    @top_origin_object
  end

  def containable?
    is_material
  end

  private

  def set_cached
    update_column(:cached, name || uri_label)

    # cached_otu_id is determined by external objects, so is never changed by an
    # update, only a create.
    return if cached_otu_id

    top_origin = taxonomic_origin_object

    if top_origin.class.name == 'Otu'
      update_column(:cached_otu_id, top_origin.id)
    else
      update_column(:cached_otu_id, top_origin.current_otu.id)
    end
  end

  def name_or_uri_not_both
    has_labelled_uri = uri.present? && uri_label.present?
    return if has_labelled_uri && !name.present?
    return if name.present? && !uri.present? && !uri_label.present?

    errors.add(:base, 'Exactly one of 1) name, or 2) uri *and* uri_label, must be present')
  end

  def top_origin_is_valid_origin
    origin = taxonomic_origin_object

    errors.add(:base, 'Anatomical parts must be endpoints of an OriginRelationship!') && return if origin.nil?

    valid = valid_old_object_classes - ['AnatomicalPart']
    t = origin.class.base_class.name
    errors.add(:base, "Class of original origin must be in [#{valid.join(', ')}], not #{t}") && return if !valid.include?(t)

    return if origin.class.name == 'Otu'

    errors.add(:base, "Original origin must have a taxon determination!") && return if !origin.taxon_determinations.exists?
  end

  def is_material_matches_origin
    origin = taxonomic_origin_object
    return if origin.nil? # invalid

    if origin.class.base_class.name == 'CollectionObject' && is_material != true
      errors.add(:base, 'CollectionObject parts must have is_material true!')
      return
    elsif origin.class.base_class.name == 'Otu' && is_material == true
      errors.add(:base, 'OTU parts must have is_material false!')
      return
    end
  end

  def is_material_matches_parent_anatomical_part
    return if inbound_origin_relationship.nil? # invalid
    parent = inbound_origin_relationship.old_object
    return if parent.class.name != 'AnatomicalPart'

    if parent.is_material != is_material
      errors.add(:base, 'is_material must match parent value!')
    end
  end

  def propagate_change_to_is_material!
    # is_material can only be changed on the top AnatomicalPart, so change the
    # value on all AnatomicalPart descendants.
    new_is_material = is_material
    current = [self]

    while(current.present?)
      nxt = []
      current.each do |o|
        o.update_column(:is_material, new_is_material)
        nxt += o.new_objects
      end

      current = nxt.filter { |x| x.class.name == 'AnatomicalPart' }
    end

  end

  # Construct an AnatomicalPart graph starting from an AnatomicalPart. Going up
  # the graph is a chain ending in the source of the AnatomicalPart, going down
  # we include everything, even after we no longer see AnatomicalParts.
  def self.construct_graph_from_mid_node(anatomical_part_id, forward_only: false)
    nodes = []
    origin_relationships = []

    origin = AnatomicalPart.find(anatomical_part_id)
    current = [origin]

    # Go down the graph: going down we show everything, since it all has origin
    # some anatomical part.
    while(current.present?)
      nxt = []
      current.each do |o|
        nodes << o
        # No restriction on old_object_type.
        r = OriginRelationship.where(old_object: o)
        origin_relationships += r
        nxt += o.new_objects
      end

      current = nxt
    end

    # Go up the graph (chain).
    if !forward_only
      current = origin
      while (current.present? && current.class.name == 'AnatomicalPart')
        r = OriginRelationship.where(new_object_id: current.id, new_object_type: 'AnatomicalPart').first
        if r.present?
          origin_relationships << r
          nodes << current.old_objects.first
        end

        current = current.old_objects.first
      end
    end

    return nodes, origin_relationships
  end

  # Construct anatomical part graph starting at a top node, like
  # CollectionObject, FieldOccurrence, OTU. This returns *all* AnatomicalPart
  # children of the top node.
  def self.construct_graph_from_top_node(node_id, node_type)
    origin = node_type.constantize.find(node_id)
    r = OriginRelationship
      .where(
        old_object_id: node_id,
        old_object_type: node_type,
        new_object_type: 'AnatomicalPart'
      )

    origin_relationships = r
    nodes = [origin]
    r.each do |rln|
      anatomical_part = rln.new_object
      new_nodes, new_origin_relationships = construct_graph_from_mid_node(
        anatomical_part.id, forward_only: true
      )
      nodes += new_nodes
      origin_relationships += new_origin_relationships
    end

  return nodes, origin_relationships
  end

  # Construct an AnatomicalPart graph starting from the direct
  # non-anatomical-part child of an anatomical part, like an Extract or a Sound.
  # @param node_type is *not* AnatomicalPart, but we assume its origin *is*.
  def self.construct_graph_from_low_node(node_id, node_type)
    origin = node_type.constantize.find(node_id)
    r = OriginRelationship
      .where(
        new_object_id: node_id,
        new_object_type: node_type,
        old_object_type: 'AnatomicalPart'
      )

    anatomical_part = r.first&.old_object # reverse paths are always a chain (for anatomical parts)

    nodes = [origin]
    origin_relationships = []
    if anatomical_part
      # This can return more children of anatomical_part than just node.
      nodes, origin_relationships = construct_graph_from_mid_node(
        anatomical_part.id
      )
    end

    return nodes, origin_relationships
  end

  def abort_if_has_descendant_anatomical_part
    if OriginRelationship.where(old_object: self).exists?
      errors.add(:base, "This part can't be deleted because it's not the end of an AnatomicalPart chain.")
      throw(:abort)
    end
  end

  def setOriginRelationshipDestroyContext
    OriginRelationshipDestroyContext.objects_in_destroy ||= Set.new
    OriginRelationshipDestroyContext.objects_in_destroy << {
      id:, type: 'AnatomicalPart'
    }

    yield

  ensure
    OriginRelationshipDestroyContext.objects_in_destroy.delete({
      id:, type: 'AnatomicalPart'
    })
  end
end

#uri_label ⇒ String

Uri label of the uri for the anatomical part.

Returns:

  • (String) 


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# File 'app/models/anatomical_part.rb', line 45

class AnatomicalPart < ApplicationRecord
  include Housekeeping
  include Shared::Uri
  include Shared::Citations
  include Shared::Confidences
  include Shared::DataAttributes
  include Shared::Depictions
  include Shared::Conveyances
  include Shared::HasPapertrail
  include Shared::Identifiers
  include Shared::AutoUuid
  # Override the :uri defined by Identifiers. Bad.
  def uri
    self[:uri]
  end
  include Shared::Loanable
  include Shared::BiologicalAssociations
  include Shared::Taxonomy
  include Shared::Notes
  include Shared::Observations
  include Shared::Containable
  include Shared::OriginRelationship
  include Shared::ProtocolRelationships
  include Shared::Tags
  include Shared::PurlDeprecation
  include Shared::IsData

  is_origin_for 'AnatomicalPart', 'Extract', 'Sequence', 'Sound'
  originates_from 'Otu', 'Specimen', 'Lot', 'CollectionObject', 'AnatomicalPart', 'FieldOccurrence'

  GRAPH_ENTRY_POINTS = [:biological_associations, :origin_relationships]

  attr_accessor :origin_object # origin of this part, only used on create
  attr_accessor :no_cached

  belongs_to :origin_otu, class_name: 'Otu', foreign_key: :cached_otu_id, inverse_of: :anatomical_parts
  belongs_to :preparation_type, inverse_of: :anatomical_parts

  # Needed so we can build the origin chain at the same time we're using it to
  # verify that a new AnitomicalPart has an OTU ancestor.
  # Probably not needed outside of creation.
  has_one :inbound_origin_relationship,
    -> { where(new_object_type: 'AnatomicalPart') },
    as: :new_object,
    class_name: 'OriginRelationship',
    inverse_of: :new_object

  accepts_nested_attributes_for :inbound_origin_relationship

  # Must run before associated origin_relationships are destroyed.
  before_destroy :abort_if_has_descendant_anatomical_part, prepend: true
  around_destroy :setOriginRelationshipDestroyContext, prepend: true

  after_save :set_cached, unless: -> { self.no_cached }
  # Runs in the update transaction, so any errors will abort the udpate.
  after_update :propagate_change_to_is_material!, if: :saved_change_to_is_material?

  validates :inbound_origin_relationship, presence: true, on: :create
  validate :name_or_uri_not_both
  validate :top_origin_is_valid_origin
  validate :is_material_matches_origin
  validate :is_material_matches_parent_anatomical_part

  def uuid_required
    is_material
  end

  # Callback on OriginRelationship#create
  def allow_origin_relationship_create?(origin_relationship)
    # Disallow if we already have a parent.
    return false if origin_relationship.new_object == self &&
      OriginRelationship.where(new_object: self).exists?

    true
  end

  # Callback on OriginRelationship#destroy
  def allow_origin_relationship_destroy?(origin_relationship)
    # Allow if we originated the destroy because we're being destroyed (relies
    # on abort_if_has_descendant_anatomical_part to catch cases where that
    # shouldn't be allowed).
    return true if OriginRelationshipDestroyContext.objects_in_destroy&.include?({
      id:, type: 'AnatomicalPart'
    })

    # Disallow if origin_relationship is part of our required ancestry chain.
    return false if origin_relationship.new_object == self

    true
  end

  # @return [Scope]
  #    the max 10 most recently used anatomical_parts
  def self.used_recently(user_id, project_id, used_on = '')
    old_types = valid_old_object_classes
    new_types = valid_new_object_classes
    return [] if !old_types.include?(used_on) && !new_types.include?(used_on)

    t = used_on.constantize.arel_table
    i = t[:updated_at].gt(1.week.ago)
      .and(t[:updated_by_id].eq(user_id))
      .and(t[:project_id].eq(project_id))

    p = AnatomicalPart.arel_table
    o = OriginRelationship.arel_table

    related = used_on.tableize
    related_klass = used_on
    if old_types.include?(used_on) && new_types.include?(used_on)
      a = AnatomicalPart.joins(:related_origin_relationships).joins("JOIN #{related} AS t1 ON t1.id = origin_relationships.old_object_id AND origin_relationships.old_object_type = '#{related_klass}'").where(i)

      b = AnatomicalPart.joins(:origin_relationships).joins("JOIN #{related} AS t2 ON t2.id = origin_relationships.new_object_id AND origin_relationships.new_object_type = '#{related_klass}'").where(i)

      ::Queries.union(AnatomicalPart, [a,b]).pluck(:id).uniq
    elsif old_types.include?(used_on)
      AnatomicalPart.joins(:related_origin_relationships).joins("JOIN #{related} ON #{related}.id = origin_relationships.old_object_id AND origin_relationships.old_object_type = '#{related_klass}'").where(i).pluck(:id).uniq
    else
      AnatomicalPart.joins(:origin_relationships).joins("JOIN #{related} ON #{related}.id = origin_relationships.new_object_id AND origin_relationships.new_object_type = '#{related_klass}'").where(i).pluck(:id).uniq
    end
  end

  # @return [Hash] anatomical_parts optimized for user selection
  def self.select_optimized(user_id, project_id, target = nil)
    r = used_recently(user_id, project_id, target)
    h = {
      quick: [],
      pinboard: AnatomicalPart.pinned_by(user_id).where(project_id:).to_a,
      recent: []
    }

    if target && !r.empty?
      n = target.tableize.to_sym
      h[:recent] = AnatomicalPart.where('"anatomical_parts"."id" IN (?)', r.first(10) ).to_a
      h[:quick] = (AnatomicalPart.pinned_by(user_id).pinboard_inserted.where(project_id:).to_a  +
        AnatomicalPart.where('"anatomical_parts"."id" IN (?)', r.first(4) ).to_a).uniq
    else
      h[:recent] = AnatomicalPart.where(project_id:, updated_by_id: user_id).order('updated_at DESC').limit(10).to_a
      h[:quick] = AnatomicalPart.pinned_by(user_id).pinboard_inserted.where(project_id:).to_a
    end

    h
  end

  # @return [Array[Array, Array]] where the first component is nodes, the second
  # component is edges, i.e. originRelationships.
  def self.graph(id, type)
    case type
    when *(AnatomicalPart.valid_old_object_classes - ['AnatomicalPart'])
      construct_graph_from_top_node(id, type)
    when *(AnatomicalPart.valid_new_object_classes - ['AnatomicalPart'])
      construct_graph_from_low_node(id, type)
    when 'AnatomicalPart'
      part = AnatomicalPart.find_by(id:)
      return [[], []] if part.nil?

      origin = part.taxonomic_origin_object
      # This constructs the full graph starting from origin - if we decide we
      # only want the chain containing the original input then call
      # graph_from_mid_node instead.
      construct_graph_from_top_node(origin.id, origin.class.base_class.name)
    end
  end

  # The top object in the OriginRelationship chain.
  def taxonomic_origin_object
    return @top_origin_object if @top_origin_object.present?

    origin = inbound_origin_relationship
    return nil if origin.nil? # invalid object

    next_parent = nil
    while (next_parent = OriginRelationship.where(new_object_id: origin.old_object_id, new_object_type: origin.old_object_type).first)
      origin = next_parent
    end

    @top_origin_object = origin.old_object
    @top_origin_object
  end

  def containable?
    is_material
  end

  private

  def set_cached
    update_column(:cached, name || uri_label)

    # cached_otu_id is determined by external objects, so is never changed by an
    # update, only a create.
    return if cached_otu_id

    top_origin = taxonomic_origin_object

    if top_origin.class.name == 'Otu'
      update_column(:cached_otu_id, top_origin.id)
    else
      update_column(:cached_otu_id, top_origin.current_otu.id)
    end
  end

  def name_or_uri_not_both
    has_labelled_uri = uri.present? && uri_label.present?
    return if has_labelled_uri && !name.present?
    return if name.present? && !uri.present? && !uri_label.present?

    errors.add(:base, 'Exactly one of 1) name, or 2) uri *and* uri_label, must be present')
  end

  def top_origin_is_valid_origin
    origin = taxonomic_origin_object

    errors.add(:base, 'Anatomical parts must be endpoints of an OriginRelationship!') && return if origin.nil?

    valid = valid_old_object_classes - ['AnatomicalPart']
    t = origin.class.base_class.name
    errors.add(:base, "Class of original origin must be in [#{valid.join(', ')}], not #{t}") && return if !valid.include?(t)

    return if origin.class.name == 'Otu'

    errors.add(:base, "Original origin must have a taxon determination!") && return if !origin.taxon_determinations.exists?
  end

  def is_material_matches_origin
    origin = taxonomic_origin_object
    return if origin.nil? # invalid

    if origin.class.base_class.name == 'CollectionObject' && is_material != true
      errors.add(:base, 'CollectionObject parts must have is_material true!')
      return
    elsif origin.class.base_class.name == 'Otu' && is_material == true
      errors.add(:base, 'OTU parts must have is_material false!')
      return
    end
  end

  def is_material_matches_parent_anatomical_part
    return if inbound_origin_relationship.nil? # invalid
    parent = inbound_origin_relationship.old_object
    return if parent.class.name != 'AnatomicalPart'

    if parent.is_material != is_material
      errors.add(:base, 'is_material must match parent value!')
    end
  end

  def propagate_change_to_is_material!
    # is_material can only be changed on the top AnatomicalPart, so change the
    # value on all AnatomicalPart descendants.
    new_is_material = is_material
    current = [self]

    while(current.present?)
      nxt = []
      current.each do |o|
        o.update_column(:is_material, new_is_material)
        nxt += o.new_objects
      end

      current = nxt.filter { |x| x.class.name == 'AnatomicalPart' }
    end

  end

  # Construct an AnatomicalPart graph starting from an AnatomicalPart. Going up
  # the graph is a chain ending in the source of the AnatomicalPart, going down
  # we include everything, even after we no longer see AnatomicalParts.
  def self.construct_graph_from_mid_node(anatomical_part_id, forward_only: false)
    nodes = []
    origin_relationships = []

    origin = AnatomicalPart.find(anatomical_part_id)
    current = [origin]

    # Go down the graph: going down we show everything, since it all has origin
    # some anatomical part.
    while(current.present?)
      nxt = []
      current.each do |o|
        nodes << o
        # No restriction on old_object_type.
        r = OriginRelationship.where(old_object: o)
        origin_relationships += r
        nxt += o.new_objects
      end

      current = nxt
    end

    # Go up the graph (chain).
    if !forward_only
      current = origin
      while (current.present? && current.class.name == 'AnatomicalPart')
        r = OriginRelationship.where(new_object_id: current.id, new_object_type: 'AnatomicalPart').first
        if r.present?
          origin_relationships << r
          nodes << current.old_objects.first
        end

        current = current.old_objects.first
      end
    end

    return nodes, origin_relationships
  end

  # Construct anatomical part graph starting at a top node, like
  # CollectionObject, FieldOccurrence, OTU. This returns *all* AnatomicalPart
  # children of the top node.
  def self.construct_graph_from_top_node(node_id, node_type)
    origin = node_type.constantize.find(node_id)
    r = OriginRelationship
      .where(
        old_object_id: node_id,
        old_object_type: node_type,
        new_object_type: 'AnatomicalPart'
      )

    origin_relationships = r
    nodes = [origin]
    r.each do |rln|
      anatomical_part = rln.new_object
      new_nodes, new_origin_relationships = construct_graph_from_mid_node(
        anatomical_part.id, forward_only: true
      )
      nodes += new_nodes
      origin_relationships += new_origin_relationships
    end

  return nodes, origin_relationships
  end

  # Construct an AnatomicalPart graph starting from the direct
  # non-anatomical-part child of an anatomical part, like an Extract or a Sound.
  # @param node_type is *not* AnatomicalPart, but we assume its origin *is*.
  def self.construct_graph_from_low_node(node_id, node_type)
    origin = node_type.constantize.find(node_id)
    r = OriginRelationship
      .where(
        new_object_id: node_id,
        new_object_type: node_type,
        old_object_type: 'AnatomicalPart'
      )

    anatomical_part = r.first&.old_object # reverse paths are always a chain (for anatomical parts)

    nodes = [origin]
    origin_relationships = []
    if anatomical_part
      # This can return more children of anatomical_part than just node.
      nodes, origin_relationships = construct_graph_from_mid_node(
        anatomical_part.id
      )
    end

    return nodes, origin_relationships
  end

  def abort_if_has_descendant_anatomical_part
    if OriginRelationship.where(old_object: self).exists?
      errors.add(:base, "This part can't be deleted because it's not the end of an AnatomicalPart chain.")
      throw(:abort)
    end
  end

  def setOriginRelationshipDestroyContext
    OriginRelationshipDestroyContext.objects_in_destroy ||= Set.new
    OriginRelationshipDestroyContext.objects_in_destroy << {
      id:, type: 'AnatomicalPart'
    }

    yield

  ensure
    OriginRelationshipDestroyContext.objects_in_destroy.delete({
      id:, type: 'AnatomicalPart'
    })
  end
end

Class Method Details

.construct_graph_from_low_node(node_id, node_type) ⇒ Object (private)

Construct an AnatomicalPart graph starting from the direct non-anatomical-part child of an anatomical part, like an Extract or a Sound.

Parameters:

  • node_type —

    is not AnatomicalPart, but we assume its origin is.



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# File 'app/models/anatomical_part.rb', line 380

def self.construct_graph_from_low_node(node_id, node_type)
  origin = node_type.constantize.find(node_id)
  r = OriginRelationship
    .where(
      new_object_id: node_id,
      new_object_type: node_type,
      old_object_type: 'AnatomicalPart'
    )

  anatomical_part = r.first&.old_object # reverse paths are always a chain (for anatomical parts)

  nodes = [origin]
  origin_relationships = []
  if anatomical_part
    # This can return more children of anatomical_part than just node.
    nodes, origin_relationships = construct_graph_from_mid_node(
      anatomical_part.id
    )
  end

  return nodes, origin_relationships
end

.construct_graph_from_mid_node(anatomical_part_id, forward_only: false) ⇒ Object (private)

Construct an AnatomicalPart graph starting from an AnatomicalPart. Going up the graph is a chain ending in the source of the AnatomicalPart, going down we include everything, even after we no longer see AnatomicalParts.



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# File 'app/models/anatomical_part.rb', line 312

def self.construct_graph_from_mid_node(anatomical_part_id, forward_only: false)
  nodes = []
  origin_relationships = []

  origin = AnatomicalPart.find(anatomical_part_id)
  current = [origin]

  # Go down the graph: going down we show everything, since it all has origin
  # some anatomical part.
  while(current.present?)
    nxt = []
    current.each do |o|
      nodes << o
      # No restriction on old_object_type.
      r = OriginRelationship.where(old_object: o)
      origin_relationships += r
      nxt += o.new_objects
    end

    current = nxt
  end

  # Go up the graph (chain).
  if !forward_only
    current = origin
    while (current.present? && current.class.name == 'AnatomicalPart')
      r = OriginRelationship.where(new_object_id: current.id, new_object_type: 'AnatomicalPart').first
      if r.present?
        origin_relationships << r
        nodes << current.old_objects.first
      end

      current = current.old_objects.first
    end
  end

  return nodes, origin_relationships
end

.construct_graph_from_top_node(node_id, node_type) ⇒ Object (private)

Construct anatomical part graph starting at a top node, like CollectionObject, FieldOccurrence, OTU. This returns all AnatomicalPart children of the top node.



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# File 'app/models/anatomical_part.rb', line 354

def self.construct_graph_from_top_node(node_id, node_type)
  origin = node_type.constantize.find(node_id)
  r = OriginRelationship
    .where(
      old_object_id: node_id,
      old_object_type: node_type,
      new_object_type: 'AnatomicalPart'
    )

  origin_relationships = r
  nodes = [origin]
  r.each do |rln|
    anatomical_part = rln.new_object
    new_nodes, new_origin_relationships = construct_graph_from_mid_node(
      anatomical_part.id, forward_only: true
    )
    nodes += new_nodes
    origin_relationships += new_origin_relationships
  end

return nodes, origin_relationships
end

.graph(id, type) ⇒ Array[Array, Array]

component is edges, i.e. originRelationships.

Returns:

  • (Array[Array, Array]) —

    where the first component is nodes, the second



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# File 'app/models/anatomical_part.rb', line 190

def self.graph(id, type)
  case type
  when *(AnatomicalPart.valid_old_object_classes - ['AnatomicalPart'])
    construct_graph_from_top_node(id, type)
  when *(AnatomicalPart.valid_new_object_classes - ['AnatomicalPart'])
    construct_graph_from_low_node(id, type)
  when 'AnatomicalPart'
    part = AnatomicalPart.find_by(id:)
    return [[], []] if part.nil?

    origin = part.taxonomic_origin_object
    # This constructs the full graph starting from origin - if we decide we
    # only want the chain containing the original input then call
    # graph_from_mid_node instead.
    construct_graph_from_top_node(origin.id, origin.class.base_class.name)
  end
end

.select_optimized(user_id, project_id, target = nil) ⇒ Hash

Returns anatomical_parts optimized for user selection.

Returns:

  • (Hash) —

    anatomical_parts optimized for user selection



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# File 'app/models/anatomical_part.rb', line 167

def self.select_optimized(user_id, project_id, target = nil)
  r = used_recently(user_id, project_id, target)
  h = {
    quick: [],
    pinboard: AnatomicalPart.pinned_by(user_id).where(project_id:).to_a,
    recent: []
  }

  if target && !r.empty?
    n = target.tableize.to_sym
    h[:recent] = AnatomicalPart.where('"anatomical_parts"."id" IN (?)', r.first(10) ).to_a
    h[:quick] = (AnatomicalPart.pinned_by(user_id).pinboard_inserted.where(project_id:).to_a  +
      AnatomicalPart.where('"anatomical_parts"."id" IN (?)', r.first(4) ).to_a).uniq
  else
    h[:recent] = AnatomicalPart.where(project_id:, updated_by_id: user_id).order('updated_at DESC').limit(10).to_a
    h[:quick] = AnatomicalPart.pinned_by(user_id).pinboard_inserted.where(project_id:).to_a
  end

  h
end

.used_recently(user_id, project_id, used_on = '') ⇒ Scope

Returns the max 10 most recently used anatomical_parts.

Returns:

  • (Scope) —

    the max 10 most recently used anatomical_parts



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# File 'app/models/anatomical_part.rb', line 138

def self.used_recently(user_id, project_id, used_on = '')
  old_types = valid_old_object_classes
  new_types = valid_new_object_classes
  return [] if !old_types.include?(used_on) && !new_types.include?(used_on)

  t = used_on.constantize.arel_table
  i = t[:updated_at].gt(1.week.ago)
    .and(t[:updated_by_id].eq(user_id))
    .and(t[:project_id].eq(project_id))

  p = AnatomicalPart.arel_table
  o = OriginRelationship.arel_table

  related = used_on.tableize
  related_klass = used_on
  if old_types.include?(used_on) && new_types.include?(used_on)
    a = AnatomicalPart.joins(:related_origin_relationships).joins("JOIN #{related} AS t1 ON t1.id = origin_relationships.old_object_id AND origin_relationships.old_object_type = '#{related_klass}'").where(i)

    b = AnatomicalPart.joins(:origin_relationships).joins("JOIN #{related} AS t2 ON t2.id = origin_relationships.new_object_id AND origin_relationships.new_object_type = '#{related_klass}'").where(i)

    ::Queries.union(AnatomicalPart, [a,b]).pluck(:id).uniq
  elsif old_types.include?(used_on)
    AnatomicalPart.joins(:related_origin_relationships).joins("JOIN #{related} ON #{related}.id = origin_relationships.old_object_id AND origin_relationships.old_object_type = '#{related_klass}'").where(i).pluck(:id).uniq
  else
    AnatomicalPart.joins(:origin_relationships).joins("JOIN #{related} ON #{related}.id = origin_relationships.new_object_id AND origin_relationships.new_object_type = '#{related_klass}'").where(i).pluck(:id).uniq
  end
end

Instance Method Details

#abort_if_has_descendant_anatomical_part ⇒ Object (private) 



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# File 'app/models/anatomical_part.rb', line 403

def abort_if_has_descendant_anatomical_part
  if OriginRelationship.where(old_object: self).exists?
    errors.add(:base, "This part can't be deleted because it's not the end of an AnatomicalPart chain.")
    throw(:abort)
  end
end

#allow_origin_relationship_create?(origin_relationship) ⇒ Boolean

Callback on OriginRelationship#create

Returns:

  • (Boolean) 


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

def allow_origin_relationship_create?(origin_relationship)
  # Disallow if we already have a parent.
  return false if origin_relationship.new_object == self &&
    OriginRelationship.where(new_object: self).exists?

  true
end

#allow_origin_relationship_destroy?(origin_relationship) ⇒ Boolean

Callback on OriginRelationship#destroy

Returns:

  • (Boolean) 


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# File 'app/models/anatomical_part.rb', line 122

def allow_origin_relationship_destroy?(origin_relationship)
  # Allow if we originated the destroy because we're being destroyed (relies
  # on abort_if_has_descendant_anatomical_part to catch cases where that
  # shouldn't be allowed).
  return true if OriginRelationshipDestroyContext.objects_in_destroy&.include?({
    id:, type: 'AnatomicalPart'
  })

  # Disallow if origin_relationship is part of our required ancestry chain.
  return false if origin_relationship.new_object == self

  true
end

#containable? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'app/models/anatomical_part.rb', line 224

def containable?
  is_material
end

#is_material_matches_origin ⇒ Object (private) 



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# File 'app/models/anatomical_part.rb', line 268

def is_material_matches_origin
  origin = taxonomic_origin_object
  return if origin.nil? # invalid

  if origin.class.base_class.name == 'CollectionObject' && is_material != true
    errors.add(:base, 'CollectionObject parts must have is_material true!')
    return
  elsif origin.class.base_class.name == 'Otu' && is_material == true
    errors.add(:base, 'OTU parts must have is_material false!')
    return
  end
end

#is_material_matches_parent_anatomical_part ⇒ Object (private) 



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# File 'app/models/anatomical_part.rb', line 281

def is_material_matches_parent_anatomical_part
  return if inbound_origin_relationship.nil? # invalid
  parent = inbound_origin_relationship.old_object
  return if parent.class.name != 'AnatomicalPart'

  if parent.is_material != is_material
    errors.add(:base, 'is_material must match parent value!')
  end
end

#name_or_uri_not_both ⇒ Object (private) 



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# File 'app/models/anatomical_part.rb', line 246

def name_or_uri_not_both
  has_labelled_uri = uri.present? && uri_label.present?
  return if has_labelled_uri && !name.present?
  return if name.present? && !uri.present? && !uri_label.present?

  errors.add(:base, 'Exactly one of 1) name, or 2) uri *and* uri_label, must be present')
end

#propagate_change_to_is_material! ⇒ Object (private) 



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# File 'app/models/anatomical_part.rb', line 291

def propagate_change_to_is_material!
  # is_material can only be changed on the top AnatomicalPart, so change the
  # value on all AnatomicalPart descendants.
  new_is_material = is_material
  current = [self]

  while(current.present?)
    nxt = []
    current.each do |o|
      o.update_column(:is_material, new_is_material)
      nxt += o.new_objects
    end

    current = nxt.filter { |x| x.class.name == 'AnatomicalPart' }
  end

end

#set_cached ⇒ Object (private) 



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# File 'app/models/anatomical_part.rb', line 230

def set_cached
  update_column(:cached, name || uri_label)

  # cached_otu_id is determined by external objects, so is never changed by an
  # update, only a create.
  return if cached_otu_id

  top_origin = taxonomic_origin_object

  if top_origin.class.name == 'Otu'
    update_column(:cached_otu_id, top_origin.id)
  else
    update_column(:cached_otu_id, top_origin.current_otu.id)
  end
end

#setOriginRelationshipDestroyContext ⇒ Object (private) 



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# File 'app/models/anatomical_part.rb', line 410

def setOriginRelationshipDestroyContext
  OriginRelationshipDestroyContext.objects_in_destroy ||= Set.new
  OriginRelationshipDestroyContext.objects_in_destroy << {
    id:, type: 'AnatomicalPart'
  }

  yield

ensure
  OriginRelationshipDestroyContext.objects_in_destroy.delete({
    id:, type: 'AnatomicalPart'
  })
end

#taxonomic_origin_object ⇒ Object

The top object in the OriginRelationship chain.



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# File 'app/models/anatomical_part.rb', line 209

def taxonomic_origin_object
  return @top_origin_object if @top_origin_object.present?

  origin = inbound_origin_relationship
  return nil if origin.nil? # invalid object

  next_parent = nil
  while (next_parent = OriginRelationship.where(new_object_id: origin.old_object_id, new_object_type: origin.old_object_type).first)
    origin = next_parent
  end

  @top_origin_object = origin.old_object
  @top_origin_object
end

#top_origin_is_valid_origin ⇒ Object (private) 



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# File 'app/models/anatomical_part.rb', line 254

def top_origin_is_valid_origin
  origin = taxonomic_origin_object

  errors.add(:base, 'Anatomical parts must be endpoints of an OriginRelationship!') && return if origin.nil?

  valid = valid_old_object_classes - ['AnatomicalPart']
  t = origin.class.base_class.name
  errors.add(:base, "Class of original origin must be in [#{valid.join(', ')}], not #{t}") && return if !valid.include?(t)

  return if origin.class.name == 'Otu'

  errors.add(:base, "Original origin must have a taxon determination!") && return if !origin.taxon_determinations.exists?
end

#uuid_required ⇒ Object 



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# File 'app/models/anatomical_part.rb', line 108

def uuid_required
  is_material
end