Class: BiologicalAssociation

Inherits:
ApplicationRecord show all
Includes:
DwcExtensions, GlobiExtensions, Housekeeping, Shared::AssertedDistributions, Shared::AutoUuid, Shared::Citations, Shared::Confidences, Shared::DataAttributes, Shared::Depictions, Shared::Identifiers, Shared::IsData, Shared::Notes, Shared::QueryBatchUpdate, Shared::Tags, SoftValidation
Defined in:
app/models/biological_association.rb

Overview

A BiologicalAssociation defines a (biological) relationship between two entities. It is an edge in the graph of biological relationships. The relationship can be between two Otus, an Otu and a Collection Object, or between two Collection Objects. For example ‘Species Aus bus is the host_of individual A.’

Defined Under Namespace

Modules: DwcExtensions, GlobiExtensions

Constant Summary collapse

GRAPH_ENTRY_POINTS = 
[:asserted_distributions].freeze

Constants included from SoftValidation

SoftValidation::ANCESTORS_WITH_SOFT_VALIDATIONS

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Methods included from Shared::QueryBatchUpdate

#query_update

Methods included from DwcExtensions

#darwin_core_extension_json, #darwin_core_extension_row, #dwc_related_resource, #dwc_related_resource_id, #dwc_relationship_according_to, #dwc_relationship_established_date, #dwc_relationship_of_resource, #dwc_relationship_of_resource_id, #dwc_relationship_remarks, #dwc_resource, #dwc_resource_id, #dwc_resource_relationship_coreid, #dwc_resource_relationship_id, #globi_extension_json

Methods included from GlobiExtensions

#globi_extension_json, #globi_extension_row, #globi_interaction_type_id, #globi_interaction_type_name, #globi_source_catalog_number, #globi_source_collection_code, #globi_source_institution_code, #globi_source_life_stage_id, #globi_source_life_stage_name, #globi_source_occurrence_id, #globi_source_sex_id, #globi_source_sex_name, #globi_source_taxon_name, #globi_source_taxon_path, #globi_source_taxon_rank, #globi_target_catalog_number, #globi_target_collection_code, #globi_target_institution_code, #globi_target_life_stage_id, #globi_target_life_stage_name, #globi_target_occurrence_id, #globi_target_sex_id, #globi_target_sex_name, #globi_target_taxon_name, #globi_target_taxon_path, #globi_target_taxon_rank

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::AutoUuid

#create_object_uuid, #generate_uuid_if_required

Methods included from Shared::Depictions

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

Methods included from Shared::Confidences

#reject_confidences

Methods included from Shared::Notes

#concatenated_notes_string, #reject_notes

Methods included from Shared::DataAttributes

#import_attributes, #internal_attributes, #keyword_value_hash, #reject_data_attributes

Methods included from Shared::Identifiers

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

Methods included from Shared::Tags

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

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 SoftValidation

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

Methods included from Housekeeping

#has_polymorphic_relationship?

Methods inherited from ApplicationRecord

transaction_with_retry

Instance Attribute Details

#biological_association_object_id ⇒ Integer

Returns Rails polymorphic, id of the object.

Returns:

  • (Integer) —

    Rails polymorphic, id of the object



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

class BiologicalAssociation < ApplicationRecord
  include Housekeeping
  include SoftValidation
  include Shared::Citations
  include Shared::Tags
  include Shared::Identifiers
  include Shared::DataAttributes
  include Shared::Notes
  include Shared::Confidences
  include Shared::Depictions
  include Shared::AutoUuid
  include Shared::AssertedDistributions
  include Shared::IsData

  include BiologicalAssociation::GlobiExtensions
  include BiologicalAssociation::DwcExtensions

  include Shared::QueryBatchUpdate

  GRAPH_ENTRY_POINTS = [:asserted_distributions].freeze

  belongs_to :biological_relationship, inverse_of: :biological_associations

  has_many :subject_biological_relationship_types, through: :biological_relationship
  has_many :object_biological_relationship_types, through: :biological_relationship

  has_many :subject_biological_properties, through: :subject_biological_relationship_types, source: :biological_property
  has_many :object_biological_properties, through: :object_biological_relationship_types, source: :biological_property

  belongs_to :biological_association_subject, polymorphic: true, inverse_of: :biological_associations
  belongs_to :biological_association_object, polymorphic: true, inverse_of: :related_biological_associations

  has_many :biological_associations_biological_associations_graphs, inverse_of: :biological_association, dependent: :destroy
  has_many :biological_associations_graphs, through: :biological_associations_biological_associations_graphs, inverse_of: :biological_associations

  validates_presence_of :biological_relationship
  validates_presence_of :biological_association_subject
  validates_presence_of :biological_association_object

  validate :association_is_unique

  validate :biological_association_subject_type_is_allowed
  validate :biological_association_object_type_is_allowed

  attr_accessor :subject_global_id
  attr_accessor :object_global_id # TODO: this is badly named

  attr_accessor :rotate

  def rotate=(value)
    s = self.biological_association_subject
    o = self.biological_association_object

    self.biological_association_subject = o
    self.biological_association_object = s
  end

  def subject_global_id=(value)
    o = GlobalID::Locator.locate(value)
    write_attribute(:biological_association_subject_id, o.id)
    write_attribute(:biological_association_subject_type, o.metamorphosize.class.name)
  end

  def object_global_id=(value)
    o = GlobalID::Locator.locate(value)
    write_attribute(:biological_association_object_id, o.id)
    write_attribute(:biological_association_object_type, o.metamorphosize.class.name)
  end

  # TODO: Why?! this is just biological_association.biological_association_subject_type
  def subject_class_name
    biological_association_subject.try(:class).base_class.name
  end

  # TODO: Why?! this is just biological_association.biological_association_object_type
  def object_class_name
    biological_association_object.try(:class).base_class.name
  end

  # !! You can not set with this method
  def subject
    biological_association_subject
  end

  # !! You can not set with this method
  def object
    biological_association_object
  end

  class << self

    def set_batch_cap(request)
      a = request.filter
      total = a.all.pluck(:biological_relationship_id).uniq

      cap = 0

      case total.size
      when 1
        cap = 5000
        request.cap_reason = 'Maximum allowed.'
      when 2
        cap = 2000
        request.cap_reason = 'Maximum allowed when 2 biological relationships present.'
      else
        cap = 25
        request.cap_reason = 'Maximum allowed when 3 or more biological relationships present.'
      end

      request.cap = cap
      request
    end

    def batch_update(params)
      request = QueryBatchRequest.new(
        klass: 'BiologicalAssociation',
        object_filter_params: params[:biological_association_query],
        object_params: params[:biological_association],
        async_cutoff: (params[:async_cutoff] || 26),
        preview: params[:preview]
      )

      set_batch_cap(request)
      query_batch_update(request)
    end

  end

  def dwc_extension_select
    BiologicalAssociation
      .joins("LEFT JOIN identifiers id_s ON id_s.identifier_object_type = biological_associations.biological_associations_subject_type AND ids_s.type = 'Identifier::Global::Uuid'" )
      .joins("LEFT JOIN identifiers id_o ON id_o.identifier_object_type = biological_associations.biological_associations_object_type AND ids_o.type = 'Identifier::Global::Uuid'" )
      .joins("LEFT JOIN identifiers id_r ON id_o.identifier_object_type = 'BiologicalRelationship' AND idr_.identifier_object_id = biological_associations.biological_relationship_id AND ids_r.type = 'Identifier::Global::Uri'" )
  end

  # @return [ActiveRecord::Relation]
  def targeted_join(target: 'subject', target_class: ::Otu)
    a = arel_table
    b = target_class.arel_table

    j = a.join(b).on(a["biological_association_#{target}_type".to_sym].eq(target_class.name).and(a["biological_assoication_#{target}_id".to_sym].eq(b[:id])))
    joins(j.join_sources)
  end

  # @return [ActiveRecord::Relation]
  def targeted_join2(target: 'subject', target_class: ::Otu)
    a = arel_table
    b = target_class.arel_table

    j = a.join(b).on(a["biological_association_#{target}_type".to_sym].eq(target_class.name).and(a["biological_assoication_#{target}_id".to_sym].eq(b[:id])))
  end

  # Not used
  # @return [ActiveRecord::Relation]
  def targeted_left_join(target: 'subject', target_class: ::Otu )
    a = arel_table
    b = target_class.arel_table

    j = a.join(b, Arel::Nodes::OuterJoin).on(a["biological_association_#{target}_type".to_sym].eq(target_class.name).and(a["biological_assoication_#{target}_id".to_sym].eq(b[:id])))
    joins(j.join_sources)
  end

  # @return [Scope]
  #    the max 10 most recently used
  def self.used_recently(user_id, project_id, used_on)
    t = case used_on
        when 'AssertedDistribution'
          AssertedDistribution.arel_table
        else
          return BiologicalAssociation.none
        end

    # i is a select manager
    i = case used_on
        when 'AssertedDistribution'
          t.project(t['asserted_distribution_object_id'], t['updated_at']).from(t)
            .where(
              t['updated_at'].gt(1.week.ago).and(
                t['asserted_distribution_object_type'].eq('BiologicalAssociation')
              )
            )
            .where(t['updated_by_id'].eq(user_id))
            .where(t['project_id'].eq(project_id))
            .order(t['updated_at'].desc)
        end

    z = i.as('recent_t')
    p = BiologicalAssociation.arel_table

    case used_on
    when 'AssertedDistribution'
      BiologicalAssociation.joins(
        Arel::Nodes::InnerJoin.new(z, Arel::Nodes::On.new(z['asserted_distribution_object_id'].eq(p['id'])))
      ).pluck(:id).uniq
    end
  end

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

    if r.empty?
      h[:quick] = BiologicalAssociation.pinned_by(user_id).pinboard_inserted.where(project_id: project_id).to_a
    else
      h[:recent] = BiologicalAssociation.where('"biological_associations"."id" IN (?)', r.first(10) ).order(updated_at: :desc).to_a
      h[:quick] = (BiologicalAssociation.pinned_by(user_id).pinboard_inserted.where(project_id: project_id).to_a +
                   BiologicalAssociation.where('"biological_associations"."id" IN (?)', r.first(4) ).order(updated_at: :desc).to_a).uniq
    end

    h
  end

  private

  def association_is_unique
    if a = BiologicalAssociation.where.not(id:).where(
        biological_association_subject:,
        biological_association_object:,
        biological_relationship:
    ).first
      # For unify purposes, self has changed either subject or object, a is the
      # identical BA we will perhaps unify with.
      if will_save_change_to_biological_association_subject_id?
        errors.add(:biological_association_subject, 'has already been taken')
      elsif will_save_change_to_biological_association_object_id?
        errors.add(:biological_association_object, 'has already been taken')
      else
        errors.add(:biological_association, 'already exists')
      end
    end
  end


  def biological_association_subject_type_is_allowed
    errors.add(:biological_association_subject_type, 'is not permitted') unless biological_association_subject && biological_association_subject.class.is_biologically_relatable?
  end

  def biological_association_object_type_is_allowed
    errors.add(:biological_association_object_type, 'is not permitted') unless biological_association_object && biological_association_object.class.is_biologically_relatable?
  end
end

#biological_association_object_type ⇒ String

Returns Rails polymorphic, type of the object (e.g. CollectionObject).

Returns:

  • (String) —

    Rails polymorphic, type of the object (e.g. CollectionObject)



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

class BiologicalAssociation < ApplicationRecord
  include Housekeeping
  include SoftValidation
  include Shared::Citations
  include Shared::Tags
  include Shared::Identifiers
  include Shared::DataAttributes
  include Shared::Notes
  include Shared::Confidences
  include Shared::Depictions
  include Shared::AutoUuid
  include Shared::AssertedDistributions
  include Shared::IsData

  include BiologicalAssociation::GlobiExtensions
  include BiologicalAssociation::DwcExtensions

  include Shared::QueryBatchUpdate

  GRAPH_ENTRY_POINTS = [:asserted_distributions].freeze

  belongs_to :biological_relationship, inverse_of: :biological_associations

  has_many :subject_biological_relationship_types, through: :biological_relationship
  has_many :object_biological_relationship_types, through: :biological_relationship

  has_many :subject_biological_properties, through: :subject_biological_relationship_types, source: :biological_property
  has_many :object_biological_properties, through: :object_biological_relationship_types, source: :biological_property

  belongs_to :biological_association_subject, polymorphic: true, inverse_of: :biological_associations
  belongs_to :biological_association_object, polymorphic: true, inverse_of: :related_biological_associations

  has_many :biological_associations_biological_associations_graphs, inverse_of: :biological_association, dependent: :destroy
  has_many :biological_associations_graphs, through: :biological_associations_biological_associations_graphs, inverse_of: :biological_associations

  validates_presence_of :biological_relationship
  validates_presence_of :biological_association_subject
  validates_presence_of :biological_association_object

  validate :association_is_unique

  validate :biological_association_subject_type_is_allowed
  validate :biological_association_object_type_is_allowed

  attr_accessor :subject_global_id
  attr_accessor :object_global_id # TODO: this is badly named

  attr_accessor :rotate

  def rotate=(value)
    s = self.biological_association_subject
    o = self.biological_association_object

    self.biological_association_subject = o
    self.biological_association_object = s
  end

  def subject_global_id=(value)
    o = GlobalID::Locator.locate(value)
    write_attribute(:biological_association_subject_id, o.id)
    write_attribute(:biological_association_subject_type, o.metamorphosize.class.name)
  end

  def object_global_id=(value)
    o = GlobalID::Locator.locate(value)
    write_attribute(:biological_association_object_id, o.id)
    write_attribute(:biological_association_object_type, o.metamorphosize.class.name)
  end

  # TODO: Why?! this is just biological_association.biological_association_subject_type
  def subject_class_name
    biological_association_subject.try(:class).base_class.name
  end

  # TODO: Why?! this is just biological_association.biological_association_object_type
  def object_class_name
    biological_association_object.try(:class).base_class.name
  end

  # !! You can not set with this method
  def subject
    biological_association_subject
  end

  # !! You can not set with this method
  def object
    biological_association_object
  end

  class << self

    def set_batch_cap(request)
      a = request.filter
      total = a.all.pluck(:biological_relationship_id).uniq

      cap = 0

      case total.size
      when 1
        cap = 5000
        request.cap_reason = 'Maximum allowed.'
      when 2
        cap = 2000
        request.cap_reason = 'Maximum allowed when 2 biological relationships present.'
      else
        cap = 25
        request.cap_reason = 'Maximum allowed when 3 or more biological relationships present.'
      end

      request.cap = cap
      request
    end

    def batch_update(params)
      request = QueryBatchRequest.new(
        klass: 'BiologicalAssociation',
        object_filter_params: params[:biological_association_query],
        object_params: params[:biological_association],
        async_cutoff: (params[:async_cutoff] || 26),
        preview: params[:preview]
      )

      set_batch_cap(request)
      query_batch_update(request)
    end

  end

  def dwc_extension_select
    BiologicalAssociation
      .joins("LEFT JOIN identifiers id_s ON id_s.identifier_object_type = biological_associations.biological_associations_subject_type AND ids_s.type = 'Identifier::Global::Uuid'" )
      .joins("LEFT JOIN identifiers id_o ON id_o.identifier_object_type = biological_associations.biological_associations_object_type AND ids_o.type = 'Identifier::Global::Uuid'" )
      .joins("LEFT JOIN identifiers id_r ON id_o.identifier_object_type = 'BiologicalRelationship' AND idr_.identifier_object_id = biological_associations.biological_relationship_id AND ids_r.type = 'Identifier::Global::Uri'" )
  end

  # @return [ActiveRecord::Relation]
  def targeted_join(target: 'subject', target_class: ::Otu)
    a = arel_table
    b = target_class.arel_table

    j = a.join(b).on(a["biological_association_#{target}_type".to_sym].eq(target_class.name).and(a["biological_assoication_#{target}_id".to_sym].eq(b[:id])))
    joins(j.join_sources)
  end

  # @return [ActiveRecord::Relation]
  def targeted_join2(target: 'subject', target_class: ::Otu)
    a = arel_table
    b = target_class.arel_table

    j = a.join(b).on(a["biological_association_#{target}_type".to_sym].eq(target_class.name).and(a["biological_assoication_#{target}_id".to_sym].eq(b[:id])))
  end

  # Not used
  # @return [ActiveRecord::Relation]
  def targeted_left_join(target: 'subject', target_class: ::Otu )
    a = arel_table
    b = target_class.arel_table

    j = a.join(b, Arel::Nodes::OuterJoin).on(a["biological_association_#{target}_type".to_sym].eq(target_class.name).and(a["biological_assoication_#{target}_id".to_sym].eq(b[:id])))
    joins(j.join_sources)
  end

  # @return [Scope]
  #    the max 10 most recently used
  def self.used_recently(user_id, project_id, used_on)
    t = case used_on
        when 'AssertedDistribution'
          AssertedDistribution.arel_table
        else
          return BiologicalAssociation.none
        end

    # i is a select manager
    i = case used_on
        when 'AssertedDistribution'
          t.project(t['asserted_distribution_object_id'], t['updated_at']).from(t)
            .where(
              t['updated_at'].gt(1.week.ago).and(
                t['asserted_distribution_object_type'].eq('BiologicalAssociation')
              )
            )
            .where(t['updated_by_id'].eq(user_id))
            .where(t['project_id'].eq(project_id))
            .order(t['updated_at'].desc)
        end

    z = i.as('recent_t')
    p = BiologicalAssociation.arel_table

    case used_on
    when 'AssertedDistribution'
      BiologicalAssociation.joins(
        Arel::Nodes::InnerJoin.new(z, Arel::Nodes::On.new(z['asserted_distribution_object_id'].eq(p['id'])))
      ).pluck(:id).uniq
    end
  end

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

    if r.empty?
      h[:quick] = BiologicalAssociation.pinned_by(user_id).pinboard_inserted.where(project_id: project_id).to_a
    else
      h[:recent] = BiologicalAssociation.where('"biological_associations"."id" IN (?)', r.first(10) ).order(updated_at: :desc).to_a
      h[:quick] = (BiologicalAssociation.pinned_by(user_id).pinboard_inserted.where(project_id: project_id).to_a +
                   BiologicalAssociation.where('"biological_associations"."id" IN (?)', r.first(4) ).order(updated_at: :desc).to_a).uniq
    end

    h
  end

  private

  def association_is_unique
    if a = BiologicalAssociation.where.not(id:).where(
        biological_association_subject:,
        biological_association_object:,
        biological_relationship:
    ).first
      # For unify purposes, self has changed either subject or object, a is the
      # identical BA we will perhaps unify with.
      if will_save_change_to_biological_association_subject_id?
        errors.add(:biological_association_subject, 'has already been taken')
      elsif will_save_change_to_biological_association_object_id?
        errors.add(:biological_association_object, 'has already been taken')
      else
        errors.add(:biological_association, 'already exists')
      end
    end
  end


  def biological_association_subject_type_is_allowed
    errors.add(:biological_association_subject_type, 'is not permitted') unless biological_association_subject && biological_association_subject.class.is_biologically_relatable?
  end

  def biological_association_object_type_is_allowed
    errors.add(:biological_association_object_type, 'is not permitted') unless biological_association_object && biological_association_object.class.is_biologically_relatable?
  end
end

#biological_association_subject_id ⇒ Integer

Returns Rails polymorphic, id of the subject of the relationship.

Returns:

  • (Integer) —

    Rails polymorphic, id of the subject of the relationship



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

class BiologicalAssociation < ApplicationRecord
  include Housekeeping
  include SoftValidation
  include Shared::Citations
  include Shared::Tags
  include Shared::Identifiers
  include Shared::DataAttributes
  include Shared::Notes
  include Shared::Confidences
  include Shared::Depictions
  include Shared::AutoUuid
  include Shared::AssertedDistributions
  include Shared::IsData

  include BiologicalAssociation::GlobiExtensions
  include BiologicalAssociation::DwcExtensions

  include Shared::QueryBatchUpdate

  GRAPH_ENTRY_POINTS = [:asserted_distributions].freeze

  belongs_to :biological_relationship, inverse_of: :biological_associations

  has_many :subject_biological_relationship_types, through: :biological_relationship
  has_many :object_biological_relationship_types, through: :biological_relationship

  has_many :subject_biological_properties, through: :subject_biological_relationship_types, source: :biological_property
  has_many :object_biological_properties, through: :object_biological_relationship_types, source: :biological_property

  belongs_to :biological_association_subject, polymorphic: true, inverse_of: :biological_associations
  belongs_to :biological_association_object, polymorphic: true, inverse_of: :related_biological_associations

  has_many :biological_associations_biological_associations_graphs, inverse_of: :biological_association, dependent: :destroy
  has_many :biological_associations_graphs, through: :biological_associations_biological_associations_graphs, inverse_of: :biological_associations

  validates_presence_of :biological_relationship
  validates_presence_of :biological_association_subject
  validates_presence_of :biological_association_object

  validate :association_is_unique

  validate :biological_association_subject_type_is_allowed
  validate :biological_association_object_type_is_allowed

  attr_accessor :subject_global_id
  attr_accessor :object_global_id # TODO: this is badly named

  attr_accessor :rotate

  def rotate=(value)
    s = self.biological_association_subject
    o = self.biological_association_object

    self.biological_association_subject = o
    self.biological_association_object = s
  end

  def subject_global_id=(value)
    o = GlobalID::Locator.locate(value)
    write_attribute(:biological_association_subject_id, o.id)
    write_attribute(:biological_association_subject_type, o.metamorphosize.class.name)
  end

  def object_global_id=(value)
    o = GlobalID::Locator.locate(value)
    write_attribute(:biological_association_object_id, o.id)
    write_attribute(:biological_association_object_type, o.metamorphosize.class.name)
  end

  # TODO: Why?! this is just biological_association.biological_association_subject_type
  def subject_class_name
    biological_association_subject.try(:class).base_class.name
  end

  # TODO: Why?! this is just biological_association.biological_association_object_type
  def object_class_name
    biological_association_object.try(:class).base_class.name
  end

  # !! You can not set with this method
  def subject
    biological_association_subject
  end

  # !! You can not set with this method
  def object
    biological_association_object
  end

  class << self

    def set_batch_cap(request)
      a = request.filter
      total = a.all.pluck(:biological_relationship_id).uniq

      cap = 0

      case total.size
      when 1
        cap = 5000
        request.cap_reason = 'Maximum allowed.'
      when 2
        cap = 2000
        request.cap_reason = 'Maximum allowed when 2 biological relationships present.'
      else
        cap = 25
        request.cap_reason = 'Maximum allowed when 3 or more biological relationships present.'
      end

      request.cap = cap
      request
    end

    def batch_update(params)
      request = QueryBatchRequest.new(
        klass: 'BiologicalAssociation',
        object_filter_params: params[:biological_association_query],
        object_params: params[:biological_association],
        async_cutoff: (params[:async_cutoff] || 26),
        preview: params[:preview]
      )

      set_batch_cap(request)
      query_batch_update(request)
    end

  end

  def dwc_extension_select
    BiologicalAssociation
      .joins("LEFT JOIN identifiers id_s ON id_s.identifier_object_type = biological_associations.biological_associations_subject_type AND ids_s.type = 'Identifier::Global::Uuid'" )
      .joins("LEFT JOIN identifiers id_o ON id_o.identifier_object_type = biological_associations.biological_associations_object_type AND ids_o.type = 'Identifier::Global::Uuid'" )
      .joins("LEFT JOIN identifiers id_r ON id_o.identifier_object_type = 'BiologicalRelationship' AND idr_.identifier_object_id = biological_associations.biological_relationship_id AND ids_r.type = 'Identifier::Global::Uri'" )
  end

  # @return [ActiveRecord::Relation]
  def targeted_join(target: 'subject', target_class: ::Otu)
    a = arel_table
    b = target_class.arel_table

    j = a.join(b).on(a["biological_association_#{target}_type".to_sym].eq(target_class.name).and(a["biological_assoication_#{target}_id".to_sym].eq(b[:id])))
    joins(j.join_sources)
  end

  # @return [ActiveRecord::Relation]
  def targeted_join2(target: 'subject', target_class: ::Otu)
    a = arel_table
    b = target_class.arel_table

    j = a.join(b).on(a["biological_association_#{target}_type".to_sym].eq(target_class.name).and(a["biological_assoication_#{target}_id".to_sym].eq(b[:id])))
  end

  # Not used
  # @return [ActiveRecord::Relation]
  def targeted_left_join(target: 'subject', target_class: ::Otu )
    a = arel_table
    b = target_class.arel_table

    j = a.join(b, Arel::Nodes::OuterJoin).on(a["biological_association_#{target}_type".to_sym].eq(target_class.name).and(a["biological_assoication_#{target}_id".to_sym].eq(b[:id])))
    joins(j.join_sources)
  end

  # @return [Scope]
  #    the max 10 most recently used
  def self.used_recently(user_id, project_id, used_on)
    t = case used_on
        when 'AssertedDistribution'
          AssertedDistribution.arel_table
        else
          return BiologicalAssociation.none
        end

    # i is a select manager
    i = case used_on
        when 'AssertedDistribution'
          t.project(t['asserted_distribution_object_id'], t['updated_at']).from(t)
            .where(
              t['updated_at'].gt(1.week.ago).and(
                t['asserted_distribution_object_type'].eq('BiologicalAssociation')
              )
            )
            .where(t['updated_by_id'].eq(user_id))
            .where(t['project_id'].eq(project_id))
            .order(t['updated_at'].desc)
        end

    z = i.as('recent_t')
    p = BiologicalAssociation.arel_table

    case used_on
    when 'AssertedDistribution'
      BiologicalAssociation.joins(
        Arel::Nodes::InnerJoin.new(z, Arel::Nodes::On.new(z['asserted_distribution_object_id'].eq(p['id'])))
      ).pluck(:id).uniq
    end
  end

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

    if r.empty?
      h[:quick] = BiologicalAssociation.pinned_by(user_id).pinboard_inserted.where(project_id: project_id).to_a
    else
      h[:recent] = BiologicalAssociation.where('"biological_associations"."id" IN (?)', r.first(10) ).order(updated_at: :desc).to_a
      h[:quick] = (BiologicalAssociation.pinned_by(user_id).pinboard_inserted.where(project_id: project_id).to_a +
                   BiologicalAssociation.where('"biological_associations"."id" IN (?)', r.first(4) ).order(updated_at: :desc).to_a).uniq
    end

    h
  end

  private

  def association_is_unique
    if a = BiologicalAssociation.where.not(id:).where(
        biological_association_subject:,
        biological_association_object:,
        biological_relationship:
    ).first
      # For unify purposes, self has changed either subject or object, a is the
      # identical BA we will perhaps unify with.
      if will_save_change_to_biological_association_subject_id?
        errors.add(:biological_association_subject, 'has already been taken')
      elsif will_save_change_to_biological_association_object_id?
        errors.add(:biological_association_object, 'has already been taken')
      else
        errors.add(:biological_association, 'already exists')
      end
    end
  end


  def biological_association_subject_type_is_allowed
    errors.add(:biological_association_subject_type, 'is not permitted') unless biological_association_subject && biological_association_subject.class.is_biologically_relatable?
  end

  def biological_association_object_type_is_allowed
    errors.add(:biological_association_object_type, 'is not permitted') unless biological_association_object && biological_association_object.class.is_biologically_relatable?
  end
end

#biological_association_subject_type ⇒ String

Returns Rails polymorphic, type fo the subject (e.g. Otu).

Returns:

  • (String) —

    Rails polymorphic, type fo the subject (e.g. Otu)



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

class BiologicalAssociation < ApplicationRecord
  include Housekeeping
  include SoftValidation
  include Shared::Citations
  include Shared::Tags
  include Shared::Identifiers
  include Shared::DataAttributes
  include Shared::Notes
  include Shared::Confidences
  include Shared::Depictions
  include Shared::AutoUuid
  include Shared::AssertedDistributions
  include Shared::IsData

  include BiologicalAssociation::GlobiExtensions
  include BiologicalAssociation::DwcExtensions

  include Shared::QueryBatchUpdate

  GRAPH_ENTRY_POINTS = [:asserted_distributions].freeze

  belongs_to :biological_relationship, inverse_of: :biological_associations

  has_many :subject_biological_relationship_types, through: :biological_relationship
  has_many :object_biological_relationship_types, through: :biological_relationship

  has_many :subject_biological_properties, through: :subject_biological_relationship_types, source: :biological_property
  has_many :object_biological_properties, through: :object_biological_relationship_types, source: :biological_property

  belongs_to :biological_association_subject, polymorphic: true, inverse_of: :biological_associations
  belongs_to :biological_association_object, polymorphic: true, inverse_of: :related_biological_associations

  has_many :biological_associations_biological_associations_graphs, inverse_of: :biological_association, dependent: :destroy
  has_many :biological_associations_graphs, through: :biological_associations_biological_associations_graphs, inverse_of: :biological_associations

  validates_presence_of :biological_relationship
  validates_presence_of :biological_association_subject
  validates_presence_of :biological_association_object

  validate :association_is_unique

  validate :biological_association_subject_type_is_allowed
  validate :biological_association_object_type_is_allowed

  attr_accessor :subject_global_id
  attr_accessor :object_global_id # TODO: this is badly named

  attr_accessor :rotate

  def rotate=(value)
    s = self.biological_association_subject
    o = self.biological_association_object

    self.biological_association_subject = o
    self.biological_association_object = s
  end

  def subject_global_id=(value)
    o = GlobalID::Locator.locate(value)
    write_attribute(:biological_association_subject_id, o.id)
    write_attribute(:biological_association_subject_type, o.metamorphosize.class.name)
  end

  def object_global_id=(value)
    o = GlobalID::Locator.locate(value)
    write_attribute(:biological_association_object_id, o.id)
    write_attribute(:biological_association_object_type, o.metamorphosize.class.name)
  end

  # TODO: Why?! this is just biological_association.biological_association_subject_type
  def subject_class_name
    biological_association_subject.try(:class).base_class.name
  end

  # TODO: Why?! this is just biological_association.biological_association_object_type
  def object_class_name
    biological_association_object.try(:class).base_class.name
  end

  # !! You can not set with this method
  def subject
    biological_association_subject
  end

  # !! You can not set with this method
  def object
    biological_association_object
  end

  class << self

    def set_batch_cap(request)
      a = request.filter
      total = a.all.pluck(:biological_relationship_id).uniq

      cap = 0

      case total.size
      when 1
        cap = 5000
        request.cap_reason = 'Maximum allowed.'
      when 2
        cap = 2000
        request.cap_reason = 'Maximum allowed when 2 biological relationships present.'
      else
        cap = 25
        request.cap_reason = 'Maximum allowed when 3 or more biological relationships present.'
      end

      request.cap = cap
      request
    end

    def batch_update(params)
      request = QueryBatchRequest.new(
        klass: 'BiologicalAssociation',
        object_filter_params: params[:biological_association_query],
        object_params: params[:biological_association],
        async_cutoff: (params[:async_cutoff] || 26),
        preview: params[:preview]
      )

      set_batch_cap(request)
      query_batch_update(request)
    end

  end

  def dwc_extension_select
    BiologicalAssociation
      .joins("LEFT JOIN identifiers id_s ON id_s.identifier_object_type = biological_associations.biological_associations_subject_type AND ids_s.type = 'Identifier::Global::Uuid'" )
      .joins("LEFT JOIN identifiers id_o ON id_o.identifier_object_type = biological_associations.biological_associations_object_type AND ids_o.type = 'Identifier::Global::Uuid'" )
      .joins("LEFT JOIN identifiers id_r ON id_o.identifier_object_type = 'BiologicalRelationship' AND idr_.identifier_object_id = biological_associations.biological_relationship_id AND ids_r.type = 'Identifier::Global::Uri'" )
  end

  # @return [ActiveRecord::Relation]
  def targeted_join(target: 'subject', target_class: ::Otu)
    a = arel_table
    b = target_class.arel_table

    j = a.join(b).on(a["biological_association_#{target}_type".to_sym].eq(target_class.name).and(a["biological_assoication_#{target}_id".to_sym].eq(b[:id])))
    joins(j.join_sources)
  end

  # @return [ActiveRecord::Relation]
  def targeted_join2(target: 'subject', target_class: ::Otu)
    a = arel_table
    b = target_class.arel_table

    j = a.join(b).on(a["biological_association_#{target}_type".to_sym].eq(target_class.name).and(a["biological_assoication_#{target}_id".to_sym].eq(b[:id])))
  end

  # Not used
  # @return [ActiveRecord::Relation]
  def targeted_left_join(target: 'subject', target_class: ::Otu )
    a = arel_table
    b = target_class.arel_table

    j = a.join(b, Arel::Nodes::OuterJoin).on(a["biological_association_#{target}_type".to_sym].eq(target_class.name).and(a["biological_assoication_#{target}_id".to_sym].eq(b[:id])))
    joins(j.join_sources)
  end

  # @return [Scope]
  #    the max 10 most recently used
  def self.used_recently(user_id, project_id, used_on)
    t = case used_on
        when 'AssertedDistribution'
          AssertedDistribution.arel_table
        else
          return BiologicalAssociation.none
        end

    # i is a select manager
    i = case used_on
        when 'AssertedDistribution'
          t.project(t['asserted_distribution_object_id'], t['updated_at']).from(t)
            .where(
              t['updated_at'].gt(1.week.ago).and(
                t['asserted_distribution_object_type'].eq('BiologicalAssociation')
              )
            )
            .where(t['updated_by_id'].eq(user_id))
            .where(t['project_id'].eq(project_id))
            .order(t['updated_at'].desc)
        end

    z = i.as('recent_t')
    p = BiologicalAssociation.arel_table

    case used_on
    when 'AssertedDistribution'
      BiologicalAssociation.joins(
        Arel::Nodes::InnerJoin.new(z, Arel::Nodes::On.new(z['asserted_distribution_object_id'].eq(p['id'])))
      ).pluck(:id).uniq
    end
  end

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

    if r.empty?
      h[:quick] = BiologicalAssociation.pinned_by(user_id).pinboard_inserted.where(project_id: project_id).to_a
    else
      h[:recent] = BiologicalAssociation.where('"biological_associations"."id" IN (?)', r.first(10) ).order(updated_at: :desc).to_a
      h[:quick] = (BiologicalAssociation.pinned_by(user_id).pinboard_inserted.where(project_id: project_id).to_a +
                   BiologicalAssociation.where('"biological_associations"."id" IN (?)', r.first(4) ).order(updated_at: :desc).to_a).uniq
    end

    h
  end

  private

  def association_is_unique
    if a = BiologicalAssociation.where.not(id:).where(
        biological_association_subject:,
        biological_association_object:,
        biological_relationship:
    ).first
      # For unify purposes, self has changed either subject or object, a is the
      # identical BA we will perhaps unify with.
      if will_save_change_to_biological_association_subject_id?
        errors.add(:biological_association_subject, 'has already been taken')
      elsif will_save_change_to_biological_association_object_id?
        errors.add(:biological_association_object, 'has already been taken')
      else
        errors.add(:biological_association, 'already exists')
      end
    end
  end


  def biological_association_subject_type_is_allowed
    errors.add(:biological_association_subject_type, 'is not permitted') unless biological_association_subject && biological_association_subject.class.is_biologically_relatable?
  end

  def biological_association_object_type_is_allowed
    errors.add(:biological_association_object_type, 'is not permitted') unless biological_association_object && biological_association_object.class.is_biologically_relatable?
  end
end

#biological_relationship_id ⇒ Integer

Returns the BiologicalRelationship id.

Returns:

  • (Integer) —

    the BiologicalRelationship id



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

class BiologicalAssociation < ApplicationRecord
  include Housekeeping
  include SoftValidation
  include Shared::Citations
  include Shared::Tags
  include Shared::Identifiers
  include Shared::DataAttributes
  include Shared::Notes
  include Shared::Confidences
  include Shared::Depictions
  include Shared::AutoUuid
  include Shared::AssertedDistributions
  include Shared::IsData

  include BiologicalAssociation::GlobiExtensions
  include BiologicalAssociation::DwcExtensions

  include Shared::QueryBatchUpdate

  GRAPH_ENTRY_POINTS = [:asserted_distributions].freeze

  belongs_to :biological_relationship, inverse_of: :biological_associations

  has_many :subject_biological_relationship_types, through: :biological_relationship
  has_many :object_biological_relationship_types, through: :biological_relationship

  has_many :subject_biological_properties, through: :subject_biological_relationship_types, source: :biological_property
  has_many :object_biological_properties, through: :object_biological_relationship_types, source: :biological_property

  belongs_to :biological_association_subject, polymorphic: true, inverse_of: :biological_associations
  belongs_to :biological_association_object, polymorphic: true, inverse_of: :related_biological_associations

  has_many :biological_associations_biological_associations_graphs, inverse_of: :biological_association, dependent: :destroy
  has_many :biological_associations_graphs, through: :biological_associations_biological_associations_graphs, inverse_of: :biological_associations

  validates_presence_of :biological_relationship
  validates_presence_of :biological_association_subject
  validates_presence_of :biological_association_object

  validate :association_is_unique

  validate :biological_association_subject_type_is_allowed
  validate :biological_association_object_type_is_allowed

  attr_accessor :subject_global_id
  attr_accessor :object_global_id # TODO: this is badly named

  attr_accessor :rotate

  def rotate=(value)
    s = self.biological_association_subject
    o = self.biological_association_object

    self.biological_association_subject = o
    self.biological_association_object = s
  end

  def subject_global_id=(value)
    o = GlobalID::Locator.locate(value)
    write_attribute(:biological_association_subject_id, o.id)
    write_attribute(:biological_association_subject_type, o.metamorphosize.class.name)
  end

  def object_global_id=(value)
    o = GlobalID::Locator.locate(value)
    write_attribute(:biological_association_object_id, o.id)
    write_attribute(:biological_association_object_type, o.metamorphosize.class.name)
  end

  # TODO: Why?! this is just biological_association.biological_association_subject_type
  def subject_class_name
    biological_association_subject.try(:class).base_class.name
  end

  # TODO: Why?! this is just biological_association.biological_association_object_type
  def object_class_name
    biological_association_object.try(:class).base_class.name
  end

  # !! You can not set with this method
  def subject
    biological_association_subject
  end

  # !! You can not set with this method
  def object
    biological_association_object
  end

  class << self

    def set_batch_cap(request)
      a = request.filter
      total = a.all.pluck(:biological_relationship_id).uniq

      cap = 0

      case total.size
      when 1
        cap = 5000
        request.cap_reason = 'Maximum allowed.'
      when 2
        cap = 2000
        request.cap_reason = 'Maximum allowed when 2 biological relationships present.'
      else
        cap = 25
        request.cap_reason = 'Maximum allowed when 3 or more biological relationships present.'
      end

      request.cap = cap
      request
    end

    def batch_update(params)
      request = QueryBatchRequest.new(
        klass: 'BiologicalAssociation',
        object_filter_params: params[:biological_association_query],
        object_params: params[:biological_association],
        async_cutoff: (params[:async_cutoff] || 26),
        preview: params[:preview]
      )

      set_batch_cap(request)
      query_batch_update(request)
    end

  end

  def dwc_extension_select
    BiologicalAssociation
      .joins("LEFT JOIN identifiers id_s ON id_s.identifier_object_type = biological_associations.biological_associations_subject_type AND ids_s.type = 'Identifier::Global::Uuid'" )
      .joins("LEFT JOIN identifiers id_o ON id_o.identifier_object_type = biological_associations.biological_associations_object_type AND ids_o.type = 'Identifier::Global::Uuid'" )
      .joins("LEFT JOIN identifiers id_r ON id_o.identifier_object_type = 'BiologicalRelationship' AND idr_.identifier_object_id = biological_associations.biological_relationship_id AND ids_r.type = 'Identifier::Global::Uri'" )
  end

  # @return [ActiveRecord::Relation]
  def targeted_join(target: 'subject', target_class: ::Otu)
    a = arel_table
    b = target_class.arel_table

    j = a.join(b).on(a["biological_association_#{target}_type".to_sym].eq(target_class.name).and(a["biological_assoication_#{target}_id".to_sym].eq(b[:id])))
    joins(j.join_sources)
  end

  # @return [ActiveRecord::Relation]
  def targeted_join2(target: 'subject', target_class: ::Otu)
    a = arel_table
    b = target_class.arel_table

    j = a.join(b).on(a["biological_association_#{target}_type".to_sym].eq(target_class.name).and(a["biological_assoication_#{target}_id".to_sym].eq(b[:id])))
  end

  # Not used
  # @return [ActiveRecord::Relation]
  def targeted_left_join(target: 'subject', target_class: ::Otu )
    a = arel_table
    b = target_class.arel_table

    j = a.join(b, Arel::Nodes::OuterJoin).on(a["biological_association_#{target}_type".to_sym].eq(target_class.name).and(a["biological_assoication_#{target}_id".to_sym].eq(b[:id])))
    joins(j.join_sources)
  end

  # @return [Scope]
  #    the max 10 most recently used
  def self.used_recently(user_id, project_id, used_on)
    t = case used_on
        when 'AssertedDistribution'
          AssertedDistribution.arel_table
        else
          return BiologicalAssociation.none
        end

    # i is a select manager
    i = case used_on
        when 'AssertedDistribution'
          t.project(t['asserted_distribution_object_id'], t['updated_at']).from(t)
            .where(
              t['updated_at'].gt(1.week.ago).and(
                t['asserted_distribution_object_type'].eq('BiologicalAssociation')
              )
            )
            .where(t['updated_by_id'].eq(user_id))
            .where(t['project_id'].eq(project_id))
            .order(t['updated_at'].desc)
        end

    z = i.as('recent_t')
    p = BiologicalAssociation.arel_table

    case used_on
    when 'AssertedDistribution'
      BiologicalAssociation.joins(
        Arel::Nodes::InnerJoin.new(z, Arel::Nodes::On.new(z['asserted_distribution_object_id'].eq(p['id'])))
      ).pluck(:id).uniq
    end
  end

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

    if r.empty?
      h[:quick] = BiologicalAssociation.pinned_by(user_id).pinboard_inserted.where(project_id: project_id).to_a
    else
      h[:recent] = BiologicalAssociation.where('"biological_associations"."id" IN (?)', r.first(10) ).order(updated_at: :desc).to_a
      h[:quick] = (BiologicalAssociation.pinned_by(user_id).pinboard_inserted.where(project_id: project_id).to_a +
                   BiologicalAssociation.where('"biological_associations"."id" IN (?)', r.first(4) ).order(updated_at: :desc).to_a).uniq
    end

    h
  end

  private

  def association_is_unique
    if a = BiologicalAssociation.where.not(id:).where(
        biological_association_subject:,
        biological_association_object:,
        biological_relationship:
    ).first
      # For unify purposes, self has changed either subject or object, a is the
      # identical BA we will perhaps unify with.
      if will_save_change_to_biological_association_subject_id?
        errors.add(:biological_association_subject, 'has already been taken')
      elsif will_save_change_to_biological_association_object_id?
        errors.add(:biological_association_object, 'has already been taken')
      else
        errors.add(:biological_association, 'already exists')
      end
    end
  end


  def biological_association_subject_type_is_allowed
    errors.add(:biological_association_subject_type, 'is not permitted') unless biological_association_subject && biological_association_subject.class.is_biologically_relatable?
  end

  def biological_association_object_type_is_allowed
    errors.add(:biological_association_object_type, 'is not permitted') unless biological_association_object && biological_association_object.class.is_biologically_relatable?
  end
end

#object_global_id ⇒ Object

TODO: this is badly named



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# File 'app/models/biological_association.rb', line 74

def object_global_id
  @object_global_id
end

#project_id ⇒ Integer

the project ID

Returns:

  • (Integer) 


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

class BiologicalAssociation < ApplicationRecord
  include Housekeeping
  include SoftValidation
  include Shared::Citations
  include Shared::Tags
  include Shared::Identifiers
  include Shared::DataAttributes
  include Shared::Notes
  include Shared::Confidences
  include Shared::Depictions
  include Shared::AutoUuid
  include Shared::AssertedDistributions
  include Shared::IsData

  include BiologicalAssociation::GlobiExtensions
  include BiologicalAssociation::DwcExtensions

  include Shared::QueryBatchUpdate

  GRAPH_ENTRY_POINTS = [:asserted_distributions].freeze

  belongs_to :biological_relationship, inverse_of: :biological_associations

  has_many :subject_biological_relationship_types, through: :biological_relationship
  has_many :object_biological_relationship_types, through: :biological_relationship

  has_many :subject_biological_properties, through: :subject_biological_relationship_types, source: :biological_property
  has_many :object_biological_properties, through: :object_biological_relationship_types, source: :biological_property

  belongs_to :biological_association_subject, polymorphic: true, inverse_of: :biological_associations
  belongs_to :biological_association_object, polymorphic: true, inverse_of: :related_biological_associations

  has_many :biological_associations_biological_associations_graphs, inverse_of: :biological_association, dependent: :destroy
  has_many :biological_associations_graphs, through: :biological_associations_biological_associations_graphs, inverse_of: :biological_associations

  validates_presence_of :biological_relationship
  validates_presence_of :biological_association_subject
  validates_presence_of :biological_association_object

  validate :association_is_unique

  validate :biological_association_subject_type_is_allowed
  validate :biological_association_object_type_is_allowed

  attr_accessor :subject_global_id
  attr_accessor :object_global_id # TODO: this is badly named

  attr_accessor :rotate

  def rotate=(value)
    s = self.biological_association_subject
    o = self.biological_association_object

    self.biological_association_subject = o
    self.biological_association_object = s
  end

  def subject_global_id=(value)
    o = GlobalID::Locator.locate(value)
    write_attribute(:biological_association_subject_id, o.id)
    write_attribute(:biological_association_subject_type, o.metamorphosize.class.name)
  end

  def object_global_id=(value)
    o = GlobalID::Locator.locate(value)
    write_attribute(:biological_association_object_id, o.id)
    write_attribute(:biological_association_object_type, o.metamorphosize.class.name)
  end

  # TODO: Why?! this is just biological_association.biological_association_subject_type
  def subject_class_name
    biological_association_subject.try(:class).base_class.name
  end

  # TODO: Why?! this is just biological_association.biological_association_object_type
  def object_class_name
    biological_association_object.try(:class).base_class.name
  end

  # !! You can not set with this method
  def subject
    biological_association_subject
  end

  # !! You can not set with this method
  def object
    biological_association_object
  end

  class << self

    def set_batch_cap(request)
      a = request.filter
      total = a.all.pluck(:biological_relationship_id).uniq

      cap = 0

      case total.size
      when 1
        cap = 5000
        request.cap_reason = 'Maximum allowed.'
      when 2
        cap = 2000
        request.cap_reason = 'Maximum allowed when 2 biological relationships present.'
      else
        cap = 25
        request.cap_reason = 'Maximum allowed when 3 or more biological relationships present.'
      end

      request.cap = cap
      request
    end

    def batch_update(params)
      request = QueryBatchRequest.new(
        klass: 'BiologicalAssociation',
        object_filter_params: params[:biological_association_query],
        object_params: params[:biological_association],
        async_cutoff: (params[:async_cutoff] || 26),
        preview: params[:preview]
      )

      set_batch_cap(request)
      query_batch_update(request)
    end

  end

  def dwc_extension_select
    BiologicalAssociation
      .joins("LEFT JOIN identifiers id_s ON id_s.identifier_object_type = biological_associations.biological_associations_subject_type AND ids_s.type = 'Identifier::Global::Uuid'" )
      .joins("LEFT JOIN identifiers id_o ON id_o.identifier_object_type = biological_associations.biological_associations_object_type AND ids_o.type = 'Identifier::Global::Uuid'" )
      .joins("LEFT JOIN identifiers id_r ON id_o.identifier_object_type = 'BiologicalRelationship' AND idr_.identifier_object_id = biological_associations.biological_relationship_id AND ids_r.type = 'Identifier::Global::Uri'" )
  end

  # @return [ActiveRecord::Relation]
  def targeted_join(target: 'subject', target_class: ::Otu)
    a = arel_table
    b = target_class.arel_table

    j = a.join(b).on(a["biological_association_#{target}_type".to_sym].eq(target_class.name).and(a["biological_assoication_#{target}_id".to_sym].eq(b[:id])))
    joins(j.join_sources)
  end

  # @return [ActiveRecord::Relation]
  def targeted_join2(target: 'subject', target_class: ::Otu)
    a = arel_table
    b = target_class.arel_table

    j = a.join(b).on(a["biological_association_#{target}_type".to_sym].eq(target_class.name).and(a["biological_assoication_#{target}_id".to_sym].eq(b[:id])))
  end

  # Not used
  # @return [ActiveRecord::Relation]
  def targeted_left_join(target: 'subject', target_class: ::Otu )
    a = arel_table
    b = target_class.arel_table

    j = a.join(b, Arel::Nodes::OuterJoin).on(a["biological_association_#{target}_type".to_sym].eq(target_class.name).and(a["biological_assoication_#{target}_id".to_sym].eq(b[:id])))
    joins(j.join_sources)
  end

  # @return [Scope]
  #    the max 10 most recently used
  def self.used_recently(user_id, project_id, used_on)
    t = case used_on
        when 'AssertedDistribution'
          AssertedDistribution.arel_table
        else
          return BiologicalAssociation.none
        end

    # i is a select manager
    i = case used_on
        when 'AssertedDistribution'
          t.project(t['asserted_distribution_object_id'], t['updated_at']).from(t)
            .where(
              t['updated_at'].gt(1.week.ago).and(
                t['asserted_distribution_object_type'].eq('BiologicalAssociation')
              )
            )
            .where(t['updated_by_id'].eq(user_id))
            .where(t['project_id'].eq(project_id))
            .order(t['updated_at'].desc)
        end

    z = i.as('recent_t')
    p = BiologicalAssociation.arel_table

    case used_on
    when 'AssertedDistribution'
      BiologicalAssociation.joins(
        Arel::Nodes::InnerJoin.new(z, Arel::Nodes::On.new(z['asserted_distribution_object_id'].eq(p['id'])))
      ).pluck(:id).uniq
    end
  end

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

    if r.empty?
      h[:quick] = BiologicalAssociation.pinned_by(user_id).pinboard_inserted.where(project_id: project_id).to_a
    else
      h[:recent] = BiologicalAssociation.where('"biological_associations"."id" IN (?)', r.first(10) ).order(updated_at: :desc).to_a
      h[:quick] = (BiologicalAssociation.pinned_by(user_id).pinboard_inserted.where(project_id: project_id).to_a +
                   BiologicalAssociation.where('"biological_associations"."id" IN (?)', r.first(4) ).order(updated_at: :desc).to_a).uniq
    end

    h
  end

  private

  def association_is_unique
    if a = BiologicalAssociation.where.not(id:).where(
        biological_association_subject:,
        biological_association_object:,
        biological_relationship:
    ).first
      # For unify purposes, self has changed either subject or object, a is the
      # identical BA we will perhaps unify with.
      if will_save_change_to_biological_association_subject_id?
        errors.add(:biological_association_subject, 'has already been taken')
      elsif will_save_change_to_biological_association_object_id?
        errors.add(:biological_association_object, 'has already been taken')
      else
        errors.add(:biological_association, 'already exists')
      end
    end
  end


  def biological_association_subject_type_is_allowed
    errors.add(:biological_association_subject_type, 'is not permitted') unless biological_association_subject && biological_association_subject.class.is_biologically_relatable?
  end

  def biological_association_object_type_is_allowed
    errors.add(:biological_association_object_type, 'is not permitted') unless biological_association_object && biological_association_object.class.is_biologically_relatable?
  end
end

#rotate ⇒ Object

Returns the value of attribute rotate.



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# File 'app/models/biological_association.rb', line 76

def rotate
  @rotate
end

#subject_global_id ⇒ Object

Returns the value of attribute subject_global_id.



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# File 'app/models/biological_association.rb', line 73

def subject_global_id
  @subject_global_id
end

Class Method Details

.batch_update(params) ⇒ Object 



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# File 'app/models/biological_association.rb', line 142

def batch_update(params)
  request = QueryBatchRequest.new(
    klass: 'BiologicalAssociation',
    object_filter_params: params[:biological_association_query],
    object_params: params[:biological_association],
    async_cutoff: (params[:async_cutoff] || 26),
    preview: params[:preview]
  )

  set_batch_cap(request)
  query_batch_update(request)
end

.select_optimized(user_id, project_id, klass) ⇒ Object 



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# File 'app/models/biological_association.rb', line 226

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

  if r.empty?
    h[:quick] = BiologicalAssociation.pinned_by(user_id).pinboard_inserted.where(project_id: project_id).to_a
  else
    h[:recent] = BiologicalAssociation.where('"biological_associations"."id" IN (?)', r.first(10) ).order(updated_at: :desc).to_a
    h[:quick] = (BiologicalAssociation.pinned_by(user_id).pinboard_inserted.where(project_id: project_id).to_a +
                 BiologicalAssociation.where('"biological_associations"."id" IN (?)', r.first(4) ).order(updated_at: :desc).to_a).uniq
  end

  h
end

.set_batch_cap(request) ⇒ Object 



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# File 'app/models/biological_association.rb', line 120

def set_batch_cap(request)
  a = request.filter
  total = a.all.pluck(:biological_relationship_id).uniq

  cap = 0

  case total.size
  when 1
    cap = 5000
    request.cap_reason = 'Maximum allowed.'
  when 2
    cap = 2000
    request.cap_reason = 'Maximum allowed when 2 biological relationships present.'
  else
    cap = 25
    request.cap_reason = 'Maximum allowed when 3 or more biological relationships present.'
  end

  request.cap = cap
  request
end

.used_recently(user_id, project_id, used_on) ⇒ Scope

Returns the max 10 most recently used.

Returns:

  • (Scope) —

    the max 10 most recently used



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# File 'app/models/biological_association.rb', line 193

def self.used_recently(user_id, project_id, used_on)
  t = case used_on
      when 'AssertedDistribution'
        AssertedDistribution.arel_table
      else
        return BiologicalAssociation.none
      end

  # i is a select manager
  i = case used_on
      when 'AssertedDistribution'
        t.project(t['asserted_distribution_object_id'], t['updated_at']).from(t)
          .where(
            t['updated_at'].gt(1.week.ago).and(
              t['asserted_distribution_object_type'].eq('BiologicalAssociation')
            )
          )
          .where(t['updated_by_id'].eq(user_id))
          .where(t['project_id'].eq(project_id))
          .order(t['updated_at'].desc)
      end

  z = i.as('recent_t')
  p = BiologicalAssociation.arel_table

  case used_on
  when 'AssertedDistribution'
    BiologicalAssociation.joins(
      Arel::Nodes::InnerJoin.new(z, Arel::Nodes::On.new(z['asserted_distribution_object_id'].eq(p['id'])))
    ).pluck(:id).uniq
  end
end

Instance Method Details

#association_is_unique ⇒ Object (private) 



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# File 'app/models/biological_association.rb', line 247

def association_is_unique
  if a = BiologicalAssociation.where.not(id:).where(
      biological_association_subject:,
      biological_association_object:,
      biological_relationship:
  ).first
    # For unify purposes, self has changed either subject or object, a is the
    # identical BA we will perhaps unify with.
    if will_save_change_to_biological_association_subject_id?
      errors.add(:biological_association_subject, 'has already been taken')
    elsif will_save_change_to_biological_association_object_id?
      errors.add(:biological_association_object, 'has already been taken')
    else
      errors.add(:biological_association, 'already exists')
    end
  end
end

#biological_association_object_type_is_allowed ⇒ Object (private) 



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# File 'app/models/biological_association.rb', line 270

def biological_association_object_type_is_allowed
  errors.add(:biological_association_object_type, 'is not permitted') unless biological_association_object && biological_association_object.class.is_biologically_relatable?
end

#biological_association_subject_type_is_allowed ⇒ Object (private) 



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# File 'app/models/biological_association.rb', line 266

def biological_association_subject_type_is_allowed
  errors.add(:biological_association_subject_type, 'is not permitted') unless biological_association_subject && biological_association_subject.class.is_biologically_relatable?
end

#dwc_extension_select ⇒ Object 



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# File 'app/models/biological_association.rb', line 157

def dwc_extension_select
  BiologicalAssociation
    .joins("LEFT JOIN identifiers id_s ON id_s.identifier_object_type = biological_associations.biological_associations_subject_type AND ids_s.type = 'Identifier::Global::Uuid'" )
    .joins("LEFT JOIN identifiers id_o ON id_o.identifier_object_type = biological_associations.biological_associations_object_type AND ids_o.type = 'Identifier::Global::Uuid'" )
    .joins("LEFT JOIN identifiers id_r ON id_o.identifier_object_type = 'BiologicalRelationship' AND idr_.identifier_object_id = biological_associations.biological_relationship_id AND ids_r.type = 'Identifier::Global::Uri'" )
end

#object ⇒ Object

!! You can not set with this method



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# File 'app/models/biological_association.rb', line 114

def object
  biological_association_object
end

#object_class_name ⇒ Object

TODO: Why?! this is just biological_association.biological_association_object_type



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

def object_class_name
  biological_association_object.try(:class).base_class.name
end

#subject ⇒ Object

!! You can not set with this method



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# File 'app/models/biological_association.rb', line 109

def subject
  biological_association_subject
end

#subject_class_name ⇒ Object

TODO: Why?! this is just biological_association.biological_association_subject_type



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# File 'app/models/biological_association.rb', line 99

def subject_class_name
  biological_association_subject.try(:class).base_class.name
end

#targeted_join(target: 'subject', target_class: ::Otu) ⇒ ActiveRecord::Relation

Returns:

  • (ActiveRecord::Relation) 


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# File 'app/models/biological_association.rb', line 165

def targeted_join(target: 'subject', target_class: ::Otu)
  a = arel_table
  b = target_class.arel_table

  j = a.join(b).on(a["biological_association_#{target}_type".to_sym].eq(target_class.name).and(a["biological_assoication_#{target}_id".to_sym].eq(b[:id])))
  joins(j.join_sources)
end

#targeted_join2(target: 'subject', target_class: ::Otu) ⇒ ActiveRecord::Relation

Returns:

  • (ActiveRecord::Relation) 


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# File 'app/models/biological_association.rb', line 174

def targeted_join2(target: 'subject', target_class: ::Otu)
  a = arel_table
  b = target_class.arel_table

  j = a.join(b).on(a["biological_association_#{target}_type".to_sym].eq(target_class.name).and(a["biological_assoication_#{target}_id".to_sym].eq(b[:id])))
end

#targeted_left_join(target: 'subject', target_class: ::Otu) ⇒ ActiveRecord::Relation

Not used

Returns:

  • (ActiveRecord::Relation) 


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# File 'app/models/biological_association.rb', line 183

def targeted_left_join(target: 'subject', target_class: ::Otu )
  a = arel_table
  b = target_class.arel_table

  j = a.join(b, Arel::Nodes::OuterJoin).on(a["biological_association_#{target}_type".to_sym].eq(target_class.name).and(a["biological_assoication_#{target}_id".to_sym].eq(b[:id])))
  joins(j.join_sources)
end