Class: BiologicalAssociation

Inherits:
ApplicationRecord show all
Includes:
DwcExtensions, GlobiExtensions, Housekeeping, 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

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_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::Notes

#concatenated_notes_string, #reject_notes

Methods included from Shared::Confidences

#reject_confidences

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::Confidences
  include Shared::Notes
  include Shared::Confidences
  include Shared::Depictions
  include Shared::AutoUuid
  include Shared::IsData

  include BiologicalAssociation::GlobiExtensions
  include BiologicalAssociation::DwcExtensions

  include Shared::QueryBatchUpdate

  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
  belongs_to :biological_association_object, polymorphic: true
  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 :biological_relationship, presence: true
  validates :biological_association_subject, presence: true
  validates :biological_association_object, presence: true

  validates_uniqueness_of :biological_association_subject_id, scope: [:biological_association_subject_type, :biological_association_object_id, :biological_association_object_type, :biological_relationship_id]

  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

  # @return [ActiveRecord::Relation]
  #def self.collection_objects_subject_join
  #  a = arel_table
  #  b = ::CollectionObject.arel_table
  #  j = a.join(b).on(a[:biological_association_subject_type].eq('CollectionObject').and(a[:biological_association_subject_id].eq(b[:id])))
  #  joins(j.join_sources)
  #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

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::Confidences
  include Shared::Notes
  include Shared::Confidences
  include Shared::Depictions
  include Shared::AutoUuid
  include Shared::IsData

  include BiologicalAssociation::GlobiExtensions
  include BiologicalAssociation::DwcExtensions

  include Shared::QueryBatchUpdate

  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
  belongs_to :biological_association_object, polymorphic: true
  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 :biological_relationship, presence: true
  validates :biological_association_subject, presence: true
  validates :biological_association_object, presence: true

  validates_uniqueness_of :biological_association_subject_id, scope: [:biological_association_subject_type, :biological_association_object_id, :biological_association_object_type, :biological_relationship_id]

  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

  # @return [ActiveRecord::Relation]
  #def self.collection_objects_subject_join
  #  a = arel_table
  #  b = ::CollectionObject.arel_table
  #  j = a.join(b).on(a[:biological_association_subject_type].eq('CollectionObject').and(a[:biological_association_subject_id].eq(b[:id])))
  #  joins(j.join_sources)
  #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

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::Confidences
  include Shared::Notes
  include Shared::Confidences
  include Shared::Depictions
  include Shared::AutoUuid
  include Shared::IsData

  include BiologicalAssociation::GlobiExtensions
  include BiologicalAssociation::DwcExtensions

  include Shared::QueryBatchUpdate

  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
  belongs_to :biological_association_object, polymorphic: true
  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 :biological_relationship, presence: true
  validates :biological_association_subject, presence: true
  validates :biological_association_object, presence: true

  validates_uniqueness_of :biological_association_subject_id, scope: [:biological_association_subject_type, :biological_association_object_id, :biological_association_object_type, :biological_relationship_id]

  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

  # @return [ActiveRecord::Relation]
  #def self.collection_objects_subject_join
  #  a = arel_table
  #  b = ::CollectionObject.arel_table
  #  j = a.join(b).on(a[:biological_association_subject_type].eq('CollectionObject').and(a[:biological_association_subject_id].eq(b[:id])))
  #  joins(j.join_sources)
  #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

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::Confidences
  include Shared::Notes
  include Shared::Confidences
  include Shared::Depictions
  include Shared::AutoUuid
  include Shared::IsData

  include BiologicalAssociation::GlobiExtensions
  include BiologicalAssociation::DwcExtensions

  include Shared::QueryBatchUpdate

  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
  belongs_to :biological_association_object, polymorphic: true
  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 :biological_relationship, presence: true
  validates :biological_association_subject, presence: true
  validates :biological_association_object, presence: true

  validates_uniqueness_of :biological_association_subject_id, scope: [:biological_association_subject_type, :biological_association_object_id, :biological_association_object_type, :biological_relationship_id]

  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

  # @return [ActiveRecord::Relation]
  #def self.collection_objects_subject_join
  #  a = arel_table
  #  b = ::CollectionObject.arel_table
  #  j = a.join(b).on(a[:biological_association_subject_type].eq('CollectionObject').and(a[:biological_association_subject_id].eq(b[:id])))
  #  joins(j.join_sources)
  #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

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::Confidences
  include Shared::Notes
  include Shared::Confidences
  include Shared::Depictions
  include Shared::AutoUuid
  include Shared::IsData

  include BiologicalAssociation::GlobiExtensions
  include BiologicalAssociation::DwcExtensions

  include Shared::QueryBatchUpdate

  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
  belongs_to :biological_association_object, polymorphic: true
  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 :biological_relationship, presence: true
  validates :biological_association_subject, presence: true
  validates :biological_association_object, presence: true

  validates_uniqueness_of :biological_association_subject_id, scope: [:biological_association_subject_type, :biological_association_object_id, :biological_association_object_type, :biological_relationship_id]

  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

  # @return [ActiveRecord::Relation]
  #def self.collection_objects_subject_join
  #  a = arel_table
  #  b = ::CollectionObject.arel_table
  #  j = a.join(b).on(a[:biological_association_subject_type].eq('CollectionObject').and(a[:biological_association_subject_id].eq(b[:id])))
  #  joins(j.join_sources)
  #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

end

#object_global_id ⇒ Object

TODO: this is badly named



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# File 'app/models/biological_association.rb', line 71

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::Confidences
  include Shared::Notes
  include Shared::Confidences
  include Shared::Depictions
  include Shared::AutoUuid
  include Shared::IsData

  include BiologicalAssociation::GlobiExtensions
  include BiologicalAssociation::DwcExtensions

  include Shared::QueryBatchUpdate

  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
  belongs_to :biological_association_object, polymorphic: true
  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 :biological_relationship, presence: true
  validates :biological_association_subject, presence: true
  validates :biological_association_object, presence: true

  validates_uniqueness_of :biological_association_subject_id, scope: [:biological_association_subject_type, :biological_association_object_id, :biological_association_object_type, :biological_relationship_id]

  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

  # @return [ActiveRecord::Relation]
  #def self.collection_objects_subject_join
  #  a = arel_table
  #  b = ::CollectionObject.arel_table
  #  j = a.join(b).on(a[:biological_association_subject_type].eq('CollectionObject').and(a[:biological_association_subject_id].eq(b[:id])))
  #  joins(j.join_sources)
  #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

end

#rotate ⇒ Object

Returns the value of attribute rotate.



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

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 70

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 139

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

.set_batch_cap(request) ⇒ Object 



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# File 'app/models/biological_association.rb', line 117

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

Instance Method Details

#dwc_extension_select ⇒ ActiveRecord::Relation

def self.collection_objects_subject_join

a = arel_table
b = ::CollectionObject.arel_table
j = a.join(b).on(a[:biological_association_subject_type].eq('CollectionObject').and(a[:biological_association_subject_id].eq(b[:id])))
joins(j.join_sources)

end

Returns:

  • (ActiveRecord::Relation) 


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# File 'app/models/biological_association.rb', line 162

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 111

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 101

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 106

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 96

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 170

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 179

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 188

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