Class: AssertedDistribution

Inherits:
ApplicationRecord show all
Includes:
DwcExtensions, Housekeeping, Shared::CitationRequired, Shared::Citations, Shared::Confidences, Shared::DataAttributes, Shared::HasPapertrail, Shared::Identifiers, Shared::IsData, Shared::IsDwcOccurrence, Shared::Maps, Shared::Notes, Shared::OriginRelationship, Shared::QueryBatchUpdate, Shared::Tags, Shared::Taxonomy, SoftValidation
Defined in:
app/models/asserted_distribution.rb

Overview

An AssertedDistribution is the Source-backed assertion that a taxon (OTU) is present in some *spatial area*. It requires a Citation indicating where/who made the assertion. In TaxonWorks the areas are drawn from GeographicAreas.

AssertedDistributions can be asserts that the source indicates that a taxon is NOT present in an area. This is a “positive negative” in , i.e. the Source can be thought of recording evidence that a taxon is not present. TaxonWorks does not differentiate between types of negative evidence.

Defined Under Namespace

Modules: DwcExtensions

Constant Summary

Constants included from DwcExtensions

DwcExtensions::DWC_OCCURRENCE_MAP

Constants included from Shared::IsDwcOccurrence

Shared::IsDwcOccurrence::DWC_DELIMITER, Shared::IsDwcOccurrence::VIEW_EXCLUSIONS

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 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 DwcExtensions

#dwc_associated_references, #dwc_country, #dwc_county, #dwc_family, #dwc_genus, #dwc_infraspecific_epithet, #dwc_kingdom, #dwc_occurrence_status, #dwc_scientific_name, #dwc_specific_epithet, #dwc_state_province, #dwc_taxon_name_authorship, #dwc_taxon_rank

Methods included from Shared::IsDwcOccurrence

#dwc_occurrence_attribute_values, #dwc_occurrence_attributes, #dwc_occurrence_id, #get_dwc_occurrence, #set_dwc_occurrence

Methods included from Shared::HasPapertrail

#attribute_updated, #attribute_updater

Methods included from Shared::Identifiers

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

Methods included from Shared::OriginRelationship

#new_objects, #old_objects, #reject_origin_relationships, #set_origin

Methods included from Shared::Confidences

#reject_confidences

Methods included from Shared::Citations

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

Methods included from Shared::DataAttributes

#import_attributes, #internal_attributes, #keyword_value_hash, #reject_data_attributes

Methods included from Shared::Tags

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

Methods included from Shared::Notes

#concatenated_notes_string, #reject_notes

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

#geographic_area_id ⇒ Integer

the geographic area ID

Returns:

  • (Integer) 


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# File 'app/models/asserted_distribution.rb', line 22

class AssertedDistribution < ApplicationRecord
  include Housekeeping
  include SoftValidation
  include Shared::Notes
  include Shared::Tags
  include Shared::DataAttributes # Why?
  include Shared::CitationRequired # !! must preceed Shared::Citations
  include Shared::Citations
  include Shared::Confidences
  include Shared::OriginRelationship
  include Shared::Identifiers
  include Shared::HasPapertrail
  include Shared::Taxonomy # at present must preceed IsDwcOccurence
  include Shared::IsDwcOccurrence
  include AssertedDistribution::DwcExtensions
  include Shared::IsData

  include Shared::Maps
  include Shared::QueryBatchUpdate

  originates_from 'Specimen', 'Lot', 'FieldOccurrence'

  # @return [Hash]
  #   of known country/state/county values
  attr_accessor :geographic_names

  belongs_to :otu, inverse_of: :asserted_distributions
  has_one :taxon_name, through: :otu
  belongs_to :geographic_area, inverse_of: :asserted_distributions

  has_one :geographic_item, through: :geographic_area, source: :default_geographic_item
  has_many :geographic_items, through: :geographic_area

  validates_presence_of :geographic_area_id, message: 'geographic area is not selected'
  validates :geographic_area, presence: true
  validates :otu, presence: true

  validates_uniqueness_of :otu, scope: [:project_id, :geographic_area, :is_absent], message: 'this geographic_area, OTU and present/absent combination already exists'
  # !! If we want to unify GeographicAreas then we need to raise a redundat error :geographic_area here, we should write a custom method
  # that checks for an error on otu then adds a record, i.e. no database calls would be made
  # validates_uniqueness_of :geographic_area_id, scope: [:project_id, :otu_id, :is_absent], message: 'this geographic_area, OTU and present/absent combination already exists'

  validate :new_records_include_citation

  # TODO: deprecate scopes referencing single wheres
  scope :with_otu_id, -> (otu_id) { where(otu_id:) }
  scope :with_is_absent, -> { where('is_absent = true') }
  scope :with_geographic_area_array, -> (geographic_area_array) { where('geographic_area_id IN (?)', geographic_area_array) }
  scope :without_is_absent, -> { where('is_absent = false OR is_absent is Null') }

  accepts_nested_attributes_for :otu, allow_destroy: false, reject_if: proc { |attributes| attributes['name'].blank? && attributes['taxon_name_id'].blank? }

  soft_validate(:sv_conflicting_geographic_area, set: :conflicting_geographic_area, name: 'conflicting geographic area', description: 'conflicting geographic area')

  # getter for attr :geographic_names
  def geographic_names
    return @geographic_names if !@geographic_names.nil?
    @geographic_names ||= geographic_area.geographic_name_classification.delete_if{|k,v| v.nil?}
    @geographic_names ||= {}
  end

  # @param [Hash] defaults
  # @return [AssertedDistribution]
  #   used to also stub an #origin_citation, as required
  def self.stub(defaults: {})
    a = AssertedDistribution.new(
      otu_id: defaults[:otu_id],
      origin_citation_attributes: {source_id: defaults[:source_id]})
    a.origin_citation = Citation.new if defaults[:source_id].blank?
    a
  end

  # rubocop:disable Style/StringHashKeys
  # TODO: DRY with helper methods
  # @return [Hash] GeoJSON feature
  def to_geo_json_feature
    retval = {
      'type' => 'Feature',
      'geometry' => RGeo::GeoJSON.encode(self.geographic_area.geographic_items.first.geo_object),
      'properties' => {'asserted_distribution' => {'id' => self.id}}
    }
    retval
  end

  # rubocop:enable Style/StringHashKeys

  # @return [True]
  #   see citable.rb
  def requires_citation?
    true
  end

  def geographic_item
    geographic_area.default_geographic_item
  end

  def has_shape?
    geographic_area.geographic_items.any?
  end

  def self.batch_update(params)
    request = QueryBatchRequest.new(
      async_cutoff: params[:async_cutoff] || 26,
      klass: 'AssertedDistribution',
      object_filter_params: params[:asserted_distribution_query],
      object_params: params[:asserted_distribution],
      preview: params[:preview],
    )

    a = request.filter

    v1 = a.all.distinct.limit(2).pluck(:geographic_area_id).uniq.count
    v2 = a.all.distinct.limit(2).pluck(:otu_id).uniq.count

    cap = 0

    if v1 > 1 && v2 > 1 # many otus, many geographic areas
      cap = 0
      request.cap_reason = 'Records include multiple OTUs *and* multiple geographic areas.'
    elsif v1 > 1
      cap = 0
      request.cap_reason = 'May not update multiple geographic areas to one.' # TODO: revist constraint
    else
      cap = 2000
    end

    request.cap = cap

    query_batch_update(request)
  end

  protected

  # @return [Boolean]
  def new_records_include_citation
    if new_record? && source.blank? && origin_citation.blank? && !citations.any?
      errors.add(:base, 'required citation is not provided')
    end
  end

  # @return [Boolean]
  def sv_conflicting_geographic_area
    unless geographic_area.nil?
      areas = [geographic_area.level0_id, geographic_area.level1_id, geographic_area.level2_id].compact
      if is_absent # this returns an array, not a single GA so test below is not right
        presence = AssertedDistribution
          .without_is_absent
          .with_geographic_area_array(areas)
          .where(otu_id:)
        soft_validations.add(:geographic_area_id, "Taxon is reported as present in #{presence.first.geographic_area.name}") unless presence.empty?
      else
        presence = AssertedDistribution
          .with_is_absent
          .where(otu_id:)
          .with_geographic_area_array(areas)
        soft_validations.add(:geographic_area_id, "Taxon is reported as missing in #{presence.first.geographic_area.name}") unless presence.empty?
      end
    end
  end

  # @param [Hash] options of e.g., {otu_id: 5, source_id: 5, geographic_areas: Array of {GeographicArea}}
  # @return [Array] an array of AssertedDistributions
  def self.stub_new(options = {})
    options.symbolize_keys!
    result = []
    options[:geographic_areas].each do |ga|
      result.push(
        AssertedDistribution.new(
          otu_id: options[:otu_id],
          geographic_area: ga,
          origin_citation_attributes: {source_id: options[:source_id]})
      )
    end
    result
  end
end

#geographic_names ⇒ Object

getter for attr :geographic_names



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# File 'app/models/asserted_distribution.rb', line 46

def geographic_names
  @geographic_names
end

#is_absent ⇒ Boolean

Returns a positive negative, when true then there exists an assertion that the taxon is not present in the spatial area.

Returns:

  • (Boolean) —

    a positive negative, when true then there exists an assertion that the taxon is not present in the spatial area



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# File 'app/models/asserted_distribution.rb', line 22

class AssertedDistribution < ApplicationRecord
  include Housekeeping
  include SoftValidation
  include Shared::Notes
  include Shared::Tags
  include Shared::DataAttributes # Why?
  include Shared::CitationRequired # !! must preceed Shared::Citations
  include Shared::Citations
  include Shared::Confidences
  include Shared::OriginRelationship
  include Shared::Identifiers
  include Shared::HasPapertrail
  include Shared::Taxonomy # at present must preceed IsDwcOccurence
  include Shared::IsDwcOccurrence
  include AssertedDistribution::DwcExtensions
  include Shared::IsData

  include Shared::Maps
  include Shared::QueryBatchUpdate

  originates_from 'Specimen', 'Lot', 'FieldOccurrence'

  # @return [Hash]
  #   of known country/state/county values
  attr_accessor :geographic_names

  belongs_to :otu, inverse_of: :asserted_distributions
  has_one :taxon_name, through: :otu
  belongs_to :geographic_area, inverse_of: :asserted_distributions

  has_one :geographic_item, through: :geographic_area, source: :default_geographic_item
  has_many :geographic_items, through: :geographic_area

  validates_presence_of :geographic_area_id, message: 'geographic area is not selected'
  validates :geographic_area, presence: true
  validates :otu, presence: true

  validates_uniqueness_of :otu, scope: [:project_id, :geographic_area, :is_absent], message: 'this geographic_area, OTU and present/absent combination already exists'
  # !! If we want to unify GeographicAreas then we need to raise a redundat error :geographic_area here, we should write a custom method
  # that checks for an error on otu then adds a record, i.e. no database calls would be made
  # validates_uniqueness_of :geographic_area_id, scope: [:project_id, :otu_id, :is_absent], message: 'this geographic_area, OTU and present/absent combination already exists'

  validate :new_records_include_citation

  # TODO: deprecate scopes referencing single wheres
  scope :with_otu_id, -> (otu_id) { where(otu_id:) }
  scope :with_is_absent, -> { where('is_absent = true') }
  scope :with_geographic_area_array, -> (geographic_area_array) { where('geographic_area_id IN (?)', geographic_area_array) }
  scope :without_is_absent, -> { where('is_absent = false OR is_absent is Null') }

  accepts_nested_attributes_for :otu, allow_destroy: false, reject_if: proc { |attributes| attributes['name'].blank? && attributes['taxon_name_id'].blank? }

  soft_validate(:sv_conflicting_geographic_area, set: :conflicting_geographic_area, name: 'conflicting geographic area', description: 'conflicting geographic area')

  # getter for attr :geographic_names
  def geographic_names
    return @geographic_names if !@geographic_names.nil?
    @geographic_names ||= geographic_area.geographic_name_classification.delete_if{|k,v| v.nil?}
    @geographic_names ||= {}
  end

  # @param [Hash] defaults
  # @return [AssertedDistribution]
  #   used to also stub an #origin_citation, as required
  def self.stub(defaults: {})
    a = AssertedDistribution.new(
      otu_id: defaults[:otu_id],
      origin_citation_attributes: {source_id: defaults[:source_id]})
    a.origin_citation = Citation.new if defaults[:source_id].blank?
    a
  end

  # rubocop:disable Style/StringHashKeys
  # TODO: DRY with helper methods
  # @return [Hash] GeoJSON feature
  def to_geo_json_feature
    retval = {
      'type' => 'Feature',
      'geometry' => RGeo::GeoJSON.encode(self.geographic_area.geographic_items.first.geo_object),
      'properties' => {'asserted_distribution' => {'id' => self.id}}
    }
    retval
  end

  # rubocop:enable Style/StringHashKeys

  # @return [True]
  #   see citable.rb
  def requires_citation?
    true
  end

  def geographic_item
    geographic_area.default_geographic_item
  end

  def has_shape?
    geographic_area.geographic_items.any?
  end

  def self.batch_update(params)
    request = QueryBatchRequest.new(
      async_cutoff: params[:async_cutoff] || 26,
      klass: 'AssertedDistribution',
      object_filter_params: params[:asserted_distribution_query],
      object_params: params[:asserted_distribution],
      preview: params[:preview],
    )

    a = request.filter

    v1 = a.all.distinct.limit(2).pluck(:geographic_area_id).uniq.count
    v2 = a.all.distinct.limit(2).pluck(:otu_id).uniq.count

    cap = 0

    if v1 > 1 && v2 > 1 # many otus, many geographic areas
      cap = 0
      request.cap_reason = 'Records include multiple OTUs *and* multiple geographic areas.'
    elsif v1 > 1
      cap = 0
      request.cap_reason = 'May not update multiple geographic areas to one.' # TODO: revist constraint
    else
      cap = 2000
    end

    request.cap = cap

    query_batch_update(request)
  end

  protected

  # @return [Boolean]
  def new_records_include_citation
    if new_record? && source.blank? && origin_citation.blank? && !citations.any?
      errors.add(:base, 'required citation is not provided')
    end
  end

  # @return [Boolean]
  def sv_conflicting_geographic_area
    unless geographic_area.nil?
      areas = [geographic_area.level0_id, geographic_area.level1_id, geographic_area.level2_id].compact
      if is_absent # this returns an array, not a single GA so test below is not right
        presence = AssertedDistribution
          .without_is_absent
          .with_geographic_area_array(areas)
          .where(otu_id:)
        soft_validations.add(:geographic_area_id, "Taxon is reported as present in #{presence.first.geographic_area.name}") unless presence.empty?
      else
        presence = AssertedDistribution
          .with_is_absent
          .where(otu_id:)
          .with_geographic_area_array(areas)
        soft_validations.add(:geographic_area_id, "Taxon is reported as missing in #{presence.first.geographic_area.name}") unless presence.empty?
      end
    end
  end

  # @param [Hash] options of e.g., {otu_id: 5, source_id: 5, geographic_areas: Array of {GeographicArea}}
  # @return [Array] an array of AssertedDistributions
  def self.stub_new(options = {})
    options.symbolize_keys!
    result = []
    options[:geographic_areas].each do |ga|
      result.push(
        AssertedDistribution.new(
          otu_id: options[:otu_id],
          geographic_area: ga,
          origin_citation_attributes: {source_id: options[:source_id]})
      )
    end
    result
  end
end

#otu_id ⇒ Integer

the OTU ID

Returns:

  • (Integer) 


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# File 'app/models/asserted_distribution.rb', line 22

class AssertedDistribution < ApplicationRecord
  include Housekeeping
  include SoftValidation
  include Shared::Notes
  include Shared::Tags
  include Shared::DataAttributes # Why?
  include Shared::CitationRequired # !! must preceed Shared::Citations
  include Shared::Citations
  include Shared::Confidences
  include Shared::OriginRelationship
  include Shared::Identifiers
  include Shared::HasPapertrail
  include Shared::Taxonomy # at present must preceed IsDwcOccurence
  include Shared::IsDwcOccurrence
  include AssertedDistribution::DwcExtensions
  include Shared::IsData

  include Shared::Maps
  include Shared::QueryBatchUpdate

  originates_from 'Specimen', 'Lot', 'FieldOccurrence'

  # @return [Hash]
  #   of known country/state/county values
  attr_accessor :geographic_names

  belongs_to :otu, inverse_of: :asserted_distributions
  has_one :taxon_name, through: :otu
  belongs_to :geographic_area, inverse_of: :asserted_distributions

  has_one :geographic_item, through: :geographic_area, source: :default_geographic_item
  has_many :geographic_items, through: :geographic_area

  validates_presence_of :geographic_area_id, message: 'geographic area is not selected'
  validates :geographic_area, presence: true
  validates :otu, presence: true

  validates_uniqueness_of :otu, scope: [:project_id, :geographic_area, :is_absent], message: 'this geographic_area, OTU and present/absent combination already exists'
  # !! If we want to unify GeographicAreas then we need to raise a redundat error :geographic_area here, we should write a custom method
  # that checks for an error on otu then adds a record, i.e. no database calls would be made
  # validates_uniqueness_of :geographic_area_id, scope: [:project_id, :otu_id, :is_absent], message: 'this geographic_area, OTU and present/absent combination already exists'

  validate :new_records_include_citation

  # TODO: deprecate scopes referencing single wheres
  scope :with_otu_id, -> (otu_id) { where(otu_id:) }
  scope :with_is_absent, -> { where('is_absent = true') }
  scope :with_geographic_area_array, -> (geographic_area_array) { where('geographic_area_id IN (?)', geographic_area_array) }
  scope :without_is_absent, -> { where('is_absent = false OR is_absent is Null') }

  accepts_nested_attributes_for :otu, allow_destroy: false, reject_if: proc { |attributes| attributes['name'].blank? && attributes['taxon_name_id'].blank? }

  soft_validate(:sv_conflicting_geographic_area, set: :conflicting_geographic_area, name: 'conflicting geographic area', description: 'conflicting geographic area')

  # getter for attr :geographic_names
  def geographic_names
    return @geographic_names if !@geographic_names.nil?
    @geographic_names ||= geographic_area.geographic_name_classification.delete_if{|k,v| v.nil?}
    @geographic_names ||= {}
  end

  # @param [Hash] defaults
  # @return [AssertedDistribution]
  #   used to also stub an #origin_citation, as required
  def self.stub(defaults: {})
    a = AssertedDistribution.new(
      otu_id: defaults[:otu_id],
      origin_citation_attributes: {source_id: defaults[:source_id]})
    a.origin_citation = Citation.new if defaults[:source_id].blank?
    a
  end

  # rubocop:disable Style/StringHashKeys
  # TODO: DRY with helper methods
  # @return [Hash] GeoJSON feature
  def to_geo_json_feature
    retval = {
      'type' => 'Feature',
      'geometry' => RGeo::GeoJSON.encode(self.geographic_area.geographic_items.first.geo_object),
      'properties' => {'asserted_distribution' => {'id' => self.id}}
    }
    retval
  end

  # rubocop:enable Style/StringHashKeys

  # @return [True]
  #   see citable.rb
  def requires_citation?
    true
  end

  def geographic_item
    geographic_area.default_geographic_item
  end

  def has_shape?
    geographic_area.geographic_items.any?
  end

  def self.batch_update(params)
    request = QueryBatchRequest.new(
      async_cutoff: params[:async_cutoff] || 26,
      klass: 'AssertedDistribution',
      object_filter_params: params[:asserted_distribution_query],
      object_params: params[:asserted_distribution],
      preview: params[:preview],
    )

    a = request.filter

    v1 = a.all.distinct.limit(2).pluck(:geographic_area_id).uniq.count
    v2 = a.all.distinct.limit(2).pluck(:otu_id).uniq.count

    cap = 0

    if v1 > 1 && v2 > 1 # many otus, many geographic areas
      cap = 0
      request.cap_reason = 'Records include multiple OTUs *and* multiple geographic areas.'
    elsif v1 > 1
      cap = 0
      request.cap_reason = 'May not update multiple geographic areas to one.' # TODO: revist constraint
    else
      cap = 2000
    end

    request.cap = cap

    query_batch_update(request)
  end

  protected

  # @return [Boolean]
  def new_records_include_citation
    if new_record? && source.blank? && origin_citation.blank? && !citations.any?
      errors.add(:base, 'required citation is not provided')
    end
  end

  # @return [Boolean]
  def sv_conflicting_geographic_area
    unless geographic_area.nil?
      areas = [geographic_area.level0_id, geographic_area.level1_id, geographic_area.level2_id].compact
      if is_absent # this returns an array, not a single GA so test below is not right
        presence = AssertedDistribution
          .without_is_absent
          .with_geographic_area_array(areas)
          .where(otu_id:)
        soft_validations.add(:geographic_area_id, "Taxon is reported as present in #{presence.first.geographic_area.name}") unless presence.empty?
      else
        presence = AssertedDistribution
          .with_is_absent
          .where(otu_id:)
          .with_geographic_area_array(areas)
        soft_validations.add(:geographic_area_id, "Taxon is reported as missing in #{presence.first.geographic_area.name}") unless presence.empty?
      end
    end
  end

  # @param [Hash] options of e.g., {otu_id: 5, source_id: 5, geographic_areas: Array of {GeographicArea}}
  # @return [Array] an array of AssertedDistributions
  def self.stub_new(options = {})
    options.symbolize_keys!
    result = []
    options[:geographic_areas].each do |ga|
      result.push(
        AssertedDistribution.new(
          otu_id: options[:otu_id],
          geographic_area: ga,
          origin_citation_attributes: {source_id: options[:source_id]})
      )
    end
    result
  end
end

#project_id ⇒ Integer

the project ID

Returns:

  • (Integer) 


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# File 'app/models/asserted_distribution.rb', line 22

class AssertedDistribution < ApplicationRecord
  include Housekeeping
  include SoftValidation
  include Shared::Notes
  include Shared::Tags
  include Shared::DataAttributes # Why?
  include Shared::CitationRequired # !! must preceed Shared::Citations
  include Shared::Citations
  include Shared::Confidences
  include Shared::OriginRelationship
  include Shared::Identifiers
  include Shared::HasPapertrail
  include Shared::Taxonomy # at present must preceed IsDwcOccurence
  include Shared::IsDwcOccurrence
  include AssertedDistribution::DwcExtensions
  include Shared::IsData

  include Shared::Maps
  include Shared::QueryBatchUpdate

  originates_from 'Specimen', 'Lot', 'FieldOccurrence'

  # @return [Hash]
  #   of known country/state/county values
  attr_accessor :geographic_names

  belongs_to :otu, inverse_of: :asserted_distributions
  has_one :taxon_name, through: :otu
  belongs_to :geographic_area, inverse_of: :asserted_distributions

  has_one :geographic_item, through: :geographic_area, source: :default_geographic_item
  has_many :geographic_items, through: :geographic_area

  validates_presence_of :geographic_area_id, message: 'geographic area is not selected'
  validates :geographic_area, presence: true
  validates :otu, presence: true

  validates_uniqueness_of :otu, scope: [:project_id, :geographic_area, :is_absent], message: 'this geographic_area, OTU and present/absent combination already exists'
  # !! If we want to unify GeographicAreas then we need to raise a redundat error :geographic_area here, we should write a custom method
  # that checks for an error on otu then adds a record, i.e. no database calls would be made
  # validates_uniqueness_of :geographic_area_id, scope: [:project_id, :otu_id, :is_absent], message: 'this geographic_area, OTU and present/absent combination already exists'

  validate :new_records_include_citation

  # TODO: deprecate scopes referencing single wheres
  scope :with_otu_id, -> (otu_id) { where(otu_id:) }
  scope :with_is_absent, -> { where('is_absent = true') }
  scope :with_geographic_area_array, -> (geographic_area_array) { where('geographic_area_id IN (?)', geographic_area_array) }
  scope :without_is_absent, -> { where('is_absent = false OR is_absent is Null') }

  accepts_nested_attributes_for :otu, allow_destroy: false, reject_if: proc { |attributes| attributes['name'].blank? && attributes['taxon_name_id'].blank? }

  soft_validate(:sv_conflicting_geographic_area, set: :conflicting_geographic_area, name: 'conflicting geographic area', description: 'conflicting geographic area')

  # getter for attr :geographic_names
  def geographic_names
    return @geographic_names if !@geographic_names.nil?
    @geographic_names ||= geographic_area.geographic_name_classification.delete_if{|k,v| v.nil?}
    @geographic_names ||= {}
  end

  # @param [Hash] defaults
  # @return [AssertedDistribution]
  #   used to also stub an #origin_citation, as required
  def self.stub(defaults: {})
    a = AssertedDistribution.new(
      otu_id: defaults[:otu_id],
      origin_citation_attributes: {source_id: defaults[:source_id]})
    a.origin_citation = Citation.new if defaults[:source_id].blank?
    a
  end

  # rubocop:disable Style/StringHashKeys
  # TODO: DRY with helper methods
  # @return [Hash] GeoJSON feature
  def to_geo_json_feature
    retval = {
      'type' => 'Feature',
      'geometry' => RGeo::GeoJSON.encode(self.geographic_area.geographic_items.first.geo_object),
      'properties' => {'asserted_distribution' => {'id' => self.id}}
    }
    retval
  end

  # rubocop:enable Style/StringHashKeys

  # @return [True]
  #   see citable.rb
  def requires_citation?
    true
  end

  def geographic_item
    geographic_area.default_geographic_item
  end

  def has_shape?
    geographic_area.geographic_items.any?
  end

  def self.batch_update(params)
    request = QueryBatchRequest.new(
      async_cutoff: params[:async_cutoff] || 26,
      klass: 'AssertedDistribution',
      object_filter_params: params[:asserted_distribution_query],
      object_params: params[:asserted_distribution],
      preview: params[:preview],
    )

    a = request.filter

    v1 = a.all.distinct.limit(2).pluck(:geographic_area_id).uniq.count
    v2 = a.all.distinct.limit(2).pluck(:otu_id).uniq.count

    cap = 0

    if v1 > 1 && v2 > 1 # many otus, many geographic areas
      cap = 0
      request.cap_reason = 'Records include multiple OTUs *and* multiple geographic areas.'
    elsif v1 > 1
      cap = 0
      request.cap_reason = 'May not update multiple geographic areas to one.' # TODO: revist constraint
    else
      cap = 2000
    end

    request.cap = cap

    query_batch_update(request)
  end

  protected

  # @return [Boolean]
  def new_records_include_citation
    if new_record? && source.blank? && origin_citation.blank? && !citations.any?
      errors.add(:base, 'required citation is not provided')
    end
  end

  # @return [Boolean]
  def sv_conflicting_geographic_area
    unless geographic_area.nil?
      areas = [geographic_area.level0_id, geographic_area.level1_id, geographic_area.level2_id].compact
      if is_absent # this returns an array, not a single GA so test below is not right
        presence = AssertedDistribution
          .without_is_absent
          .with_geographic_area_array(areas)
          .where(otu_id:)
        soft_validations.add(:geographic_area_id, "Taxon is reported as present in #{presence.first.geographic_area.name}") unless presence.empty?
      else
        presence = AssertedDistribution
          .with_is_absent
          .where(otu_id:)
          .with_geographic_area_array(areas)
        soft_validations.add(:geographic_area_id, "Taxon is reported as missing in #{presence.first.geographic_area.name}") unless presence.empty?
      end
    end
  end

  # @param [Hash] options of e.g., {otu_id: 5, source_id: 5, geographic_areas: Array of {GeographicArea}}
  # @return [Array] an array of AssertedDistributions
  def self.stub_new(options = {})
    options.symbolize_keys!
    result = []
    options[:geographic_areas].each do |ga|
      result.push(
        AssertedDistribution.new(
          otu_id: options[:otu_id],
          geographic_area: ga,
          origin_citation_attributes: {source_id: options[:source_id]})
      )
    end
    result
  end
end

Class Method Details

.batch_update(params) ⇒ Object 



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

def self.batch_update(params)
  request = QueryBatchRequest.new(
    async_cutoff: params[:async_cutoff] || 26,
    klass: 'AssertedDistribution',
    object_filter_params: params[:asserted_distribution_query],
    object_params: params[:asserted_distribution],
    preview: params[:preview],
  )

  a = request.filter

  v1 = a.all.distinct.limit(2).pluck(:geographic_area_id).uniq.count
  v2 = a.all.distinct.limit(2).pluck(:otu_id).uniq.count

  cap = 0

  if v1 > 1 && v2 > 1 # many otus, many geographic areas
    cap = 0
    request.cap_reason = 'Records include multiple OTUs *and* multiple geographic areas.'
  elsif v1 > 1
    cap = 0
    request.cap_reason = 'May not update multiple geographic areas to one.' # TODO: revist constraint
  else
    cap = 2000
  end

  request.cap = cap

  query_batch_update(request)
end

.stub(defaults: {}) ⇒ AssertedDistribution

Returns used to also stub an #origin_citation, as required.

Parameters:

  • defaults (Hash) (defaults to: {})

Returns:



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# File 'app/models/asserted_distribution.rb', line 86

def self.stub(defaults: {})
  a = AssertedDistribution.new(
    otu_id: defaults[:otu_id],
    origin_citation_attributes: {source_id: defaults[:source_id]})
  a.origin_citation = Citation.new if defaults[:source_id].blank?
  a
end

.stub_new(options = {}) ⇒ Array (protected)

Returns an array of AssertedDistributions.

Parameters:

  • options (Hash) (defaults to: {}) —

    of e.g., 5, source_id: 5, geographic_areas: Array of {GeographicArea}

Returns:

  • (Array) —

    an array of AssertedDistributions



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# File 'app/models/asserted_distribution.rb', line 184

def self.stub_new(options = {})
  options.symbolize_keys!
  result = []
  options[:geographic_areas].each do |ga|
    result.push(
      AssertedDistribution.new(
        otu_id: options[:otu_id],
        geographic_area: ga,
        origin_citation_attributes: {source_id: options[:source_id]})
    )
  end
  result
end

Instance Method Details

#geographic_item ⇒ Object 



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

def geographic_item
  geographic_area.default_geographic_item
end

#has_shape? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'app/models/asserted_distribution.rb', line 118

def has_shape?
  geographic_area.geographic_items.any?
end

#new_records_include_citation ⇒ Boolean (protected)

Returns:

  • (Boolean) 


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# File 'app/models/asserted_distribution.rb', line 156

def new_records_include_citation
  if new_record? && source.blank? && origin_citation.blank? && !citations.any?
    errors.add(:base, 'required citation is not provided')
  end
end

#requires_citation? ⇒ True

Returns see citable.rb.

Returns:

  • (True) —

    see citable.rb



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# File 'app/models/asserted_distribution.rb', line 110

def requires_citation?
  true
end

#sv_conflicting_geographic_area ⇒ Boolean (protected)

Returns:

  • (Boolean) 


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# File 'app/models/asserted_distribution.rb', line 163

def sv_conflicting_geographic_area
  unless geographic_area.nil?
    areas = [geographic_area.level0_id, geographic_area.level1_id, geographic_area.level2_id].compact
    if is_absent # this returns an array, not a single GA so test below is not right
      presence = AssertedDistribution
        .without_is_absent
        .with_geographic_area_array(areas)
        .where(otu_id:)
      soft_validations.add(:geographic_area_id, "Taxon is reported as present in #{presence.first.geographic_area.name}") unless presence.empty?
    else
      presence = AssertedDistribution
        .with_is_absent
        .where(otu_id:)
        .with_geographic_area_array(areas)
      soft_validations.add(:geographic_area_id, "Taxon is reported as missing in #{presence.first.geographic_area.name}") unless presence.empty?
    end
  end
end

#to_geo_json_feature ⇒ Hash

rubocop:disable Style/StringHashKeys TODO: DRY with helper methods

Returns:

  • (Hash) —

    GeoJSON feature



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# File 'app/models/asserted_distribution.rb', line 97

def to_geo_json_feature
  retval = {
    'type' => 'Feature',
    'geometry' => RGeo::GeoJSON.encode(self.geographic_area.geographic_items.first.geo_object),
    'properties' => {'asserted_distribution' => {'id' => self.id}}
  }
  retval
end