Class: CollectionProfile

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

Overview

A collection profile, extensible, but currently sensu INHS/Colin Favret. See Favret, C., et al. “Profiling natural history collections: A method for quantitative and comparative health assessment.” Collection Forum. Vol. 22. No. 1-2. 2007.

Data is validated against a .yml definition in config/initializers/constants/data/collection_profile_indices.yml That file is loaded to COLLECTION_PROFILE_INDICES[:dry][1]

Constant Summary

Constants included from SoftValidation

SoftValidation::ANCESTORS_WITH_SOFT_VALIDATIONS

Instance Attribute Summary collapse

Instance Method Summary collapse

Methods included from Shared::IsData

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

Methods included from Shared::Tags

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

Methods included from Shared::Notes

#concatenated_notes_string, #reject_notes

Methods included from Shared::Identifiers

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

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

#arrangement_level ⇒ Integer

Returns See Favret et al. (2007) (cited above).

Returns:

  • (Integer) —

    See Favret et al. (2007) (cited above)



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# File 'app/models/collection_profile.rb', line 64

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

  belongs_to :container, inverse_of: :collection_profiles
  belongs_to :otu

  # Once created the intent is that CollectionProfiles are #dup(ed), not
  # edited.  If there was a data error pass true here
  attr_accessor :force_update

  scope :with_collection_type_string, -> (type_string) {where(collection_type: type_string)}
  scope :with_container_id, -> (container) {where(container_id: container)}
  scope :with_otu_id, -> (otu) {where(otu_id: otu)}

  validates :conservation_status,
            :processing_state,
            :container_condition,
            :condition_of_labels,
            :identification_level,
            :arrangement_level,
            :data_quality,
            :computerization_level,
            :collection_type, presence: true

  validate :validate_type,
           :validate_number,
           :validate_indices

  validate :prevent_editing, unless: -> {self.force_update}

  # region Profile indices

  # @return [Array]
  #   set of all provided indecies, if any is not provided return an empty array
  def collection_profile_indices
    i = [self.conservation_status,
         self.processing_state,
         self.container_condition,
         self.condition_of_labels,
         self.identification_level,
         self.arrangement_level,
         self.data_quality,
         self.computerization_level].compact
    i.size == 8 ? i : []
  end

  # @return [Float, nil]
  #    the average of all 8 indecies
  def average_profile_index
    i = self.collection_profile_indices
    i.empty? ? nil : i.sum / i.size.to_f
  end

  #endregion

  private

  def validate_type
    unless self.collection_type.blank?
      errors.add(:collection_type, 'Invalid profile type') if COLLECTION_PROFILE_INDICES[:Favret][self.collection_type.to_sym].nil?
    end
  end

  def validate_number
    t = self.collection_type.to_s
    if self.number_of_collection_objects.nil? && self.number_of_containers.nil?
      errors.add(:number_of_collection_objects, 'At least one number of specimens or number of containers should be specified')
      errors.add(:number_of_containers, 'At least one number of specimens or number of containers should be specified')
    elsif t == 'dry' && self.number_of_collection_objects.nil?
      errors.add(:number_of_collection_objects, 'Number of specimens should be specified')
    elsif (t == 'wet' || t == 'slide') && self.number_of_containers.nil?
      errors.add(:number_of_containers, 'Number of slides or vials should be specified')
    end
  end

  def validate_indices
    unless self.collection_type.blank?
      ct = self.collection_type.to_sym

      COLLECTION_PROFILE_INDICES[:Favret][ct].each_key do |a|
        v = self.send(a)
        unless v.nil?
          errors.add(a.to_sym, 'Invalid entry') if COLLECTION_PROFILE_INDICES[:Favret][ct][a.to_sym][v].nil?
        end
      end
    end
  end

  def prevent_editing
    unless self.new_record? || (self.created_at == self.updated_at) # a little strange, handles Factories?!
      errors.add(:base, 'Collection profile should not be updated. Updated version should be saved as a new record')
    end
  end

end

#collection_type ⇒ String

Returns one of ‘wet’, ‘dry’, ‘slide’ sensu Favret. Model is extensible via editing .yml and new profile types.

Returns:

  • (String) —

    one of ‘wet’, ‘dry’, ‘slide’ sensu Favret. Model is extensible via editing .yml and new profile types.



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# File 'app/models/collection_profile.rb', line 64

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

  belongs_to :container, inverse_of: :collection_profiles
  belongs_to :otu

  # Once created the intent is that CollectionProfiles are #dup(ed), not
  # edited.  If there was a data error pass true here
  attr_accessor :force_update

  scope :with_collection_type_string, -> (type_string) {where(collection_type: type_string)}
  scope :with_container_id, -> (container) {where(container_id: container)}
  scope :with_otu_id, -> (otu) {where(otu_id: otu)}

  validates :conservation_status,
            :processing_state,
            :container_condition,
            :condition_of_labels,
            :identification_level,
            :arrangement_level,
            :data_quality,
            :computerization_level,
            :collection_type, presence: true

  validate :validate_type,
           :validate_number,
           :validate_indices

  validate :prevent_editing, unless: -> {self.force_update}

  # region Profile indices

  # @return [Array]
  #   set of all provided indecies, if any is not provided return an empty array
  def collection_profile_indices
    i = [self.conservation_status,
         self.processing_state,
         self.container_condition,
         self.condition_of_labels,
         self.identification_level,
         self.arrangement_level,
         self.data_quality,
         self.computerization_level].compact
    i.size == 8 ? i : []
  end

  # @return [Float, nil]
  #    the average of all 8 indecies
  def average_profile_index
    i = self.collection_profile_indices
    i.empty? ? nil : i.sum / i.size.to_f
  end

  #endregion

  private

  def validate_type
    unless self.collection_type.blank?
      errors.add(:collection_type, 'Invalid profile type') if COLLECTION_PROFILE_INDICES[:Favret][self.collection_type.to_sym].nil?
    end
  end

  def validate_number
    t = self.collection_type.to_s
    if self.number_of_collection_objects.nil? && self.number_of_containers.nil?
      errors.add(:number_of_collection_objects, 'At least one number of specimens or number of containers should be specified')
      errors.add(:number_of_containers, 'At least one number of specimens or number of containers should be specified')
    elsif t == 'dry' && self.number_of_collection_objects.nil?
      errors.add(:number_of_collection_objects, 'Number of specimens should be specified')
    elsif (t == 'wet' || t == 'slide') && self.number_of_containers.nil?
      errors.add(:number_of_containers, 'Number of slides or vials should be specified')
    end
  end

  def validate_indices
    unless self.collection_type.blank?
      ct = self.collection_type.to_sym

      COLLECTION_PROFILE_INDICES[:Favret][ct].each_key do |a|
        v = self.send(a)
        unless v.nil?
          errors.add(a.to_sym, 'Invalid entry') if COLLECTION_PROFILE_INDICES[:Favret][ct][a.to_sym][v].nil?
        end
      end
    end
  end

  def prevent_editing
    unless self.new_record? || (self.created_at == self.updated_at) # a little strange, handles Factories?!
      errors.add(:base, 'Collection profile should not be updated. Updated version should be saved as a new record')
    end
  end

end

#computerization_level ⇒ Integer

Returns See Favret et al. (2007) (cited above).

Returns:

  • (Integer) —

    See Favret et al. (2007) (cited above)



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# File 'app/models/collection_profile.rb', line 64

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

  belongs_to :container, inverse_of: :collection_profiles
  belongs_to :otu

  # Once created the intent is that CollectionProfiles are #dup(ed), not
  # edited.  If there was a data error pass true here
  attr_accessor :force_update

  scope :with_collection_type_string, -> (type_string) {where(collection_type: type_string)}
  scope :with_container_id, -> (container) {where(container_id: container)}
  scope :with_otu_id, -> (otu) {where(otu_id: otu)}

  validates :conservation_status,
            :processing_state,
            :container_condition,
            :condition_of_labels,
            :identification_level,
            :arrangement_level,
            :data_quality,
            :computerization_level,
            :collection_type, presence: true

  validate :validate_type,
           :validate_number,
           :validate_indices

  validate :prevent_editing, unless: -> {self.force_update}

  # region Profile indices

  # @return [Array]
  #   set of all provided indecies, if any is not provided return an empty array
  def collection_profile_indices
    i = [self.conservation_status,
         self.processing_state,
         self.container_condition,
         self.condition_of_labels,
         self.identification_level,
         self.arrangement_level,
         self.data_quality,
         self.computerization_level].compact
    i.size == 8 ? i : []
  end

  # @return [Float, nil]
  #    the average of all 8 indecies
  def average_profile_index
    i = self.collection_profile_indices
    i.empty? ? nil : i.sum / i.size.to_f
  end

  #endregion

  private

  def validate_type
    unless self.collection_type.blank?
      errors.add(:collection_type, 'Invalid profile type') if COLLECTION_PROFILE_INDICES[:Favret][self.collection_type.to_sym].nil?
    end
  end

  def validate_number
    t = self.collection_type.to_s
    if self.number_of_collection_objects.nil? && self.number_of_containers.nil?
      errors.add(:number_of_collection_objects, 'At least one number of specimens or number of containers should be specified')
      errors.add(:number_of_containers, 'At least one number of specimens or number of containers should be specified')
    elsif t == 'dry' && self.number_of_collection_objects.nil?
      errors.add(:number_of_collection_objects, 'Number of specimens should be specified')
    elsif (t == 'wet' || t == 'slide') && self.number_of_containers.nil?
      errors.add(:number_of_containers, 'Number of slides or vials should be specified')
    end
  end

  def validate_indices
    unless self.collection_type.blank?
      ct = self.collection_type.to_sym

      COLLECTION_PROFILE_INDICES[:Favret][ct].each_key do |a|
        v = self.send(a)
        unless v.nil?
          errors.add(a.to_sym, 'Invalid entry') if COLLECTION_PROFILE_INDICES[:Favret][ct][a.to_sym][v].nil?
        end
      end
    end
  end

  def prevent_editing
    unless self.new_record? || (self.created_at == self.updated_at) # a little strange, handles Factories?!
      errors.add(:base, 'Collection profile should not be updated. Updated version should be saved as a new record')
    end
  end

end

#condition_of_labels ⇒ Integer

Returns See Favret et al. (2007) (cited above).

Returns:

  • (Integer) —

    See Favret et al. (2007) (cited above)



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# File 'app/models/collection_profile.rb', line 64

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

  belongs_to :container, inverse_of: :collection_profiles
  belongs_to :otu

  # Once created the intent is that CollectionProfiles are #dup(ed), not
  # edited.  If there was a data error pass true here
  attr_accessor :force_update

  scope :with_collection_type_string, -> (type_string) {where(collection_type: type_string)}
  scope :with_container_id, -> (container) {where(container_id: container)}
  scope :with_otu_id, -> (otu) {where(otu_id: otu)}

  validates :conservation_status,
            :processing_state,
            :container_condition,
            :condition_of_labels,
            :identification_level,
            :arrangement_level,
            :data_quality,
            :computerization_level,
            :collection_type, presence: true

  validate :validate_type,
           :validate_number,
           :validate_indices

  validate :prevent_editing, unless: -> {self.force_update}

  # region Profile indices

  # @return [Array]
  #   set of all provided indecies, if any is not provided return an empty array
  def collection_profile_indices
    i = [self.conservation_status,
         self.processing_state,
         self.container_condition,
         self.condition_of_labels,
         self.identification_level,
         self.arrangement_level,
         self.data_quality,
         self.computerization_level].compact
    i.size == 8 ? i : []
  end

  # @return [Float, nil]
  #    the average of all 8 indecies
  def average_profile_index
    i = self.collection_profile_indices
    i.empty? ? nil : i.sum / i.size.to_f
  end

  #endregion

  private

  def validate_type
    unless self.collection_type.blank?
      errors.add(:collection_type, 'Invalid profile type') if COLLECTION_PROFILE_INDICES[:Favret][self.collection_type.to_sym].nil?
    end
  end

  def validate_number
    t = self.collection_type.to_s
    if self.number_of_collection_objects.nil? && self.number_of_containers.nil?
      errors.add(:number_of_collection_objects, 'At least one number of specimens or number of containers should be specified')
      errors.add(:number_of_containers, 'At least one number of specimens or number of containers should be specified')
    elsif t == 'dry' && self.number_of_collection_objects.nil?
      errors.add(:number_of_collection_objects, 'Number of specimens should be specified')
    elsif (t == 'wet' || t == 'slide') && self.number_of_containers.nil?
      errors.add(:number_of_containers, 'Number of slides or vials should be specified')
    end
  end

  def validate_indices
    unless self.collection_type.blank?
      ct = self.collection_type.to_sym

      COLLECTION_PROFILE_INDICES[:Favret][ct].each_key do |a|
        v = self.send(a)
        unless v.nil?
          errors.add(a.to_sym, 'Invalid entry') if COLLECTION_PROFILE_INDICES[:Favret][ct][a.to_sym][v].nil?
        end
      end
    end
  end

  def prevent_editing
    unless self.new_record? || (self.created_at == self.updated_at) # a little strange, handles Factories?!
      errors.add(:base, 'Collection profile should not be updated. Updated version should be saved as a new record')
    end
  end

end

#conservation_status ⇒ Integer

Returns See Favret et al. (2007) (cited above).

Returns:

  • (Integer) —

    See Favret et al. (2007) (cited above)



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# File 'app/models/collection_profile.rb', line 64

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

  belongs_to :container, inverse_of: :collection_profiles
  belongs_to :otu

  # Once created the intent is that CollectionProfiles are #dup(ed), not
  # edited.  If there was a data error pass true here
  attr_accessor :force_update

  scope :with_collection_type_string, -> (type_string) {where(collection_type: type_string)}
  scope :with_container_id, -> (container) {where(container_id: container)}
  scope :with_otu_id, -> (otu) {where(otu_id: otu)}

  validates :conservation_status,
            :processing_state,
            :container_condition,
            :condition_of_labels,
            :identification_level,
            :arrangement_level,
            :data_quality,
            :computerization_level,
            :collection_type, presence: true

  validate :validate_type,
           :validate_number,
           :validate_indices

  validate :prevent_editing, unless: -> {self.force_update}

  # region Profile indices

  # @return [Array]
  #   set of all provided indecies, if any is not provided return an empty array
  def collection_profile_indices
    i = [self.conservation_status,
         self.processing_state,
         self.container_condition,
         self.condition_of_labels,
         self.identification_level,
         self.arrangement_level,
         self.data_quality,
         self.computerization_level].compact
    i.size == 8 ? i : []
  end

  # @return [Float, nil]
  #    the average of all 8 indecies
  def average_profile_index
    i = self.collection_profile_indices
    i.empty? ? nil : i.sum / i.size.to_f
  end

  #endregion

  private

  def validate_type
    unless self.collection_type.blank?
      errors.add(:collection_type, 'Invalid profile type') if COLLECTION_PROFILE_INDICES[:Favret][self.collection_type.to_sym].nil?
    end
  end

  def validate_number
    t = self.collection_type.to_s
    if self.number_of_collection_objects.nil? && self.number_of_containers.nil?
      errors.add(:number_of_collection_objects, 'At least one number of specimens or number of containers should be specified')
      errors.add(:number_of_containers, 'At least one number of specimens or number of containers should be specified')
    elsif t == 'dry' && self.number_of_collection_objects.nil?
      errors.add(:number_of_collection_objects, 'Number of specimens should be specified')
    elsif (t == 'wet' || t == 'slide') && self.number_of_containers.nil?
      errors.add(:number_of_containers, 'Number of slides or vials should be specified')
    end
  end

  def validate_indices
    unless self.collection_type.blank?
      ct = self.collection_type.to_sym

      COLLECTION_PROFILE_INDICES[:Favret][ct].each_key do |a|
        v = self.send(a)
        unless v.nil?
          errors.add(a.to_sym, 'Invalid entry') if COLLECTION_PROFILE_INDICES[:Favret][ct][a.to_sym][v].nil?
        end
      end
    end
  end

  def prevent_editing
    unless self.new_record? || (self.created_at == self.updated_at) # a little strange, handles Factories?!
      errors.add(:base, 'Collection profile should not be updated. Updated version should be saved as a new record')
    end
  end

end

#container_condition ⇒ Integer

Returns See Favret et al. (2007) (cited above).

Returns:

  • (Integer) —

    See Favret et al. (2007) (cited above)



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# File 'app/models/collection_profile.rb', line 64

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

  belongs_to :container, inverse_of: :collection_profiles
  belongs_to :otu

  # Once created the intent is that CollectionProfiles are #dup(ed), not
  # edited.  If there was a data error pass true here
  attr_accessor :force_update

  scope :with_collection_type_string, -> (type_string) {where(collection_type: type_string)}
  scope :with_container_id, -> (container) {where(container_id: container)}
  scope :with_otu_id, -> (otu) {where(otu_id: otu)}

  validates :conservation_status,
            :processing_state,
            :container_condition,
            :condition_of_labels,
            :identification_level,
            :arrangement_level,
            :data_quality,
            :computerization_level,
            :collection_type, presence: true

  validate :validate_type,
           :validate_number,
           :validate_indices

  validate :prevent_editing, unless: -> {self.force_update}

  # region Profile indices

  # @return [Array]
  #   set of all provided indecies, if any is not provided return an empty array
  def collection_profile_indices
    i = [self.conservation_status,
         self.processing_state,
         self.container_condition,
         self.condition_of_labels,
         self.identification_level,
         self.arrangement_level,
         self.data_quality,
         self.computerization_level].compact
    i.size == 8 ? i : []
  end

  # @return [Float, nil]
  #    the average of all 8 indecies
  def average_profile_index
    i = self.collection_profile_indices
    i.empty? ? nil : i.sum / i.size.to_f
  end

  #endregion

  private

  def validate_type
    unless self.collection_type.blank?
      errors.add(:collection_type, 'Invalid profile type') if COLLECTION_PROFILE_INDICES[:Favret][self.collection_type.to_sym].nil?
    end
  end

  def validate_number
    t = self.collection_type.to_s
    if self.number_of_collection_objects.nil? && self.number_of_containers.nil?
      errors.add(:number_of_collection_objects, 'At least one number of specimens or number of containers should be specified')
      errors.add(:number_of_containers, 'At least one number of specimens or number of containers should be specified')
    elsif t == 'dry' && self.number_of_collection_objects.nil?
      errors.add(:number_of_collection_objects, 'Number of specimens should be specified')
    elsif (t == 'wet' || t == 'slide') && self.number_of_containers.nil?
      errors.add(:number_of_containers, 'Number of slides or vials should be specified')
    end
  end

  def validate_indices
    unless self.collection_type.blank?
      ct = self.collection_type.to_sym

      COLLECTION_PROFILE_INDICES[:Favret][ct].each_key do |a|
        v = self.send(a)
        unless v.nil?
          errors.add(a.to_sym, 'Invalid entry') if COLLECTION_PROFILE_INDICES[:Favret][ct][a.to_sym][v].nil?
        end
      end
    end
  end

  def prevent_editing
    unless self.new_record? || (self.created_at == self.updated_at) # a little strange, handles Factories?!
      errors.add(:base, 'Collection profile should not be updated. Updated version should be saved as a new record')
    end
  end

end

#container_id ⇒ Integer

Returns the (physical) Container beign profiled.

Returns:

  • (Integer) —

    the (physical) Container beign profiled



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# File 'app/models/collection_profile.rb', line 64

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

  belongs_to :container, inverse_of: :collection_profiles
  belongs_to :otu

  # Once created the intent is that CollectionProfiles are #dup(ed), not
  # edited.  If there was a data error pass true here
  attr_accessor :force_update

  scope :with_collection_type_string, -> (type_string) {where(collection_type: type_string)}
  scope :with_container_id, -> (container) {where(container_id: container)}
  scope :with_otu_id, -> (otu) {where(otu_id: otu)}

  validates :conservation_status,
            :processing_state,
            :container_condition,
            :condition_of_labels,
            :identification_level,
            :arrangement_level,
            :data_quality,
            :computerization_level,
            :collection_type, presence: true

  validate :validate_type,
           :validate_number,
           :validate_indices

  validate :prevent_editing, unless: -> {self.force_update}

  # region Profile indices

  # @return [Array]
  #   set of all provided indecies, if any is not provided return an empty array
  def collection_profile_indices
    i = [self.conservation_status,
         self.processing_state,
         self.container_condition,
         self.condition_of_labels,
         self.identification_level,
         self.arrangement_level,
         self.data_quality,
         self.computerization_level].compact
    i.size == 8 ? i : []
  end

  # @return [Float, nil]
  #    the average of all 8 indecies
  def average_profile_index
    i = self.collection_profile_indices
    i.empty? ? nil : i.sum / i.size.to_f
  end

  #endregion

  private

  def validate_type
    unless self.collection_type.blank?
      errors.add(:collection_type, 'Invalid profile type') if COLLECTION_PROFILE_INDICES[:Favret][self.collection_type.to_sym].nil?
    end
  end

  def validate_number
    t = self.collection_type.to_s
    if self.number_of_collection_objects.nil? && self.number_of_containers.nil?
      errors.add(:number_of_collection_objects, 'At least one number of specimens or number of containers should be specified')
      errors.add(:number_of_containers, 'At least one number of specimens or number of containers should be specified')
    elsif t == 'dry' && self.number_of_collection_objects.nil?
      errors.add(:number_of_collection_objects, 'Number of specimens should be specified')
    elsif (t == 'wet' || t == 'slide') && self.number_of_containers.nil?
      errors.add(:number_of_containers, 'Number of slides or vials should be specified')
    end
  end

  def validate_indices
    unless self.collection_type.blank?
      ct = self.collection_type.to_sym

      COLLECTION_PROFILE_INDICES[:Favret][ct].each_key do |a|
        v = self.send(a)
        unless v.nil?
          errors.add(a.to_sym, 'Invalid entry') if COLLECTION_PROFILE_INDICES[:Favret][ct][a.to_sym][v].nil?
        end
      end
    end
  end

  def prevent_editing
    unless self.new_record? || (self.created_at == self.updated_at) # a little strange, handles Factories?!
      errors.add(:base, 'Collection profile should not be updated. Updated version should be saved as a new record')
    end
  end

end

#data_quality ⇒ Integer

Returns See Favret et al. (2007) (cited above).

Returns:

  • (Integer) —

    See Favret et al. (2007) (cited above)



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# File 'app/models/collection_profile.rb', line 64

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

  belongs_to :container, inverse_of: :collection_profiles
  belongs_to :otu

  # Once created the intent is that CollectionProfiles are #dup(ed), not
  # edited.  If there was a data error pass true here
  attr_accessor :force_update

  scope :with_collection_type_string, -> (type_string) {where(collection_type: type_string)}
  scope :with_container_id, -> (container) {where(container_id: container)}
  scope :with_otu_id, -> (otu) {where(otu_id: otu)}

  validates :conservation_status,
            :processing_state,
            :container_condition,
            :condition_of_labels,
            :identification_level,
            :arrangement_level,
            :data_quality,
            :computerization_level,
            :collection_type, presence: true

  validate :validate_type,
           :validate_number,
           :validate_indices

  validate :prevent_editing, unless: -> {self.force_update}

  # region Profile indices

  # @return [Array]
  #   set of all provided indecies, if any is not provided return an empty array
  def collection_profile_indices
    i = [self.conservation_status,
         self.processing_state,
         self.container_condition,
         self.condition_of_labels,
         self.identification_level,
         self.arrangement_level,
         self.data_quality,
         self.computerization_level].compact
    i.size == 8 ? i : []
  end

  # @return [Float, nil]
  #    the average of all 8 indecies
  def average_profile_index
    i = self.collection_profile_indices
    i.empty? ? nil : i.sum / i.size.to_f
  end

  #endregion

  private

  def validate_type
    unless self.collection_type.blank?
      errors.add(:collection_type, 'Invalid profile type') if COLLECTION_PROFILE_INDICES[:Favret][self.collection_type.to_sym].nil?
    end
  end

  def validate_number
    t = self.collection_type.to_s
    if self.number_of_collection_objects.nil? && self.number_of_containers.nil?
      errors.add(:number_of_collection_objects, 'At least one number of specimens or number of containers should be specified')
      errors.add(:number_of_containers, 'At least one number of specimens or number of containers should be specified')
    elsif t == 'dry' && self.number_of_collection_objects.nil?
      errors.add(:number_of_collection_objects, 'Number of specimens should be specified')
    elsif (t == 'wet' || t == 'slide') && self.number_of_containers.nil?
      errors.add(:number_of_containers, 'Number of slides or vials should be specified')
    end
  end

  def validate_indices
    unless self.collection_type.blank?
      ct = self.collection_type.to_sym

      COLLECTION_PROFILE_INDICES[:Favret][ct].each_key do |a|
        v = self.send(a)
        unless v.nil?
          errors.add(a.to_sym, 'Invalid entry') if COLLECTION_PROFILE_INDICES[:Favret][ct][a.to_sym][v].nil?
        end
      end
    end
  end

  def prevent_editing
    unless self.new_record? || (self.created_at == self.updated_at) # a little strange, handles Factories?!
      errors.add(:base, 'Collection profile should not be updated. Updated version should be saved as a new record')
    end
  end

end

#force_update ⇒ Object

Once created the intent is that CollectionProfiles are #dup(ed), not edited. If there was a data error pass true here



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

def force_update
  @force_update
end

#identification_level ⇒ Integer

Returns See Favret et al. (2007) (cited above).

Returns:

  • (Integer) —

    See Favret et al. (2007) (cited above)



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# File 'app/models/collection_profile.rb', line 64

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

  belongs_to :container, inverse_of: :collection_profiles
  belongs_to :otu

  # Once created the intent is that CollectionProfiles are #dup(ed), not
  # edited.  If there was a data error pass true here
  attr_accessor :force_update

  scope :with_collection_type_string, -> (type_string) {where(collection_type: type_string)}
  scope :with_container_id, -> (container) {where(container_id: container)}
  scope :with_otu_id, -> (otu) {where(otu_id: otu)}

  validates :conservation_status,
            :processing_state,
            :container_condition,
            :condition_of_labels,
            :identification_level,
            :arrangement_level,
            :data_quality,
            :computerization_level,
            :collection_type, presence: true

  validate :validate_type,
           :validate_number,
           :validate_indices

  validate :prevent_editing, unless: -> {self.force_update}

  # region Profile indices

  # @return [Array]
  #   set of all provided indecies, if any is not provided return an empty array
  def collection_profile_indices
    i = [self.conservation_status,
         self.processing_state,
         self.container_condition,
         self.condition_of_labels,
         self.identification_level,
         self.arrangement_level,
         self.data_quality,
         self.computerization_level].compact
    i.size == 8 ? i : []
  end

  # @return [Float, nil]
  #    the average of all 8 indecies
  def average_profile_index
    i = self.collection_profile_indices
    i.empty? ? nil : i.sum / i.size.to_f
  end

  #endregion

  private

  def validate_type
    unless self.collection_type.blank?
      errors.add(:collection_type, 'Invalid profile type') if COLLECTION_PROFILE_INDICES[:Favret][self.collection_type.to_sym].nil?
    end
  end

  def validate_number
    t = self.collection_type.to_s
    if self.number_of_collection_objects.nil? && self.number_of_containers.nil?
      errors.add(:number_of_collection_objects, 'At least one number of specimens or number of containers should be specified')
      errors.add(:number_of_containers, 'At least one number of specimens or number of containers should be specified')
    elsif t == 'dry' && self.number_of_collection_objects.nil?
      errors.add(:number_of_collection_objects, 'Number of specimens should be specified')
    elsif (t == 'wet' || t == 'slide') && self.number_of_containers.nil?
      errors.add(:number_of_containers, 'Number of slides or vials should be specified')
    end
  end

  def validate_indices
    unless self.collection_type.blank?
      ct = self.collection_type.to_sym

      COLLECTION_PROFILE_INDICES[:Favret][ct].each_key do |a|
        v = self.send(a)
        unless v.nil?
          errors.add(a.to_sym, 'Invalid entry') if COLLECTION_PROFILE_INDICES[:Favret][ct][a.to_sym][v].nil?
        end
      end
    end
  end

  def prevent_editing
    unless self.new_record? || (self.created_at == self.updated_at) # a little strange, handles Factories?!
      errors.add(:base, 'Collection profile should not be updated. Updated version should be saved as a new record')
    end
  end

end

#number_of_collection_objects ⇒ Integer

Returns a count of the number of collection objects in this container (asserted, not as calculated in TW).

Returns:

  • (Integer) —

    a count of the number of collection objects in this container (asserted, not as calculated in TW)



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# File 'app/models/collection_profile.rb', line 64

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

  belongs_to :container, inverse_of: :collection_profiles
  belongs_to :otu

  # Once created the intent is that CollectionProfiles are #dup(ed), not
  # edited.  If there was a data error pass true here
  attr_accessor :force_update

  scope :with_collection_type_string, -> (type_string) {where(collection_type: type_string)}
  scope :with_container_id, -> (container) {where(container_id: container)}
  scope :with_otu_id, -> (otu) {where(otu_id: otu)}

  validates :conservation_status,
            :processing_state,
            :container_condition,
            :condition_of_labels,
            :identification_level,
            :arrangement_level,
            :data_quality,
            :computerization_level,
            :collection_type, presence: true

  validate :validate_type,
           :validate_number,
           :validate_indices

  validate :prevent_editing, unless: -> {self.force_update}

  # region Profile indices

  # @return [Array]
  #   set of all provided indecies, if any is not provided return an empty array
  def collection_profile_indices
    i = [self.conservation_status,
         self.processing_state,
         self.container_condition,
         self.condition_of_labels,
         self.identification_level,
         self.arrangement_level,
         self.data_quality,
         self.computerization_level].compact
    i.size == 8 ? i : []
  end

  # @return [Float, nil]
  #    the average of all 8 indecies
  def average_profile_index
    i = self.collection_profile_indices
    i.empty? ? nil : i.sum / i.size.to_f
  end

  #endregion

  private

  def validate_type
    unless self.collection_type.blank?
      errors.add(:collection_type, 'Invalid profile type') if COLLECTION_PROFILE_INDICES[:Favret][self.collection_type.to_sym].nil?
    end
  end

  def validate_number
    t = self.collection_type.to_s
    if self.number_of_collection_objects.nil? && self.number_of_containers.nil?
      errors.add(:number_of_collection_objects, 'At least one number of specimens or number of containers should be specified')
      errors.add(:number_of_containers, 'At least one number of specimens or number of containers should be specified')
    elsif t == 'dry' && self.number_of_collection_objects.nil?
      errors.add(:number_of_collection_objects, 'Number of specimens should be specified')
    elsif (t == 'wet' || t == 'slide') && self.number_of_containers.nil?
      errors.add(:number_of_containers, 'Number of slides or vials should be specified')
    end
  end

  def validate_indices
    unless self.collection_type.blank?
      ct = self.collection_type.to_sym

      COLLECTION_PROFILE_INDICES[:Favret][ct].each_key do |a|
        v = self.send(a)
        unless v.nil?
          errors.add(a.to_sym, 'Invalid entry') if COLLECTION_PROFILE_INDICES[:Favret][ct][a.to_sym][v].nil?
        end
      end
    end
  end

  def prevent_editing
    unless self.new_record? || (self.created_at == self.updated_at) # a little strange, handles Factories?!
      errors.add(:base, 'Collection profile should not be updated. Updated version should be saved as a new record')
    end
  end

end

#number_of_containers ⇒ Integer

Returns a count of the number of containers inside this container (asserted, not as calculated in TW).

Returns:

  • (Integer) —

    a count of the number of containers inside this container (asserted, not as calculated in TW)



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# File 'app/models/collection_profile.rb', line 64

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

  belongs_to :container, inverse_of: :collection_profiles
  belongs_to :otu

  # Once created the intent is that CollectionProfiles are #dup(ed), not
  # edited.  If there was a data error pass true here
  attr_accessor :force_update

  scope :with_collection_type_string, -> (type_string) {where(collection_type: type_string)}
  scope :with_container_id, -> (container) {where(container_id: container)}
  scope :with_otu_id, -> (otu) {where(otu_id: otu)}

  validates :conservation_status,
            :processing_state,
            :container_condition,
            :condition_of_labels,
            :identification_level,
            :arrangement_level,
            :data_quality,
            :computerization_level,
            :collection_type, presence: true

  validate :validate_type,
           :validate_number,
           :validate_indices

  validate :prevent_editing, unless: -> {self.force_update}

  # region Profile indices

  # @return [Array]
  #   set of all provided indecies, if any is not provided return an empty array
  def collection_profile_indices
    i = [self.conservation_status,
         self.processing_state,
         self.container_condition,
         self.condition_of_labels,
         self.identification_level,
         self.arrangement_level,
         self.data_quality,
         self.computerization_level].compact
    i.size == 8 ? i : []
  end

  # @return [Float, nil]
  #    the average of all 8 indecies
  def average_profile_index
    i = self.collection_profile_indices
    i.empty? ? nil : i.sum / i.size.to_f
  end

  #endregion

  private

  def validate_type
    unless self.collection_type.blank?
      errors.add(:collection_type, 'Invalid profile type') if COLLECTION_PROFILE_INDICES[:Favret][self.collection_type.to_sym].nil?
    end
  end

  def validate_number
    t = self.collection_type.to_s
    if self.number_of_collection_objects.nil? && self.number_of_containers.nil?
      errors.add(:number_of_collection_objects, 'At least one number of specimens or number of containers should be specified')
      errors.add(:number_of_containers, 'At least one number of specimens or number of containers should be specified')
    elsif t == 'dry' && self.number_of_collection_objects.nil?
      errors.add(:number_of_collection_objects, 'Number of specimens should be specified')
    elsif (t == 'wet' || t == 'slide') && self.number_of_containers.nil?
      errors.add(:number_of_containers, 'Number of slides or vials should be specified')
    end
  end

  def validate_indices
    unless self.collection_type.blank?
      ct = self.collection_type.to_sym

      COLLECTION_PROFILE_INDICES[:Favret][ct].each_key do |a|
        v = self.send(a)
        unless v.nil?
          errors.add(a.to_sym, 'Invalid entry') if COLLECTION_PROFILE_INDICES[:Favret][ct][a.to_sym][v].nil?
        end
      end
    end
  end

  def prevent_editing
    unless self.new_record? || (self.created_at == self.updated_at) # a little strange, handles Factories?!
      errors.add(:base, 'Collection profile should not be updated. Updated version should be saved as a new record')
    end
  end

end

#otu_id ⇒ Integer

Returns the encompassing taxon found in this container.

Returns:

  • (Integer) —

    the encompassing taxon found in this container



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# File 'app/models/collection_profile.rb', line 64

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

  belongs_to :container, inverse_of: :collection_profiles
  belongs_to :otu

  # Once created the intent is that CollectionProfiles are #dup(ed), not
  # edited.  If there was a data error pass true here
  attr_accessor :force_update

  scope :with_collection_type_string, -> (type_string) {where(collection_type: type_string)}
  scope :with_container_id, -> (container) {where(container_id: container)}
  scope :with_otu_id, -> (otu) {where(otu_id: otu)}

  validates :conservation_status,
            :processing_state,
            :container_condition,
            :condition_of_labels,
            :identification_level,
            :arrangement_level,
            :data_quality,
            :computerization_level,
            :collection_type, presence: true

  validate :validate_type,
           :validate_number,
           :validate_indices

  validate :prevent_editing, unless: -> {self.force_update}

  # region Profile indices

  # @return [Array]
  #   set of all provided indecies, if any is not provided return an empty array
  def collection_profile_indices
    i = [self.conservation_status,
         self.processing_state,
         self.container_condition,
         self.condition_of_labels,
         self.identification_level,
         self.arrangement_level,
         self.data_quality,
         self.computerization_level].compact
    i.size == 8 ? i : []
  end

  # @return [Float, nil]
  #    the average of all 8 indecies
  def average_profile_index
    i = self.collection_profile_indices
    i.empty? ? nil : i.sum / i.size.to_f
  end

  #endregion

  private

  def validate_type
    unless self.collection_type.blank?
      errors.add(:collection_type, 'Invalid profile type') if COLLECTION_PROFILE_INDICES[:Favret][self.collection_type.to_sym].nil?
    end
  end

  def validate_number
    t = self.collection_type.to_s
    if self.number_of_collection_objects.nil? && self.number_of_containers.nil?
      errors.add(:number_of_collection_objects, 'At least one number of specimens or number of containers should be specified')
      errors.add(:number_of_containers, 'At least one number of specimens or number of containers should be specified')
    elsif t == 'dry' && self.number_of_collection_objects.nil?
      errors.add(:number_of_collection_objects, 'Number of specimens should be specified')
    elsif (t == 'wet' || t == 'slide') && self.number_of_containers.nil?
      errors.add(:number_of_containers, 'Number of slides or vials should be specified')
    end
  end

  def validate_indices
    unless self.collection_type.blank?
      ct = self.collection_type.to_sym

      COLLECTION_PROFILE_INDICES[:Favret][ct].each_key do |a|
        v = self.send(a)
        unless v.nil?
          errors.add(a.to_sym, 'Invalid entry') if COLLECTION_PROFILE_INDICES[:Favret][ct][a.to_sym][v].nil?
        end
      end
    end
  end

  def prevent_editing
    unless self.new_record? || (self.created_at == self.updated_at) # a little strange, handles Factories?!
      errors.add(:base, 'Collection profile should not be updated. Updated version should be saved as a new record')
    end
  end

end

#processing_state ⇒ Integer

Returns See Favret et al. (2007) (cited above).

Returns:

  • (Integer) —

    See Favret et al. (2007) (cited above)



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# File 'app/models/collection_profile.rb', line 64

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

  belongs_to :container, inverse_of: :collection_profiles
  belongs_to :otu

  # Once created the intent is that CollectionProfiles are #dup(ed), not
  # edited.  If there was a data error pass true here
  attr_accessor :force_update

  scope :with_collection_type_string, -> (type_string) {where(collection_type: type_string)}
  scope :with_container_id, -> (container) {where(container_id: container)}
  scope :with_otu_id, -> (otu) {where(otu_id: otu)}

  validates :conservation_status,
            :processing_state,
            :container_condition,
            :condition_of_labels,
            :identification_level,
            :arrangement_level,
            :data_quality,
            :computerization_level,
            :collection_type, presence: true

  validate :validate_type,
           :validate_number,
           :validate_indices

  validate :prevent_editing, unless: -> {self.force_update}

  # region Profile indices

  # @return [Array]
  #   set of all provided indecies, if any is not provided return an empty array
  def collection_profile_indices
    i = [self.conservation_status,
         self.processing_state,
         self.container_condition,
         self.condition_of_labels,
         self.identification_level,
         self.arrangement_level,
         self.data_quality,
         self.computerization_level].compact
    i.size == 8 ? i : []
  end

  # @return [Float, nil]
  #    the average of all 8 indecies
  def average_profile_index
    i = self.collection_profile_indices
    i.empty? ? nil : i.sum / i.size.to_f
  end

  #endregion

  private

  def validate_type
    unless self.collection_type.blank?
      errors.add(:collection_type, 'Invalid profile type') if COLLECTION_PROFILE_INDICES[:Favret][self.collection_type.to_sym].nil?
    end
  end

  def validate_number
    t = self.collection_type.to_s
    if self.number_of_collection_objects.nil? && self.number_of_containers.nil?
      errors.add(:number_of_collection_objects, 'At least one number of specimens or number of containers should be specified')
      errors.add(:number_of_containers, 'At least one number of specimens or number of containers should be specified')
    elsif t == 'dry' && self.number_of_collection_objects.nil?
      errors.add(:number_of_collection_objects, 'Number of specimens should be specified')
    elsif (t == 'wet' || t == 'slide') && self.number_of_containers.nil?
      errors.add(:number_of_containers, 'Number of slides or vials should be specified')
    end
  end

  def validate_indices
    unless self.collection_type.blank?
      ct = self.collection_type.to_sym

      COLLECTION_PROFILE_INDICES[:Favret][ct].each_key do |a|
        v = self.send(a)
        unless v.nil?
          errors.add(a.to_sym, 'Invalid entry') if COLLECTION_PROFILE_INDICES[:Favret][ct][a.to_sym][v].nil?
        end
      end
    end
  end

  def prevent_editing
    unless self.new_record? || (self.created_at == self.updated_at) # a little strange, handles Factories?!
      errors.add(:base, 'Collection profile should not be updated. Updated version should be saved as a new record')
    end
  end

end

#project_id ⇒ Integer

Returns the Project ID.

Returns:

  • (Integer) —

    the Project ID



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# File 'app/models/collection_profile.rb', line 64

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

  belongs_to :container, inverse_of: :collection_profiles
  belongs_to :otu

  # Once created the intent is that CollectionProfiles are #dup(ed), not
  # edited.  If there was a data error pass true here
  attr_accessor :force_update

  scope :with_collection_type_string, -> (type_string) {where(collection_type: type_string)}
  scope :with_container_id, -> (container) {where(container_id: container)}
  scope :with_otu_id, -> (otu) {where(otu_id: otu)}

  validates :conservation_status,
            :processing_state,
            :container_condition,
            :condition_of_labels,
            :identification_level,
            :arrangement_level,
            :data_quality,
            :computerization_level,
            :collection_type, presence: true

  validate :validate_type,
           :validate_number,
           :validate_indices

  validate :prevent_editing, unless: -> {self.force_update}

  # region Profile indices

  # @return [Array]
  #   set of all provided indecies, if any is not provided return an empty array
  def collection_profile_indices
    i = [self.conservation_status,
         self.processing_state,
         self.container_condition,
         self.condition_of_labels,
         self.identification_level,
         self.arrangement_level,
         self.data_quality,
         self.computerization_level].compact
    i.size == 8 ? i : []
  end

  # @return [Float, nil]
  #    the average of all 8 indecies
  def average_profile_index
    i = self.collection_profile_indices
    i.empty? ? nil : i.sum / i.size.to_f
  end

  #endregion

  private

  def validate_type
    unless self.collection_type.blank?
      errors.add(:collection_type, 'Invalid profile type') if COLLECTION_PROFILE_INDICES[:Favret][self.collection_type.to_sym].nil?
    end
  end

  def validate_number
    t = self.collection_type.to_s
    if self.number_of_collection_objects.nil? && self.number_of_containers.nil?
      errors.add(:number_of_collection_objects, 'At least one number of specimens or number of containers should be specified')
      errors.add(:number_of_containers, 'At least one number of specimens or number of containers should be specified')
    elsif t == 'dry' && self.number_of_collection_objects.nil?
      errors.add(:number_of_collection_objects, 'Number of specimens should be specified')
    elsif (t == 'wet' || t == 'slide') && self.number_of_containers.nil?
      errors.add(:number_of_containers, 'Number of slides or vials should be specified')
    end
  end

  def validate_indices
    unless self.collection_type.blank?
      ct = self.collection_type.to_sym

      COLLECTION_PROFILE_INDICES[:Favret][ct].each_key do |a|
        v = self.send(a)
        unless v.nil?
          errors.add(a.to_sym, 'Invalid entry') if COLLECTION_PROFILE_INDICES[:Favret][ct][a.to_sym][v].nil?
        end
      end
    end
  end

  def prevent_editing
    unless self.new_record? || (self.created_at == self.updated_at) # a little strange, handles Factories?!
      errors.add(:base, 'Collection profile should not be updated. Updated version should be saved as a new record')
    end
  end

end

Instance Method Details

#average_profile_index ⇒ Float?

Returns the average of all 8 indecies.

Returns:

  • (Float, nil) —

    the average of all 8 indecies



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

def average_profile_index
  i = self.collection_profile_indices
  i.empty? ? nil : i.sum / i.size.to_f
end

#collection_profile_indices ⇒ Array

Returns set of all provided indecies, if any is not provided return an empty array.

Returns:

  • (Array) —

    set of all provided indecies, if any is not provided return an empty array



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# File 'app/models/collection_profile.rb', line 103

def collection_profile_indices
  i = [self.conservation_status,
       self.processing_state,
       self.container_condition,
       self.condition_of_labels,
       self.identification_level,
       self.arrangement_level,
       self.data_quality,
       self.computerization_level].compact
  i.size == 8 ? i : []
end

#prevent_editing ⇒ Object (private) 



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

def prevent_editing
  unless self.new_record? || (self.created_at == self.updated_at) # a little strange, handles Factories?!
    errors.add(:base, 'Collection profile should not be updated. Updated version should be saved as a new record')
  end
end

#validate_indices ⇒ Object (private) 



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# File 'app/models/collection_profile.rb', line 144

def validate_indices
  unless self.collection_type.blank?
    ct = self.collection_type.to_sym

    COLLECTION_PROFILE_INDICES[:Favret][ct].each_key do |a|
      v = self.send(a)
      unless v.nil?
        errors.add(a.to_sym, 'Invalid entry') if COLLECTION_PROFILE_INDICES[:Favret][ct][a.to_sym][v].nil?
      end
    end
  end
end

#validate_number ⇒ Object (private) 



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# File 'app/models/collection_profile.rb', line 132

def validate_number
  t = self.collection_type.to_s
  if self.number_of_collection_objects.nil? && self.number_of_containers.nil?
    errors.add(:number_of_collection_objects, 'At least one number of specimens or number of containers should be specified')
    errors.add(:number_of_containers, 'At least one number of specimens or number of containers should be specified')
  elsif t == 'dry' && self.number_of_collection_objects.nil?
    errors.add(:number_of_collection_objects, 'Number of specimens should be specified')
  elsif (t == 'wet' || t == 'slide') && self.number_of_containers.nil?
    errors.add(:number_of_containers, 'Number of slides or vials should be specified')
  end
end

#validate_type ⇒ Object (private) 



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# File 'app/models/collection_profile.rb', line 126

def validate_type
  unless self.collection_type.blank?
    errors.add(:collection_type, 'Invalid profile type') if COLLECTION_PROFILE_INDICES[:Favret][self.collection_type.to_sym].nil?
  end
end