Class: Extract

Inherits:
ApplicationRecord show all
Includes:
Housekeeping, Shared::Identifiers, Shared::IsData, Shared::OriginRelationship, Shared::ProtocolRelationships
Defined in:
app/models/extract.rb

Overview

An Extract is the quantified physical entity that originated from a CollectionObject. Extracts are linked to their origin through an OriginRelationship.

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::OriginRelationship

#new_objects, #old_objects, #reject_origin_relationships, #set_origin

Methods included from Shared::ProtocolRelationships

#protocolled?

Methods included from Shared::Identifiers

#identified?, #next_by_identifier, #previous_by_identifier, #reject_identifiers

Methods included from Housekeeping

#has_polymorphic_relationship?

Methods inherited from ApplicationRecord

transaction_with_retry

Instance Attribute Details

#concentration_unit ⇒ Numeric

Returns # @Merfoo, define with David.

Returns:

  • (Numeric) —

    # @Merfoo, define with David



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# File 'app/models/extract.rb', line 36

class Extract < ApplicationRecord
  include Housekeeping
  include Shared::Identifiers
  include Shared::ProtocolRelationships
  include Shared::OriginRelationship
  include Shared::IsData

  is_origin_for 'Extract', 'Sequence'
  originates_from 'Extract', 'Specimen', 'Lot', 'RangedLot', 'Otu'

  has_many :sequences, through: :origin_relationships, source: :new_object, source_type: 'Sequence'

  validates_presence_of :quantity_value
  attr_accessor :is_made_now

  before_validation :set_made, if: -> {is_made_now}

  validates_presence_of :quantity_value
  validates_presence_of :quantity_unit

  validates :quantity_unit, with: :validate_units

  validates :year_made, date_year: { allow_blank: false }
  validates :month_made, date_month: { allow_blank: false }
  validates :day_made, date_day: { allow_blank: false }

  protected

  def set_made
    write_attribute(:year_made, Time.now.year)
    write_attribute(:month_made, Time.now.month)
    write_attribute(:day_made, Time.now.day)
  end

  def validate_units
    begin
      RubyUnits::Unit.new(quantity_unit)
    rescue ArgumentError, 'Unit not recognized'
      errors.add(:quantity_unit, "'#{quantity_unit}' is an invalid quantity_unit")
    end
  end


end

#concentration_value ⇒ Numeric

Returns # @Merfoo, define with David.

Returns:

  • (Numeric) —

    # @Merfoo, define with David



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# File 'app/models/extract.rb', line 36

class Extract < ApplicationRecord
  include Housekeeping
  include Shared::Identifiers
  include Shared::ProtocolRelationships
  include Shared::OriginRelationship
  include Shared::IsData

  is_origin_for 'Extract', 'Sequence'
  originates_from 'Extract', 'Specimen', 'Lot', 'RangedLot', 'Otu'

  has_many :sequences, through: :origin_relationships, source: :new_object, source_type: 'Sequence'

  validates_presence_of :quantity_value
  attr_accessor :is_made_now

  before_validation :set_made, if: -> {is_made_now}

  validates_presence_of :quantity_value
  validates_presence_of :quantity_unit

  validates :quantity_unit, with: :validate_units

  validates :year_made, date_year: { allow_blank: false }
  validates :month_made, date_month: { allow_blank: false }
  validates :day_made, date_day: { allow_blank: false }

  protected

  def set_made
    write_attribute(:year_made, Time.now.year)
    write_attribute(:month_made, Time.now.month)
    write_attribute(:day_made, Time.now.day)
  end

  def validate_units
    begin
      RubyUnits::Unit.new(quantity_unit)
    rescue ArgumentError, 'Unit not recognized'
      errors.add(:quantity_unit, "'#{quantity_unit}' is an invalid quantity_unit")
    end
  end


end

#day_made ⇒ Integer

Returns 2 digit day the extract originated.

Returns:

  • (Integer) —

    2 digit day the extract originated



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# File 'app/models/extract.rb', line 36

class Extract < ApplicationRecord
  include Housekeeping
  include Shared::Identifiers
  include Shared::ProtocolRelationships
  include Shared::OriginRelationship
  include Shared::IsData

  is_origin_for 'Extract', 'Sequence'
  originates_from 'Extract', 'Specimen', 'Lot', 'RangedLot', 'Otu'

  has_many :sequences, through: :origin_relationships, source: :new_object, source_type: 'Sequence'

  validates_presence_of :quantity_value
  attr_accessor :is_made_now

  before_validation :set_made, if: -> {is_made_now}

  validates_presence_of :quantity_value
  validates_presence_of :quantity_unit

  validates :quantity_unit, with: :validate_units

  validates :year_made, date_year: { allow_blank: false }
  validates :month_made, date_month: { allow_blank: false }
  validates :day_made, date_day: { allow_blank: false }

  protected

  def set_made
    write_attribute(:year_made, Time.now.year)
    write_attribute(:month_made, Time.now.month)
    write_attribute(:day_made, Time.now.day)
  end

  def validate_units
    begin
      RubyUnits::Unit.new(quantity_unit)
    rescue ArgumentError, 'Unit not recognized'
      errors.add(:quantity_unit, "'#{quantity_unit}' is an invalid quantity_unit")
    end
  end


end

#is_made_now ⇒ Object

Returns the value of attribute is_made_now.



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# File 'app/models/extract.rb', line 49

def is_made_now
  @is_made_now
end

#month_made ⇒ Integer

Returns 2 digit month the extract originated.

Returns:

  • (Integer) —

    2 digit month the extract originated



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# File 'app/models/extract.rb', line 36

class Extract < ApplicationRecord
  include Housekeeping
  include Shared::Identifiers
  include Shared::ProtocolRelationships
  include Shared::OriginRelationship
  include Shared::IsData

  is_origin_for 'Extract', 'Sequence'
  originates_from 'Extract', 'Specimen', 'Lot', 'RangedLot', 'Otu'

  has_many :sequences, through: :origin_relationships, source: :new_object, source_type: 'Sequence'

  validates_presence_of :quantity_value
  attr_accessor :is_made_now

  before_validation :set_made, if: -> {is_made_now}

  validates_presence_of :quantity_value
  validates_presence_of :quantity_unit

  validates :quantity_unit, with: :validate_units

  validates :year_made, date_year: { allow_blank: false }
  validates :month_made, date_month: { allow_blank: false }
  validates :day_made, date_day: { allow_blank: false }

  protected

  def set_made
    write_attribute(:year_made, Time.now.year)
    write_attribute(:month_made, Time.now.month)
    write_attribute(:day_made, Time.now.day)
  end

  def validate_units
    begin
      RubyUnits::Unit.new(quantity_unit)
    rescue ArgumentError, 'Unit not recognized'
      errors.add(:quantity_unit, "'#{quantity_unit}' is an invalid quantity_unit")
    end
  end


end

#quantity_unit ⇒ Numeric

Returns # @Merfoo, define with David.

Returns:

  • (Numeric) —

    # @Merfoo, define with David



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# File 'app/models/extract.rb', line 36

class Extract < ApplicationRecord
  include Housekeeping
  include Shared::Identifiers
  include Shared::ProtocolRelationships
  include Shared::OriginRelationship
  include Shared::IsData

  is_origin_for 'Extract', 'Sequence'
  originates_from 'Extract', 'Specimen', 'Lot', 'RangedLot', 'Otu'

  has_many :sequences, through: :origin_relationships, source: :new_object, source_type: 'Sequence'

  validates_presence_of :quantity_value
  attr_accessor :is_made_now

  before_validation :set_made, if: -> {is_made_now}

  validates_presence_of :quantity_value
  validates_presence_of :quantity_unit

  validates :quantity_unit, with: :validate_units

  validates :year_made, date_year: { allow_blank: false }
  validates :month_made, date_month: { allow_blank: false }
  validates :day_made, date_day: { allow_blank: false }

  protected

  def set_made
    write_attribute(:year_made, Time.now.year)
    write_attribute(:month_made, Time.now.month)
    write_attribute(:day_made, Time.now.day)
  end

  def validate_units
    begin
      RubyUnits::Unit.new(quantity_unit)
    rescue ArgumentError, 'Unit not recognized'
      errors.add(:quantity_unit, "'#{quantity_unit}' is an invalid quantity_unit")
    end
  end


end

#quantity_value ⇒ Numeric

Returns # @Merfoo, define with David.

Returns:

  • (Numeric) —

    # @Merfoo, define with David



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# File 'app/models/extract.rb', line 36

class Extract < ApplicationRecord
  include Housekeeping
  include Shared::Identifiers
  include Shared::ProtocolRelationships
  include Shared::OriginRelationship
  include Shared::IsData

  is_origin_for 'Extract', 'Sequence'
  originates_from 'Extract', 'Specimen', 'Lot', 'RangedLot', 'Otu'

  has_many :sequences, through: :origin_relationships, source: :new_object, source_type: 'Sequence'

  validates_presence_of :quantity_value
  attr_accessor :is_made_now

  before_validation :set_made, if: -> {is_made_now}

  validates_presence_of :quantity_value
  validates_presence_of :quantity_unit

  validates :quantity_unit, with: :validate_units

  validates :year_made, date_year: { allow_blank: false }
  validates :month_made, date_month: { allow_blank: false }
  validates :day_made, date_day: { allow_blank: false }

  protected

  def set_made
    write_attribute(:year_made, Time.now.year)
    write_attribute(:month_made, Time.now.month)
    write_attribute(:day_made, Time.now.day)
  end

  def validate_units
    begin
      RubyUnits::Unit.new(quantity_unit)
    rescue ArgumentError, 'Unit not recognized'
      errors.add(:quantity_unit, "'#{quantity_unit}' is an invalid quantity_unit")
    end
  end


end

#verbatim_anatomical_origin ⇒ String

Returns proxy for a OriginRelationship to an AnatomicalClass.

Returns:

  • (String) —

    proxy for a OriginRelationship to an AnatomicalClass



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# File 'app/models/extract.rb', line 36

class Extract < ApplicationRecord
  include Housekeeping
  include Shared::Identifiers
  include Shared::ProtocolRelationships
  include Shared::OriginRelationship
  include Shared::IsData

  is_origin_for 'Extract', 'Sequence'
  originates_from 'Extract', 'Specimen', 'Lot', 'RangedLot', 'Otu'

  has_many :sequences, through: :origin_relationships, source: :new_object, source_type: 'Sequence'

  validates_presence_of :quantity_value
  attr_accessor :is_made_now

  before_validation :set_made, if: -> {is_made_now}

  validates_presence_of :quantity_value
  validates_presence_of :quantity_unit

  validates :quantity_unit, with: :validate_units

  validates :year_made, date_year: { allow_blank: false }
  validates :month_made, date_month: { allow_blank: false }
  validates :day_made, date_day: { allow_blank: false }

  protected

  def set_made
    write_attribute(:year_made, Time.now.year)
    write_attribute(:month_made, Time.now.month)
    write_attribute(:day_made, Time.now.day)
  end

  def validate_units
    begin
      RubyUnits::Unit.new(quantity_unit)
    rescue ArgumentError, 'Unit not recognized'
      errors.add(:quantity_unit, "'#{quantity_unit}' is an invalid quantity_unit")
    end
  end


end

#year_made ⇒ Integer

Returns 4 digit year the extract originated.

Returns:

  • (Integer) —

    4 digit year the extract originated



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# File 'app/models/extract.rb', line 36

class Extract < ApplicationRecord
  include Housekeeping
  include Shared::Identifiers
  include Shared::ProtocolRelationships
  include Shared::OriginRelationship
  include Shared::IsData

  is_origin_for 'Extract', 'Sequence'
  originates_from 'Extract', 'Specimen', 'Lot', 'RangedLot', 'Otu'

  has_many :sequences, through: :origin_relationships, source: :new_object, source_type: 'Sequence'

  validates_presence_of :quantity_value
  attr_accessor :is_made_now

  before_validation :set_made, if: -> {is_made_now}

  validates_presence_of :quantity_value
  validates_presence_of :quantity_unit

  validates :quantity_unit, with: :validate_units

  validates :year_made, date_year: { allow_blank: false }
  validates :month_made, date_month: { allow_blank: false }
  validates :day_made, date_day: { allow_blank: false }

  protected

  def set_made
    write_attribute(:year_made, Time.now.year)
    write_attribute(:month_made, Time.now.month)
    write_attribute(:day_made, Time.now.day)
  end

  def validate_units
    begin
      RubyUnits::Unit.new(quantity_unit)
    rescue ArgumentError, 'Unit not recognized'
      errors.add(:quantity_unit, "'#{quantity_unit}' is an invalid quantity_unit")
    end
  end


end

Instance Method Details

#set_made ⇒ Object (protected) 



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

def set_made
  write_attribute(:year_made, Time.now.year)
  write_attribute(:month_made, Time.now.month)
  write_attribute(:day_made, Time.now.day)
end

#validate_units ⇒ Object (protected) 



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# File 'app/models/extract.rb', line 70

def validate_units
  begin
    RubyUnits::Unit.new(quantity_unit)
  rescue ArgumentError, 'Unit not recognized'
    errors.add(:quantity_unit, "'#{quantity_unit}' is an invalid quantity_unit")
  end
end