Class: CollectionObject::BiologicalCollectionObject

Inherits:
CollectionObject
  • Object
show all
Includes:
DwcExtensions, Shared::IsDwcOccurrence
Defined in:
app/models/collection_object/biological_collection_object.rb

Overview

A collection object that is classified as being biological in origin.

!! See also CollectionObject::BiologicalExtensions

Direct Known Subclasses

Lot, RangedLot, Specimen

Constant Summary

Constants included from Shared::IsDwcOccurrence

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

Instance Method Summary collapse

Methods included from Shared::IsDwcOccurrence

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

Instance Method Details

#current_taxon_determination=(taxon_determination) ⇒ Object 



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# File 'app/models/collection_object/biological_collection_object.rb', line 51

def current_taxon_determination=(taxon_determination)
  if taxon_determinations.include?(taxon_determination)
    taxon_determination.move_to_top
  end
end

#reorder_determinations_by(attribute = :date) ⇒ Boolean

Returns nil values are sent to the bottom.

Returns:

  • (Boolean) —

    nil values are sent to the bottom



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# File 'app/models/collection_object/biological_collection_object.rb', line 59

def reorder_determinations_by(attribute = :date)
  determinations = []
  if attribute == :date
    determinations = taxon_determinations.sort{|a, b| (b.sort_date || Time.utc(1, 1))  <=> (a.sort_date || Time.utc(1,1)) }
  else
    determinations = taxon_determinations.order(attribute)
  end

  begin
    TaxonDetermination.transaction do
      determinations.each_with_index do |td, i|
        td.update_column(:position, i + 1)
      end
    end
  rescue
    return false
  end
  return true
end

#sv_determined_before_collected ⇒ Object (protected) 



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# File 'app/models/collection_object/biological_collection_object.rb', line 93

def sv_determined_before_collected
  ce = collecting_event
  return true if ce.nil? || ce.start_date_year.nil?
  #ce_date = ce.start_date_year.to_s + '/' + sprintf( '%02d', ce.start_date_month.to_i) + "/" + sprintf( '%02d', ce.start_date_day.to_i)
  #ce_date = ce.end_date_year.to_s + '/' + sprintf( '%02d', ce.end_date_month.to_i) + "/" + sprintf( '%02d', ce.end_date_day.to_i) unless ce.end_date_year.nil?
  ce_date = Utilities::Dates.nomenclature_date(ce.start_date_day, ce.start_date_month, ce.start_date_year)
  ce_date = Utilities::Dates.nomenclature_date(ce.end_date_day, ce.end_date_month, ce.end_date_year) unless ce.end_date_year.nil?
  taxon_determinations.each do |d|
    next if d.year_made.nil?
    #d_date = d.year_made.to_s + '/' + sprintf( '%02d', d.month_made.to_i) + "/" + sprintf( '%02d', d.day_made.to_i)
    d_date = Utilities::Dates.nomenclature_date(d.day_made, d.month_made, d.year_made)
    soft_validations.add(:base, 'Determination is preceding the collecting date') if d_date < ce_date
  end
end

#sv_fix_missing_determination ⇒ Object (protected) 



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# File 'app/models/collection_object/biological_collection_object.rb', line 85

def sv_fix_missing_determination
  if !taxon_determinations.any? && type_materials.any?
    tn = type_materials.first.protonym_id
    otu = Otu.find_or_create_by(taxon_name_id: tn, name: nil).try(:id)
    td = taxon_determinations.create(otu_id: otu) unless otu.nil?
  end
end

#sv_missing_biocuration_classification ⇒ Object (protected) 



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# File 'app/models/collection_object/biological_collection_object.rb', line 120

def sv_missing_biocuration_classification
  soft_validations.add(:repository_id, 'Biocuration is not specified') if !biocuration_classifications.any?
end

#sv_missing_collecting_event ⇒ Object (protected) 



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# File 'app/models/collection_object/biological_collection_object.rb', line 108

def sv_missing_collecting_event
  soft_validations.add(:collecting_event_id, 'Collecting event is not selected') if collecting_event_id.nil?
end

#sv_missing_determination ⇒ Object (protected) 



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# File 'app/models/collection_object/biological_collection_object.rb', line 81

def sv_missing_determination
  soft_validations.add(:base, 'Determination is missing', success_message: 'Determination was added', failure_message: 'The determination was not added') if !taxon_determinations.any?
end

#sv_missing_preparation_type ⇒ Object (protected) 



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# File 'app/models/collection_object/biological_collection_object.rb', line 112

def sv_missing_preparation_type
  soft_validations.add(:preparation_type_id, 'Preparation type is not selected') if preparation_type_id.nil?
end

#sv_missing_repository ⇒ Object (protected) 



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# File 'app/models/collection_object/biological_collection_object.rb', line 116

def sv_missing_repository
  soft_validations.add(:repository_id, 'Repository is not selected') if repository_id.nil?
end