Class: BatchLoad::Import::TaxonNames::NomenInterpreter

Inherits:
BatchLoad::Import show all
Defined in:
lib/batch_load/import/taxon_names/nomen_interpreter.rb

Constant Summary collapse

SAVE_ORDER = 
[:original_taxon_name, :taxon_name, :taxon_name_relationship, :otu]

Instance Attribute Summary collapse

Attributes inherited from BatchLoad::Import

#create_attempted, #csv, #errors, #file, #file_errors, #import_level, #processed, #processed_rows, #project, #successful_rows, #total_data_lines, #total_lines, #user, #user_header_map, #user_id

Instance Method Summary collapse

Methods inherited from BatchLoad::Import

#all_objects, #create, #create_attempted?, #import_level_ok?, #line_strict_level_ok?, #processed?, #ready_to_create?, #save_order, #sorted_processed_rows, #strict_level_ok?, #total_records_created, #user_map, #valid?, #valid_objects, #warn_level_ok?

Constructor Details

#initialize(nomenclature_code: nil, parent_taxon_name_id: nil, also_create_otu: false, **args) ⇒ NomenInterpreter

Returns a new instance of NomenInterpreter.

Parameters:

  • args (Hash) 


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# File 'lib/batch_load/import/taxon_names/nomen_interpreter.rb', line 23

def initialize(nomenclature_code: nil, parent_taxon_name_id: nil, also_create_otu: false, **args)
  @nomenclature_code = nomenclature_code.presence
  @parent_taxon_name_id = parent_taxon_name_id.presence
  @also_create_otu = also_create_otu.presence

  super(**args)
end

Instance Attribute Details

#also_create_otu ⇒ Object

Whether to create an OTU as well

Returns:

  • Boolean



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# File 'lib/batch_load/import/taxon_names/nomen_interpreter.rb', line 15

def also_create_otu
  @also_create_otu
end

#base_taxon_name_id ⇒ Object

The default parent if otherwise not provided



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# File 'lib/batch_load/import/taxon_names/nomen_interpreter.rb', line 8

def base_taxon_name_id
  @base_taxon_name_id
end

#nomenclature_code ⇒ Object

The code (Rank Class) that new names will use. Required.



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# File 'lib/batch_load/import/taxon_names/nomen_interpreter.rb', line 11

def nomenclature_code
  @nomenclature_code
end

#parent_taxon_name_id ⇒ Object

The id of the parent taxon name, computed automatically as Root if not provided



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# File 'lib/batch_load/import/taxon_names/nomen_interpreter.rb', line 5

def parent_taxon_name_id
  @parent_taxon_name_id
end

#project_id ⇒ Object

Required to handle some defaults



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# File 'lib/batch_load/import/taxon_names/nomen_interpreter.rb', line 18

def project_id
  @project_id
end

Instance Method Details

#build ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/batch_load/import/taxon_names/nomen_interpreter.rb', line 201

def build
  if valid?
    build_taxon_names
    @processed = true
  end
end

#build_taxon_names ⇒ Integer

rubocop:disable Metrics/MethodLength

Returns:

  • (Integer) 


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# File 'lib/batch_load/import/taxon_names/nomen_interpreter.rb', line 50

def build_taxon_names
  @total_data_lines = 0
  i = 0
  taxon_names = {}

  csv.each_with_index do |row, i|

    parse_result = BatchLoad::RowParse.new
    parse_result.row_number = i # check vs. header etc.

    parse_result.objects[:original_taxon_name] = []
    parse_result.objects[:taxon_name] = []
    parse_result.objects[:taxon_name_relationship] = []
    parse_result.objects[:otu] = []

    @processed_rows[i] = parse_result

    begin
      next if ['complex', 'species group', 'series', 'variety', 'unidentified'].include?(row['rank'])

      rank = Ranks.lookup(@nomenclature_code.to_sym, row['rank'])

      parse_result.parse_errors.push 'Unknown rank.' if rank.blank?

      protonym_attributes = {
        name: row['taxon_name'],
        year_of_publication: year_of_publication(row['author_year']),
        rank_class: rank,
        by: user,
        project:,
        verbatim_author: verbatim_author(row['author_year']),

        # People are not created at this point
        #  taxon_name_authors_attributes: taxon_name_authors_attributes(verbatim_author(row['author_year']))
      }

      # Not implemented

      # if row['original_name']
      #   original_protonym_attributes = {
      #     verbatim_name: row['original_name'],
      #     name: row['original_name'].split(' ')[-1],
      #     year_of_publication: year_of_publication(row['author_year']),
      #     rank_class: Ranks.lookup(@nomenclature_code.to_sym, row['original_rank']),
      #     parent: parent_taxon_name,
      #     by: user,
      #     project:,
      #     verbatim_author: verbatim_author(row['author_year']),
      #     taxon_name_authors_attributes: taxon_name_authors_attributes(verbatim_author(row['author_year']))
      #   }

      #   original_protonym = Protonym.new(original_protonym_attributes)

      #   if row['original_rank'] == 'genus'
      #     protonym_attributes[:original_genus] = original_protonym
      #   elsif row['original_rank'] == 'subgenus'
      #     protonym_attributes[:original_subgenus] = original_protonym
      #   elsif row['original_rank'] == 'species'
      #     protonym_attributes[:original_species] = original_protonym
      #   elsif row['original_rank'] == 'subspecies'
      #     protonym_attributes[:original_subspecies] = original_protonym
      #   end

      #   parse_result.objects[:original_taxon_name].push original_protonym
      # end

      p = Protonym.new(protonym_attributes)

      # row data
      taxon_name_id = row['id']
      parent_id = row['parent_id']

      taxon_names[taxon_name_id] = p

      if parent_id.blank?
        p.parent_id = parent_taxon_name_id
      else
        if taxon_names[parent_id]
          p.parent = taxon_names[parent_id]
        else
          parse_result.parse_errors.push 'Parent ID is not defined at this point! Row out of order?'
        end
      end

      # TaxonNameRelationship
      related_name_id = row['related_name_id']

      if taxon_names[related_name_id].present?
        related_name_nomen_class = nil

        begin
          related_name_nomen_class = row['related_name_nomen_class'].safe_constantize

          if related_name_nomen_class.ancestors.include?(TaxonNameRelationship)

            taxon_name_relationship = related_name_nomen_class.new(
              subject_taxon_name: p, object_taxon_name: taxon_names[related_name_id]
            )

            parse_result.objects[:taxon_name_relationship].push taxon_name_relationship
          end
        rescue NameError
          parse_result.parse_errors.push 'Unknown taxon name relationship'
        end
      end

      # TaxonNameClassification

      # TODO: add to index, not here
      if name_nomen_classification = row['name_nomen_classification']
        begin
          if c = name_nomen_classification.safe_constantize
            p.taxon_name_classifications_attributes = [ {type: name_nomen_classification} ]
          end
        rescue NameError
          parse_result.parse_errors.push 'Unknown taxon name classification'
        end
      end

      # There is an OTU linked to the taxon name.
      if row['taxon_concept_name'].present? || row['guid'].present?
        taxon_concept_identifier_nomen = {}

        if row['guid'].present?
          taxon_concept_identifier_nomen = {
            type: 'Identifier::Global::Uri',
            identifier: row['guid'] }
        end

        otu = Otu.new(name: row['taxon_concept_name'], taxon_name: p, identifiers_attributes: [taxon_concept_identifier_nomen] )

        parse_result.objects[:otu].push(otu)
      else

        # Note we are not technically using the param like TaxonName.new(), so we can't just set the attribute
        # So we hack in the OTUs 'manually".  This also lets us see them in the result
        if also_create_otu
          parse_result.objects[:otu].push Otu.new(taxon_name: p)
        end
      end

      parse_result.objects[:taxon_name].push p
      @total_data_lines += 1 if p.present?
    end
  end

  @total_lines = i
end

#root_taxon_name ⇒ String

Returns:

  • (String) 


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# File 'lib/batch_load/import/taxon_names/nomen_interpreter.rb', line 41

def root_taxon_name
  Project.find(@project_id).root_taxon_name
end

#verbatim_author(author_year) ⇒ String? (private)

TODO: unify parsing to somewhere else

Parameters:

  • author_year (String)

Returns:

  • (String, nil) —

    just the author name, wiht parens left on



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# File 'lib/batch_load/import/taxon_names/nomen_interpreter.rb', line 220

def verbatim_author(author_year)
  return nil if author_year.blank?
  author_year.gsub(/\,+\s*\d\d\d\d/, '')
end

#year_of_publication(author_year) ⇒ String? (private)

Parameters:

  • author_year (String)

Returns:

  • (String, nil) 


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# File 'lib/batch_load/import/taxon_names/nomen_interpreter.rb', line 212

def year_of_publication(author_year)
  return nil if author_year.blank?
  author_year&.match(/\d\d\d\d/)&.to_s
end