Class: Autoselect::TaxonName::CatalogueOfLifeCreator

Inherits:
Object
  • Object
show all
Defined in:
lib/autoselect/taxon_name/catalogue_of_life_creator.rb

Overview

Creates TaxonName records (and CoL URI identifiers) from a Catalog of Life selection.

Receives an ordered list of rows (distal → proximal, i.e. kingdom first, target last). Each row represents one name to be created or an existing TaxonName to be used as a parent. Rows with a taxonworks_id are already in the project; if the row immediately above them was just inserted (a rank CoL reports that TaxonWorks' real chain skipped), the existing record is reparented onto it. Otherwise it's used as-is as a parent anchor and left untouched, and it must already be under the row above it - if not, the rows don't describe TaxonWorks' real lineage and the request is refused.

Defined Under Namespace

Classes: CreationError

Instance Method Summary collapse

Constructor Details

#initialize(rows:, project_id:, user_id:, col_code: nil) ⇒ CatalogueOfLifeCreator

Returns a new instance of CatalogueOfLifeCreator.



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# File 'lib/autoselect/taxon_name/catalogue_of_life_creator.rb', line 49

def initialize(rows:, project_id:, user_id:, col_code: nil)
  @rows = rows
  @project_id = project_id.to_i
  @user_id = user_id.to_i
  @col_code = col_code.to_s.downcase.presence
end

Instance Method Details

#call ⇒ Hash

Returns { taxon_name_id: Integer, created_ids: Array }.

Returns:

  • (Hash) —

    { taxon_name_id: Integer, created_ids: Array }

Raises:

  • (CreationError) —

    if any record fails validation; the transaction is fully rolled back.



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# File 'lib/autoselect/taxon_name/catalogue_of_life_creator.rb', line 59

def call
  parent_id = project_root_id
  # Whether parent_id is a row created in this call (a skipped
  # unknown-rank row leaves it as it was).
  parent_created = false
  created_ids = []

  matched_ids = @rows.filter_map { |row|
    row[:taxonworks_id].presence&.to_i
  }
  current_parent_ids = ::TaxonName
    .where(id: matched_ids, project_id: @project_id)
    .pluck(:id, :parent_id).to_h

  unknown_ids = matched_ids - current_parent_ids.keys
  if unknown_ids.any?
    raise CreationError.new("Unknown TaxonName id(s) for this project: #{unknown_ids.join(', ')}")
  end

  refuse_non_accepted()
  # An ancestor at a rank TaxonWorks doesn't have is skipped below, but
  # the target can't be: the result is whatever was created last, so
  # skipping it would hand back its parent as the record.
  refuse_unknown_target_rank()

  ::ActiveRecord::Base.transaction do
    @rows.each do |row|
      if row[:taxonworks_id].present?
        existing_id = row[:taxonworks_id].to_i

        if current_parent_ids[existing_id] != parent_id
          existing = ::TaxonName.where(project_id: @project_id).find(existing_id)

          # Only a row just created directly above (a rank CoL reports
          # that TaxonWorks' real chain skipped) reattaches this existing
          # record. Any other mismatch means the rows don't describe
          # TaxonWorks' real lineage (a stale modal, a hand-made
          # request) - refuse rather than move a curated record.
          if !parent_created
            raise CreationError.new(
              "#{existing.cached} isn't under the record above it in " \
                'this request; the classification may have changed - ' \
                'reopen and try again.',
              col_name: row[:col_name],
              col_id: row[:col_id]
            )
          end

          begin
            existing.update!(parent_id:)
          rescue ::ActiveRecord::RecordInvalid => e
            raise CreationError.new(
              "Reparenting #{existing.cached}: #{e.record.errors.full_messages.join(', ')}",
              col_name: row[:col_name],
              col_id: row[:col_id]
            )
          end
        end

        parent_id = existing_id
        parent_created = false
        next
      end

      rank_class = resolve_rank_class(row[:col_rank])

      # Skip rows whose rank is entirely unknown to TaxonWorks — we cannot
      # create a valid Protonym without a rank_class (e.g. CoL-only ranks
      # like 'domain').
      next if rank_class.nil?

      author, year = ::Vendor::Colrapi::NameTranslation
        .split_authorship(row[:col_authorship], row[:col_year])

      begin
        tn = ::TaxonName.create!(
          type: 'Protonym',
          name: ::Vendor::Colrapi::NameTranslation
            .protonym_name(row[:col_name], row[:col_rank]),
          parent_id:,
          rank_class:,
          verbatim_author: author,
          year_of_publication: year,
          project_id: @project_id,
          by: @user_id,
        )
      rescue ::ActiveRecord::RecordInvalid => e
        raise CreationError.new(
          e.record.errors.full_messages.join(', '),
          col_name: row[:col_name],
          col_id: row[:col_id]
        )
      end

      create_col_identifier(tn, row) if row[:col_id].present?

      created_ids << tn.id
      parent_id = tn.id
      parent_created = true
    end
  end

  { taxon_name_id: parent_id, created_ids: }
end

#create_col_identifier(taxon_name, row) ⇒ Object (private)

Records the CoL taxon id as a ChecklistBank URI identifier on the freshly-created name.



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# File 'lib/autoselect/taxon_name/catalogue_of_life_creator.rb', line 173

def create_col_identifier(taxon_name, row)
  ::Identifier::Global::Uri::ChecklistBank.create!(
    taxon_id: row[:col_id],
    dataset_id: row[:dataset_id],
    identifier_object: taxon_name,
    project_id: @project_id,
    by: @user_id
  )
rescue ::ActiveRecord::RecordInvalid => e
  raise CreationError.new(
    "CoL identifier for #{row[:col_name]}: " \
      "#{e.record.errors.full_messages.join(', ')}",
    col_name: row[:col_name],
    col_id: row[:col_id]
  )
end

#project_root_id ⇒ Object (private)

Returns the TaxonName id of the project's Root node.



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# File 'lib/autoselect/taxon_name/catalogue_of_life_creator.rb', line 167

def project_root_id
  ::Project.find(@project_id).root_taxon_name.id
end

#refuse_non_accepted ⇒ Object (private)

CoL gives a non-accepted name (synonym, misapplied, ...) only its accepted name's classification, nothing of its own, so there's no sound place to create it. The modal already disables Create for it; this is the server-side guard. A row with a taxonworks_id isn't created, so an existing name is still used.

Raises:



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# File 'lib/autoselect/taxon_name/catalogue_of_life_creator.rb', line 195

def refuse_non_accepted
  row = @rows.find do |r|
    r[:taxonworks_id].blank? && r[:col_status].present? &&
      !::Vendor::Colrapi::COL_ACCEPTED_STATUSES
        .include?(r[:col_status].to_s.downcase)
  end
  return if row.nil?

  raise CreationError.new(
    "#{row[:col_name]} is a #{row[:col_status]} in Catalogue of Life, " \
      "which has no classification of its own for it - it can't be " \
      'created from here.',
    col_name: row[:col_name],
    col_id: row[:col_id]
  )
end

#refuse_unknown_target_rank ⇒ Object (private)

Raises:



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# File 'lib/autoselect/taxon_name/catalogue_of_life_creator.rb', line 212

def refuse_unknown_target_rank
  target = @rows.last
  return if target.nil? || target[:taxonworks_id].present?
  return if resolve_rank_class(target[:col_rank])

  raise CreationError.new(
    "Rank #{target[:col_rank]} isn't a TaxonWorks rank - " \
      "#{target[:col_name]} can't be created.",
    col_name: target[:col_name],
    col_id: target[:col_id]
  )
end

#resolve_rank_class(rank_string) ⇒ Object (private)

Maps a human-readable CoL rank string to a TaxonWorks rank_class string. Returns nil for unknown ranks.



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# File 'lib/autoselect/taxon_name/catalogue_of_life_creator.rb', line 227

def resolve_rank_class(rank_string)
  ::Vendor::Colrapi.rank_class_for(rank_string, col_code: @col_code)
end