Contents

class GenomerPluginValidate::Validator::BadProductField < Genomer::Plugin
  include GenomerPluginValidate::Validator

  ERROR = "Bad product field for '%s:' "

  def run
    [
      hypothetical_products,
      domain_related_like_ending_products,
      nterm_products,
      all_caps_products
    ].flatten
  end

  def products_matching(re)
    annotations_by_attribute("product").
      map{|(product,entries)| entries.map{|i| [i.id,product]}}.
      flatten(1).
      map{|(id,product)| [id, re.match(product)]}.
      select{|(_,match)| match}.
      map{|(id,match)| [id,match.to_a[1].downcase]}
  end

  def hypothetical_products
    products_matching(/^([Hh]ypothetical)(?! protein)/).
      map{|i| (ERROR + "start with 'putative' instead of '%s.'") % i}
  end

  def domain_related_like_ending_products
    products_matching(/([Dd]omain|[Rr]elated|[Ll]ike).?$/).
      map{|i| (ERROR + "products ending with '%s' are not allowed.") % i}
  end

  def nterm_products
    products_matching(/(?!\B)([Nn][-\s][Tt]erm(inal)?)/).
      map{|i| (ERROR + "'N-terminal' or variations are not allowed.") % i}
  end

  def all_caps_products
    products_matching(/^([A-Z\s-]+)$/).
      map(&:first).
      map{|i| (ERROR + "all caps product fields are not allowed.") % i}
  end

end

Version data entries

2 entries across 2 versions & 1 rubygems

Version	Path
genomer-plugin-validate-0.0.2	lib/genomer-plugin-validate/validator/bad_product_field.rb
genomer-plugin-validate-0.0.1	lib/genomer-plugin-validate/validator/bad_product_field.rb