Class: Identifier::Global::GenBankAccessionCode

Inherits:
Identifier::Global show all
Defined in:
app/models/identifier/global/gen_bank_accession_code.rb

Overview

From NCBI-GenBank Flat File Release 220.0 at ftp.ncbi.nih.gov/genbank/gbrel.txt section 3.4.6 ACCESSION format There are 2 formats, one format with 1 upper case letter followed by 5 numbers and another format with 2 upper case letters followed by 6 numbers Format 1: A12345 Format 2: AB123456 For use with GenBank sequences

Constant Summary

Constants included from SoftValidation

SoftValidation::ANCESTORS_WITH_SOFT_VALIDATIONS

Constants included from Shared::DualAnnotator

Shared::DualAnnotator::ALWAYS_COMMUNITY

Instance Attribute Summary

Attributes inherited from Identifier::Global

#relation

Attributes inherited from Identifier

#cached, #cached_numeric_identifier, #identifier, #identifier_object_id, #namespace_id, #project_id, #type

Instance Method Summary collapse

Methods inherited from Identifier::Global

#build_cached, #is_global?, #permit_only_one_global_without_relation_supplied_per_type, #sv_resolves?

Methods included from SoftValidation

#clear_soft_validations, #fix_for, #fix_soft_validations, #soft_fixed?, #soft_valid?, #soft_validate, #soft_validated?, #soft_validations, #soft_validators

Methods inherited from Identifier

#build_cached, #build_cached_numeric_identifier, #is_global?, #is_local?, prototype_identifier, #set_cached, #type_name

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::Labels

#labeled?

Methods included from Housekeeping

#has_polymorphic_relationship?

Methods included from Shared::PolymorphicAnnotator

#annotated_object_is_persisted?

Methods inherited from ApplicationRecord

transaction_with_retry

Instance Method Details

#sequences_only ⇒ Object (private) 



31
32
33
 
# File 'app/models/identifier/global/gen_bank_accession_code.rb', line 31

def sequences_only
  errors.add(:identifier_object_type, 'is not a Sequence') if identifier_object_type != 'Sequence'
end

#valid_gen_bank_accession_code ⇒ Object 



13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
 
# File 'app/models/identifier/global/gen_bank_accession_code.rb', line 13

def valid_gen_bank_accession_code
  if identifier.present?
    matched = false

    if /\A[A-Z][A-Z][0-9]{6}\Z/.match(identifier)
      matched = true
    elsif /\A[A-Z][0-9]{5}\Z/.match(identifier)
      matched = true
    end

    if !matched
      errors.add(:identifier, 'invalid format')
    end
  end
end