Module: Briard::Readers::CrossrefReader

Included in:
MetadataUtils
Defined in:
lib/briard/readers/crossref_reader.rb

Instance Method Summary collapse

Instance Method Details

#crossref_alternate_identifiers(bibliographic_metadata) ⇒ Object 



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# File 'lib/briard/readers/crossref_reader.rb', line 239

def crossref_alternate_identifiers(bibliographic_metadata)
  if bibliographic_metadata.dig('publisher_item', 'item_number').present?
    Array.wrap(bibliographic_metadata.dig('publisher_item', 'item_number')).map do |item|
      if item.is_a?(String)
        { 'identifier' => item,
          'identifierType' => 'Publisher ID' }
      else
        { 'identifier' => item.fetch('__content__', nil),
          'identifierType' => item.fetch('item_number_type', nil) || 'Publisher ID' }
      end
    end
  elsif parse_attributes(bibliographic_metadata.fetch('item_number', nil)).present?
    [{ 'identifier' => parse_attributes(bibliographic_metadata.fetch('item_number', nil)),
       'identifierType' => parse_attributes(bibliographic_metadata.dig('item_number',
                                                                       'item_number_type')) || 'Publisher ID' }]
  elsif parse_attributes(bibliographic_metadata.fetch('isbn', nil)).present?
    [{ 'identifier' => parse_attributes(bibliographic_metadata.fetch('isbn', nil), first: true),
       'identifierType' => 'ISBN' }]
  else
    []
  end
end

#crossref_date_published(bibliographic_metadata) ⇒ Object 



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# File 'lib/briard/readers/crossref_reader.rb', line 373

def crossref_date_published(bibliographic_metadata)
  pub_date = Array.wrap(bibliographic_metadata.fetch('publication_date', nil)).presence ||
             Array.wrap(bibliographic_metadata.fetch('acceptance_date', nil))
  return unless pub_date.present?

  get_date_from_parts(pub_date.first['year'], pub_date.first['month'], pub_date.first['day'])
end

#crossref_description(bibliographic_metadata) ⇒ Object 



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# File 'lib/briard/readers/crossref_reader.rb', line 262

def crossref_description(bibliographic_metadata)
  abstract = Array.wrap(bibliographic_metadata['abstract']).map do |r|
    { 'descriptionType' => 'Abstract',
      'description' => sanitize(parse_attributes(r, content: 'p')) }.compact
  end

  description = Array.wrap(bibliographic_metadata['description']).map do |r|
    { 'descriptionType' => 'Other', 'description' => sanitize(parse_attributes(r)) }.compact
  end

  (abstract + description)
end

#crossref_funding_reference(program_metadata) ⇒ Object 



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# File 'lib/briard/readers/crossref_reader.rb', line 337

def crossref_funding_reference(program_metadata)
  fundref = Array.wrap(program_metadata).find { |a| a['name'] == 'fundref' } || {}
  Array.wrap(fundref.fetch('assertion', [])).select do |a|
    a['name'] == 'fundgroup' && a['assertion'].present?
  end.map do |f|
    funder_identifier = nil
    funder_identifier_type = nil
    funder_name = nil
    award_title = nil
    award_number = nil
    award_uri = nil

    Array.wrap(f.fetch('assertion')).each do |a|
      case a.fetch('name')
      when 'award_number'
        award_number = a.fetch('__content__', nil)
        award_uri = a.fetch('awardURI', nil)
      when 'funder_name'
        funder_name = a.fetch('__content__', nil).to_s.squish.presence
        funder_identifier = validate_funder_doi(a.dig('assertion', '__content__'))
        funder_identifier_type = 'Crossref Funder ID' if funder_identifier.present?
      end
    end

    # funder_name is required in DataCite
    next unless funder_name.present?

    { 'funderIdentifier' => funder_identifier,
      'funderIdentifierType' => funder_identifier_type,
      'funderName' => funder_name,
      'awardTitle' => award_title,
      'awardNumber' => award_number,
      'awardUri' => award_uri }.compact
  end.compact
end

#crossref_is_part_of(model_metadata) ⇒ Object 



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# File 'lib/briard/readers/crossref_reader.rb', line 381

def crossref_is_part_of(model_metadata)
  if model_metadata.present? && model_metadata.fetch('issn', nil).present?
    { 'relatedIdentifier' => normalize_issn(model_metadata.fetch('issn', nil)),
      'relationType' => 'IsPartOf',
      'relatedIdentifierType' => 'ISSN',
      'resourceTypeGeneral' => 'Collection' }.compact
  elsif model_metadata.present? && model_metadata.fetch('relatedIdentifier', nil).present?
    { 'relatedIdentifier' => model_metadata.fetch('relatedIdentifier', nil),
      'relationType' => 'IsPartOf',
      'relatedIdentifierType' => 'DOI' }.compact
  end
end

#crossref_license(program_metadata) ⇒ Object 



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# File 'lib/briard/readers/crossref_reader.rb', line 275

def crossref_license(program_metadata)
  access_indicator = Array.wrap(program_metadata).find { |m| m['name'] == 'AccessIndicators' }
  if access_indicator.present?
    Array.wrap(access_indicator['license_ref']).map do |license|
      hsh_to_spdx('rightsURI' => parse_attributes(license))
    end.uniq
  else
    []
  end
end

#crossref_people(bibliographic_metadata, contributor_role) ⇒ Object 



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# File 'lib/briard/readers/crossref_reader.rb', line 286

def crossref_people(bibliographic_metadata, contributor_role)
  person = bibliographic_metadata.dig('contributors',
                                      'person_name') || bibliographic_metadata['person_name']
  organization = Array.wrap(bibliographic_metadata.dig('contributors', 'organization'))
  if contributor_role == 'author' && Array.wrap(person).select do |a|
       a['contributor_role'] == 'author'
     end.blank? && Array.wrap(organization).select do |a|
                     a['contributor_role'] == 'author'
                   end.blank?
    person = [{ 'name' => ':(unav)', 'contributor_role' => 'author' }]
  end

  (Array.wrap(person) + Array.wrap(organization)).select do |a|
    a['contributor_role'] == contributor_role
  end.map do |a|
    name_identifiers = if normalize_orcid(parse_attributes(a['ORCID'])).present?
                         [{
                           'nameIdentifier' => normalize_orcid(parse_attributes(a['ORCID'])), 'nameIdentifierScheme' => 'ORCID', 'schemeUri' => 'https://orcid.org'
                         }]
                       end
    if a['surname'].present? || a['given_name'].present? || name_identifiers.present?
      given_name = parse_attributes(a['given_name'])
      family_name = parse_attributes(a['surname'])
      affiliation = Array.wrap(a['affiliation']).map do |a|
        if a.is_a?(Hash)
          a
        elsif a.is_a?(Hash) && a.key?('__content__') && a['__content__'].strip.blank?
          nil
        elsif a.is_a?(Hash) && a.key?('__content__')
          { 'name' => a['__content__'] }
        elsif a.strip.blank?
          nil
        elsif a.is_a?(String)
          { 'name' => a }
        end
      end.compact

      { 'nameType' => 'Personal',
        'nameIdentifiers' => name_identifiers,
        'name' => [family_name, given_name].compact.join(', '),
        'givenName' => given_name,
        'familyName' => family_name,
        'affiliation' => affiliation.presence,
        'contributorType' => contributor_role == 'editor' ? 'Editor' : nil }.compact
    else
      { 'nameType' => 'Organizational',
        'name' => a['name'] || a['__content__'] }
    end
  end
end

#crossref_references(bibliographic_metadata) ⇒ Object 



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# File 'lib/briard/readers/crossref_reader.rb', line 394

def crossref_references(bibliographic_metadata)
  refs = bibliographic_metadata.dig('citation_list', 'citation')
  Array.wrap(refs).select { |a| a['doi'].present? }.map do |c|
    next unless c['doi'].present?

    { 'relatedIdentifier' => parse_attributes(c['doi']).downcase,
      'relationType' => 'References',
      'relatedIdentifierType' => 'DOI' }.compact
  end.compact.unwrap
end

#get_crossref(id: nil, **_options) ⇒ Object

CrossRef types from api.crossref.org/types



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# File 'lib/briard/readers/crossref_reader.rb', line 7

def get_crossref(id: nil, **_options)
  return { 'string' => nil, 'state' => 'not_found' } unless id.present?

  doi = doi_from_url(id)
  url = "https://api.crossref.org/works/#{doi}/transform/application/vnd.crossref.unixsd+xml"
  response = Maremma.get(url, accept: 'text/xml;charset=utf-8', raw: true)
  string = response.body.fetch('data', nil)
  string = Nokogiri::XML(string, nil, 'UTF-8', &:noblanks).to_s if string.present?

  { 'string' => string }
end

#read_crossref(string: nil, **options) ⇒ Object 



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# File 'lib/briard/readers/crossref_reader.rb', line 19

def read_crossref(string: nil, **options)
  read_options = ActiveSupport::HashWithIndifferentAccess.new(options.except(:doi, :id, :url,
                                                                             :sandbox, :validate, :ra))

  if string.present?
    m = Maremma.from_xml(string).dig('crossref_result', 'query_result', 'body', 'query',
                                     'doi_record') || {}
    meta = m.dig('doi_record', 'crossref', 'error').nil? ? m : {}

    # query contains information from outside metadata schema, e.g. publisher name
    query = Maremma.from_xml(string).dig('crossref_result', 'query_result', 'body',
                                         'query') || {}
  else
    meta = {}
    query = {}
  end

  # model should be one of book, conference, database, dissertation, journal, peer_review, posted_content,
  # report_paper, sa_component, standard
  model = meta['crossref'].to_h.keys.last

  resource_type = nil
  bibliographic_metadata = {}
  program_metadata = {}
  journal_metadata = nil
  journal_issue = {}
  journal_metadata = nil
  publisher = query.dig('crm_item', 0)
  publisher = nil unless publisher.is_a?(String)

  case model
  when 'book'
    book_metadata = meta.dig('crossref', 'book', 'book_metadata')
    book_series_metadata = meta.dig('crossref', 'book', 'book_series_metadata')
    book_set_metadata = meta.dig('crossref', 'book', 'book_set_metadata')
    bibliographic_metadata = meta.dig('crossref', 'book',
                                      'content_item') || book_metadata || book_series_metadata || book_set_metadata
    resource_type = if bibliographic_metadata.fetch('component_type', nil)
                      "book-#{bibliographic_metadata.fetch('component_type')}"
                    else
                      'book'
                    end
    # publisher = if book_metadata.present?
    #               book_metadata.dig("publisher", "publisher_name")
    #             elsif book_series_metadata.present?
    #               book_series_metadata.dig("publisher", "publisher_name")
    #             end
  when 'conference'
    event_metadata = meta.dig('crossref', 'conference', 'event_metadata') || {}
    bibliographic_metadata = meta.dig('crossref', 'conference', 'conference_paper').to_h
  when 'journal'
    journal_metadata = meta.dig('crossref', 'journal', 'journal_metadata') || {}
    journal_issue = meta.dig('crossref', 'journal', 'journal_issue') || {}
    journal_article = meta.dig('crossref', 'journal', 'journal_article') || {}
    bibliographic_metadata = journal_article.presence || journal_issue.presence || journal_metadata
    program_metadata = bibliographic_metadata.dig('crossmark', 'custom_metadata',
                                                  'program') || bibliographic_metadata['program']
    resource_type = if journal_article.present?
                      'journal_article'
                    elsif journal_issue.present?
                      'journal_issue'
                    else
                      'journal'
                    end
  when 'posted_content'
    bibliographic_metadata = meta.dig('crossref', 'posted_content').to_h
    publisher ||= bibliographic_metadata.dig('institution', 'institution_name')
  when 'sa_component'
    bibliographic_metadata = meta.dig('crossref', 'sa_component', 'component_list',
                                      'component').to_h
    related_identifier = Array.wrap(query.to_h['crm_item']).find do |cr|
      cr['name'] == 'relation'
    end
    journal_metadata = { 'relatedIdentifier' => related_identifier.to_h.fetch('__content',
                                                                              nil) }
  when 'database'
    bibliographic_metadata = meta.dig('crossref', 'database', 'dataset').to_h
    resource_type = 'dataset'
  when 'report_paper'
    bibliographic_metadata = meta.dig('crossref', 'report_paper',
                                      'report_paper_metadata').to_h
    resource_type = 'report'
  when 'peer_review'
    bibliographic_metadata = meta.dig('crossref', 'peer_review')
  when 'dissertation'
    bibliographic_metadata = meta.dig('crossref', 'dissertation')
  end

  resource_type = (resource_type || model).to_s.underscore.camelcase.presence
  schema_org = Briard::Utils::CR_TO_SO_TRANSLATIONS[resource_type] || 'CreativeWork'
  types = {
    'resourceTypeGeneral' => Briard::Utils::CR_TO_DC_TRANSLATIONS[resource_type],
    'resourceType' => resource_type,
    'schemaOrg' => schema_org,
    'citeproc' => Briard::Utils::CR_TO_CP_TRANSLATIONS[resource_type] || 'article-journal',
    'bibtex' => Briard::Utils::CR_TO_BIB_TRANSLATIONS[resource_type] || 'misc',
    'ris' => Briard::Utils::CR_TO_RIS_TRANSLATIONS[resource_type] || 'GEN'
  }.compact

  titles = if bibliographic_metadata['titles'].present?
             Array.wrap(bibliographic_metadata['titles']).map do |r|
               if r.blank? || (r['title'].blank? && r['original_language_title'].blank?)
                 nil
               elsif r['title'].is_a?(String)
                 { 'title' => sanitize(r['title']) }
               elsif r['original_language_title'].present?
                 { 'title' => sanitize(r.dig('original_language_title', '__content__')),
                   'lang' => r.dig('original_language_title', 'language') }
               else
                 { 'title' => sanitize(r.dig('title', '__content__')) }.compact
               end
             end.compact
           else
             [{ 'title' => ':(unav)' }]
           end

  date_published = crossref_date_published(bibliographic_metadata)
  if date_published.present?
    date_published = { 'date' => date_published, 'dateType' => 'Issued' }
  else
    date_published = Array.wrap(query.to_h['crm_item']).find { |cr| cr['name'] == 'created' }
    if date_published.present?
      date_published = { 'date' => date_published.fetch('__content__', '')[0..9],
                         'dateType' => 'Issued' }
    end
  end
  date_updated = Array.wrap(query.to_h['crm_item']).find { |cr| cr['name'] == 'last-update' }
  if date_updated.present?
    date_updated = { 'date' => date_updated.fetch('__content__', nil),
                     'dateType' => 'Updated' }
  end

  date_registered = Array.wrap(query.to_h['crm_item']).find do |cr|
    cr['name'] == 'deposit-timestamp'
  end
  if date_registered.present?
    date_registered = get_datetime_from_time(date_registered.fetch('__content__', nil))
  end

  # check that date is valid iso8601 date
  date_published = nil unless Date.edtf(date_published.to_h['date']).present?
  date_updated = nil unless Date.edtf(date_updated.to_h['date']).present?

  dates = [date_published, date_updated].compact
  publication_year = date_published.to_h.fetch('date', '')[0..3].presence

  state = meta.present? || read_options.present? ? 'findable' : 'not_found'

  related_identifiers = Array.wrap(crossref_is_part_of(journal_metadata)) + Array.wrap(crossref_references(bibliographic_metadata))

  container = if journal_metadata.present?
                issn = normalize_issn(journal_metadata.to_h.fetch('issn', nil))

                { 'type' => 'Journal',
                  'identifier' => issn,
                  'identifierType' => issn.present? ? 'ISSN' : nil,
                  'title' => parse_attributes(journal_metadata.to_h['full_title']),
                  'volume' => parse_attributes(journal_issue.dig('journal_volume', 'volume')),
                  'issue' => parse_attributes(journal_issue['issue']),
                  'firstPage' => bibliographic_metadata.dig('pages',
                                                            'first_page') || parse_attributes(journal_article.to_h.dig('publisher_item', 'item_number'),
                                                                                              first: true),
                  'lastPage' => bibliographic_metadata.dig('pages', 'last_page') }.compact

              # By using book_metadata, we can account for where resource_type is `BookChapter` and not assume its a whole book
              elsif book_metadata.present?
                identifiers = crossref_alternate_identifiers(book_metadata)

                {
                  'type' => 'Book',
                  'title' => book_metadata.dig('titles', 'title'),
                  'firstPage' => bibliographic_metadata.dig('pages', 'first_page'),
                  'lastPage' => bibliographic_metadata.dig('pages', 'last_page'),
                  'identifiers' => identifiers
                }.compact

              elsif book_series_metadata.to_h.fetch('series_metadata', nil).present?
                issn = normalize_issn(book_series_metadata.dig('series_metadata', 'issn'))

                { 'type' => 'Book Series',
                  'identifier' => issn,
                  'identifierType' => issn.present? ? 'ISSN' : nil,
                  'title' => book_series_metadata.dig('series_metadata', 'titles', 'title'),
                  'volume' => bibliographic_metadata.fetch('volume', nil) }.compact
              end

  id = normalize_doi(options[:doi] || options[:id] || bibliographic_metadata.dig('doi_data',
                                                                                 'doi'))

  # Let sections override this in case of alternative metadata structures, such as book chapters, which
  # have their meta inside `content_item`, but the main book indentifers inside of `book_metadata`
  identifiers ||= crossref_alternate_identifiers(bibliographic_metadata)

  { 'id' => id,
    'types' => types,
    'doi' => doi_from_url(id),
    'url' => parse_attributes(bibliographic_metadata.dig('doi_data', 'resource'),
                              first: true),
    'titles' => titles,
    'identifiers' => identifiers,
    'creators' => crossref_people(bibliographic_metadata, 'author'),
    'contributors' => crossref_people(bibliographic_metadata, 'editor'),
    'funding_references' => crossref_funding_reference(program_metadata),
    'publisher' => publisher,
    'container' => container,
    'agency' => agency = options[:ra] || 'Crossref',
    'related_identifiers' => related_identifiers,
    'dates' => dates,
    'publication_year' => publication_year,
    'descriptions' => crossref_description(bibliographic_metadata),
    'rights_list' => crossref_license(program_metadata),
    'version_info' => nil,
    'subjects' => nil,
    'language' => nil,
    'sizes' => nil,
    'schema_version' => 'http://datacite.org/schema/kernel-4',
    'state' => state,
    'date_registered' => date_registered }.merge(read_options)
end