Module: Bolognese::Readers::CrossrefReader

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

Constant Summary collapse

CONTACT_EMAIL =

CrossRef types from api.crossref.org/types

"[email protected]"

Instance Method Summary collapse

Instance Method Details

#crossref_alternate_identifiers(bibliographic_metadata) ⇒ Object 



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# File 'lib/bolognese/readers/crossref_reader.rb', line 144

def crossref_alternate_identifiers(bibliographic_metadata)
  if bibliographic_metadata.dig("publisher_item", "item_number").present?
    { "identifier" => parse_attributes(bibliographic_metadata.dig("publisher_item", "item_number")),
      "identifierType" => "Publisher ID" }
  elsif parse_attributes(bibliographic_metadata.fetch("item_number", nil)).present?
    { "identifier" => parse_attributes(bibliographic_metadata.fetch("item_number", nil)),
      "identifierType" => "Publisher ID" }
  end
end

#crossref_date_published(bibliographic_metadata) ⇒ Object 



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# File 'lib/bolognese/readers/crossref_reader.rb', line 207

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))
  if pub_date.present?
    get_date_from_parts(pub_date.first["year"], pub_date.first["month"], pub_date.first["day"])
  else
    nil
  end
end

#crossref_description(bibliographic_metadata) ⇒ Object 



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# File 'lib/bolognese/readers/crossref_reader.rb', line 154

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

  description = Array.wrap(bibliographic_metadata.dig("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/bolognese/readers/crossref_reader.rb', line 190

def crossref_funding_reference(program_metadata)
  fundref = Array.wrap(program_metadata).find { |a| a["name"] == "fundref" } || {}
  Array.wrap(fundref.fetch("assertion", [])).select { |a| a["name"] == "fundgroup" }.map do |f|
    f = Array.wrap(f.fetch("assertion", nil)).first
    funder_identifier = normalize_id(f.dig("assertion", "__content__"))
    funder_identifier_type = funder_identifier.present? ?  "Crossref Funder ID" : nil
    award_title = f.fetch("awardTitle", nil).present? ? f.fetch("awardTitle") : nil

    { "funderIdentifier" => funder_identifier,
      "funderIdentifierType" => funder_identifier_type,
      "funderName" => f.fetch("__content__", nil).to_s.strip.presence,
      "awardTitle" => award_title,
      "awardNumber" => f.dig("awardNumber", "__content__"),
      "awardUri" => f.dig("awardNumber", "awardURI") }.compact
  end
end

#crossref_is_part_of(model_metadata) ⇒ Object 



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# File 'lib/bolognese/readers/crossref_reader.rb', line 217

def crossref_is_part_of(model_metadata)
  if model_metadata.present? && model_metadata.fetch("issn", nil).present?
    { "relatedIdentifier" => parse_attributes(model_metadata.fetch("issn", nil), first: true),
      "relationType" => "IsPartOf",
      "relatedIdentifierType" => "ISSN",
      "resourceTypeGeneral" => "Collection" }.compact
  else
    nil
  end
end

#crossref_license(program_metadata) ⇒ Object 



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# File 'lib/bolognese/readers/crossref_reader.rb', line 166

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|
      { "rightsUri" => normalize_url(parse_attributes(license)) }
    end.uniq
  else
    nil
  end
end

#crossref_people(bibliographic_metadata, contributor_role) ⇒ Object 



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# File 'lib/bolognese/readers/crossref_reader.rb', line 177

def crossref_people(bibliographic_metadata, contributor_role)
  person = bibliographic_metadata.dig("contributors", "person_name")
  Array.wrap(person).select { |a| a["contributor_role"] == contributor_role }.map do |a|
    name_identifiers = normalize_orcid(parse_attributes(a["ORCID"])).present? ? [{ "nameIdentifier" => normalize_orcid(parse_attributes(a["ORCID"])), "nameIdentifierScheme" => "ORCID" }] : nil
    { "nameType" => "Personal",
      "nameIdentifiers" => name_identifiers,
      "name" => [a["surname"], a["given_name"]].join(", "),
      "givenName" => a["given_name"],
      "familyName" => a["surname"],
      "contributorType" => contributor_role == "editor" ? "Editor" : nil }.compact
  end.unwrap
end

#crossref_references(bibliographic_metadata) ⇒ Object 



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# File 'lib/bolognese/readers/crossref_reader.rb', line 228

def crossref_references(bibliographic_metadata)
  refs = bibliographic_metadata.dig("citation_list", "citation")
  Array.wrap(refs).select { |a| a["doi"].present? }.map do |c|
    if c["doi"].present?
      { "relatedIdentifier" => parse_attributes(c["doi"]).downcase,
        "relationType" => "References",
        "relatedIdentifierType" => "DOI" }.compact
    else
      nil
    end
  end.compact.unwrap
end

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



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# File 'lib/bolognese/readers/crossref_reader.rb', line 10

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

  doi = doi_from_url(id)
  url = "http://www.crossref.org/openurl/?id=doi:#{doi}&noredirect=true&pid=#{CONTACT_EMAIL}&format=unixref"
  response = Maremma.get(url, accept: "text/xml", 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/bolognese/readers/crossref_reader.rb', line 22

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

  if string.present?
    m = Maremma.from_xml(string).dig("doi_records", "doi_record") || {}
    meta = m.dig("crossref", "error").nil? ? m : {}
  else
    meta = {}
  end

  # model should be one of book, conference, database, dissertation, journal, peer_review, posted_content,
  # report-paper, sa_component, standard
  model = meta.dig("crossref").to_h.keys.first

  resource_type = nil
  bibliographic_metadata = {}
  program_metadata = {}
  journal_metadata = nil
  journal_issue = {}
  publisher = "(:unav)"

  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").to_h
    resource_type = bibliographic_metadata.fetch("component_type", nil) ? "book-" + bibliographic_metadata.fetch("component_type") : "book"
    publisher = book_metadata.dig("publisher", "publisher_name")
  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") || {}
    bibliographic_metadata = meta.dig("crossref", "journal", "journal_article").to_h
    program_metadata = bibliographic_metadata.dig("crossmark", "custom_metadata", "program") || bibliographic_metadata.dig("program")
    journal_issue = meta.dig("crossref", "journal", "journal_issue") || {}
    journal_article = meta.dig("crossref", "journal", "journal_article") || {}

    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
  end

  resource_type = (resource_type || model).to_s.underscore.camelcase.presence
  schema_org = Bolognese::Utils::CR_TO_SO_TRANSLATIONS[resource_type] || "ScholarlyArticle"
  types = {
    "resourceTypeGeneral" => Bolognese::Utils::SO_TO_DC_TRANSLATIONS[schema_org],
    "resourceType" => resource_type,
    "schemaOrg" => schema_org,
    "citeproc" => Bolognese::Utils::CR_TO_CP_TRANSLATIONS[resource_type] || "article-journal",
    "bibtex" => Bolognese::Utils::CR_TO_BIB_TRANSLATIONS[resource_type] || "misc",
    "ris" => Bolognese::Utils::CR_TO_RIS_TRANSLATIONS[resource_type] || "JOUR"
  }.compact

  # Crossref servers run on Eastern Time
  Time.zone = 'Eastern Time (US & Canada)'
  dates = [
    { "date" => crossref_date_published(bibliographic_metadata),
      "dateType" => "Issued" },
    { "date" => Time.zone.parse(meta.fetch("timestamp", "2018-01-01")).utc.iso8601,
      "dateType" => "Updated" }
  ]
  publication_year = crossref_date_published(bibliographic_metadata).present? ? crossref_date_published(bibliographic_metadata)[0..3] : nil
  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? || book_metadata.present?
    issn = parse_attributes(journal_metadata.to_h.fetch("issn", nil), first: true)

    { "type" => "Journal",
      "identifier" => issn,
      "identifierType" => issn.present? ? "ISSN" : nil,
      "title" => journal_metadata.to_h["full_title"],
      "volume" => journal_issue.dig("journal_volume", "volume"),
      "issue" => journal_issue.dig("issue"),
      "firstPage" => bibliographic_metadata.dig("pages", "first_page"),
      "lastPage" => bibliographic_metadata.dig("pages", "last_page") }.compact
  else
    nil
  end

  identifiers = [{ "identifierType" => "DOI", "identifier" => normalize_doi(options[:doi] || options[:id] || bibliographic_metadata.dig("doi_data", "doi")) }, crossref_alternate_identifiers(bibliographic_metadata)].compact

  id = Array.wrap(identifiers).first.to_h.fetch("identifier", nil)
  doi = Array.wrap(identifiers).find { |r| r["identifierType"] == "DOI" }.to_h.fetch("identifier", nil)

  { "id" => id,
    "types" => types,
    "doi" => doi_from_url(doi),
    "url" => bibliographic_metadata.dig("doi_data", "resource"),
    "titles" => [{ "title" => parse_attributes(bibliographic_metadata.dig("titles", "title")) }],
    "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" => "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" => nil,
    "state" => state
  }.merge(read_options)
end