Module: Bolognese::Readers::CrossrefReader

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

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 211

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" => "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/bolognese/readers/crossref_reader.rb', line 329

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 233

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 294

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" && a["assertion"].present? }.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|
      if a.fetch("name") == "award_number"
        award_number = a.fetch("__content__", nil)
        award_uri = a.fetch("awardURI", nil)
      elsif a.fetch("name") == "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
    if funder_name.present?
      { "funderIdentifier" => funder_identifier,
        "funderIdentifierType" => funder_identifier_type,
        "funderName" => funder_name,
        "awardTitle" => award_title,
        "awardNumber" => award_number,
        "awardUri" => award_uri }.compact
    else
      nil
    end
  end.compact
end

#crossref_is_part_of(model_metadata) ⇒ Object 



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# File 'lib/bolognese/readers/crossref_reader.rb', line 339

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
  else
    nil
  end
end

#crossref_license(program_metadata) ⇒ Object 



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# File 'lib/bolognese/readers/crossref_reader.rb', line 245

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/bolognese/readers/crossref_reader.rb', line 256

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

  (Array.wrap(person) + Array.wrap(organization)).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", "schemeUri"=>"https://orcid.org" }] : nil
    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.key?("__content__") && a["__content__"].strip.blank?
          nil
        elsif a.is_a?(Hash) && a.key?("__content__")
          { "name" => a["__content__"] }
        elsif a.is_a?(Hash)
          a
        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/bolognese/readers/crossref_reader.rb', line 354

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

CrossRef types from api.crossref.org/types



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# File 'lib/bolognese/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", 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 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.dig("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 = bibliographic_metadata.fetch("component_type", nil) ? "book-" + bibliographic_metadata.fetch("component_type") : "book"
    # 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.dig("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 { |cr| cr["name"] == "relation" }
    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 = Bolognese::Utils::CR_TO_SO_TRANSLATIONS[resource_type] || "ScholarlyArticle"
  types = {
    "resourceTypeGeneral" => Bolognese::Utils::CR_TO_DC_TRANSLATIONS[resource_type],
    "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

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

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

  # 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.dig("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" => nil,
    "state" => state,
    "date_registered" => date_registered
  }.merge(read_options)
end