Module: Bolognese::Readers::DataciteReader

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

Instance Method Summary collapse

Instance Method Details

#datacite_date(dates, date_type) ⇒ Object 



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# File 'lib/bolognese/readers/datacite_reader.rb', line 160

def datacite_date(dates, date_type)
  dd = dates.find { |d| d["dateType"] == date_type } || {}
  dd.fetch("__content__", nil)
end

#datacite_funder_contributor(meta) ⇒ Object 



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# File 'lib/bolognese/readers/datacite_reader.rb', line 183

def datacite_funder_contributor(meta)
  Array.wrap(meta.dig("contributors", "contributor")).reduce([]) do |sum, f|
    if f["contributorType"] == "Funder"
      # handle special case of OpenAIRE metadata
      id = f.dig("nameIdentifier", "__content__").to_s.start_with?("info:eu-repo/grantAgreement/EC") ? "https://doi.org/10.13039/501100000780" : nil

      funder = { "type" => "Organization",
                 "id" => id,
                 "name" => f["contributorName"] }.compact
      if f.dig("nameIdentifier", "nameIdentifierScheme") == "info"
        sum << { "type" => "Award",
                 "identifier" => f.dig("nameIdentifier", "__content__").split("/").last,
                 "funder" => funder }
      else
        sum << funder
      end
    else
      sum
    end
  end
end

#datacite_funding_reference(meta) ⇒ Object 



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# File 'lib/bolognese/readers/datacite_reader.rb', line 165

def datacite_funding_reference(meta)
  Array.wrap(meta.dig("fundingReferences", "fundingReference")).map do |f|
    funder_id = parse_attributes(f["funderIdentifier"])
    funder = { "type" => "Organization",
               "id" => normalize_id(funder_id),
               "name" => f["funderName"] }.compact
    if f["awardNumber"].present? || f["awardTitle"].present?
      { "type" => "Award",
        "name" => f.fetch("awardTitle", nil),
        "identifier" => f["awardNumber"].is_a?(Hash) ? f.dig("awardNumber", "__content__") : f["awardNumber"],
        "url" => f["awardNumber"].is_a?(Hash) ? f.dig("awardNumber", "awardURI") : nil,
        "funder" => funder }.compact
    else
      funder
    end
  end.uniq
end

#datacite_has_part(meta) ⇒ Object 



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# File 'lib/bolognese/readers/datacite_reader.rb', line 220

def datacite_has_part(meta)
  datacite_related_identifier(meta, relation_type: "HasPart")
end

#datacite_is_identical_to(meta) ⇒ Object 



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# File 'lib/bolognese/readers/datacite_reader.rb', line 212

def datacite_is_identical_to(meta)
  datacite_related_identifier(meta, relation_type: "IsIdenticalTo")
end

#datacite_is_new_version_of(meta) ⇒ Object 



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

def datacite_is_new_version_of(meta)
  datacite_related_identifier(meta, relation_type: "IsNewVersionOf")
end

#datacite_is_original_form_of(meta) ⇒ Object 



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# File 'lib/bolognese/readers/datacite_reader.rb', line 236

def datacite_is_original_form_of(meta)
  datacite_related_identifier(meta, relation_type: "IsOriginalFormOf")
end

#datacite_is_part_of(meta) ⇒ Object 



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# File 'lib/bolognese/readers/datacite_reader.rb', line 216

def datacite_is_part_of(meta)
  datacite_related_identifier(meta, relation_type: "IsPartOf")
end

#datacite_is_previous_version_of(meta) ⇒ Object 



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# File 'lib/bolognese/readers/datacite_reader.rb', line 224

def datacite_is_previous_version_of(meta)
  datacite_related_identifier(meta, relation_type: "IsPreviousVersionOf")
end

#datacite_is_referenced_by(meta) ⇒ Object 



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# File 'lib/bolognese/readers/datacite_reader.rb', line 244

def datacite_is_referenced_by(meta)
  datacite_related_identifier(meta, relation_type: "IsCitedBy IsReferencedBy").presence
end

#datacite_is_reviewed_by(meta) ⇒ Object 



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# File 'lib/bolognese/readers/datacite_reader.rb', line 260

def datacite_is_reviewed_by(meta)
  datacite_related_identifier(meta, relation_type: "IsReviewedBy").presence
end

#datacite_is_supplement_to(meta) ⇒ Object 



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# File 'lib/bolognese/readers/datacite_reader.rb', line 248

def datacite_is_supplement_to(meta)
  datacite_related_identifier(meta, relation_type: "IsSupplementTo")
end

#datacite_is_supplemented_by(meta) ⇒ Object 



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# File 'lib/bolognese/readers/datacite_reader.rb', line 252

def datacite_is_supplemented_by(meta)
  datacite_related_identifier(meta, relation_type: "isSupplementedBy")
end

#datacite_is_variant_form_of(meta) ⇒ Object 



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# File 'lib/bolognese/readers/datacite_reader.rb', line 232

def datacite_is_variant_form_of(meta)
  datacite_related_identifier(meta, relation_type: "IsVariantFormOf")
end

#datacite_references(meta) ⇒ Object 



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# File 'lib/bolognese/readers/datacite_reader.rb', line 240

def datacite_references(meta)
  datacite_related_identifier(meta, relation_type: "References Cites").presence
end

#datacite_related_identifier(meta, relation_type: nil) ⇒ Object 



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# File 'lib/bolognese/readers/datacite_reader.rb', line 205

def datacite_related_identifier(meta, relation_type: nil)
  arr = Array.wrap(meta.dig("relatedIdentifiers", "relatedIdentifier")).select { |r| %w(DOI URL).include?(r["relatedIdentifierType"]) }
  arr = arr.select { |r| relation_type.split(" ").include?(r["relationType"]) } if relation_type.present?

  arr.map { |work| { "type" => "CreativeWork", "id" => normalize_id(work["__content__"]) } }.unwrap
end

#datacite_reviews(meta) ⇒ Object 



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# File 'lib/bolognese/readers/datacite_reader.rb', line 256

def datacite_reviews(meta)
  datacite_related_identifier(meta, relation_type: "Reviews").presence
end

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



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# File 'lib/bolognese/readers/datacite_reader.rb', line 6

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

  search_url = doi_search(id, options)
  doi = doi_from_url(id)
  params = { q: doi,
             fl: "doi,url,xml,state,allocator_symbol,datacentre_symbol,media,minted,updated",
             defType: "edismax",
             wt: "json" }
  search_url += "?" + URI.encode_www_form(params)

  response = Maremma.get search_url
  attributes = response.body.dig("data", "response", "docs").first
  return { "string" => nil, "state" => "not_found" } unless attributes.present?

  string = attributes.fetch('xml', nil)
  string = Base64.decode64(string) if string.present?

  if string.present?
    doc = Nokogiri::XML(string, nil, 'UTF-8', &:noblanks)

    # remove leading and trailing whitespace in text nodes
    doc.xpath("//text()").each do |node|
      if node.content =~ /\S/
        node.content = node.content.strip
      else
        node.remove
      end
    end
    string = doc.to_xml(:indent => 2)
  end

  content_url = Array.wrap(attributes.fetch("media", nil)).map do |media|
    media.split(":", 2).last
  end.compact

  { "string" => string,
    "b_url" => attributes.fetch("url", nil),
    "state" => attributes.fetch("state", nil),
    "date_registered" => attributes.fetch("minted", nil),
    "date_updated" => attributes.fetch("updated", nil),
    "provider_id" => attributes.fetch("allocator_symbol", nil),
    "client_id" => attributes.fetch("datacentre_symbol", nil),
    "content_url" => content_url }
end

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



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# File 'lib/bolognese/readers/datacite_reader.rb', line 52

def read_datacite(string: nil, **options)
  doc = Nokogiri::XML(string, nil, 'UTF-8', &:noblanks)
  ns = doc.collect_namespaces.find { |k, v| v.start_with?("http://datacite.org/schema/kernel") }
  schema_version = Array.wrap(ns).last || "http://datacite.org/schema/kernel-4"
  doc.remove_namespaces!
  string = doc.to_xml(:indent => 2)
  
  meta = Maremma.from_xml(string).to_h.fetch("resource", {})

  # validate only when option is set, as this step is expensive and
  # not needed if XML comes from DataCite MDS
  if options[:validate]
    errors = datacite_errors(xml: string, schema_version: schema_version)
    return { "errors" => errors } if errors.present?
  end

  if options[:doi]
    id = normalize_doi(options[:doi], sandbox: options[:sandbox])
  else
    id = normalize_doi(meta.dig("identifier", "__content__") || options[:id], sandbox: options[:sandbox])
  end

  doi = doi_from_url(id)
  resource_type_general = meta.dig("resourceType", "resourceTypeGeneral")
  additional_type = meta.fetch("resourceType", {}).fetch("__content__", nil)
  type = Bolognese::Utils::CR_TO_SO_TRANSLATIONS[additional_type.to_s.underscore.camelcase] || Bolognese::Utils::DC_TO_SO_TRANSLATIONS[resource_type_general.to_s.dasherize] || "CreativeWork"
  title = Array.wrap(meta.dig("titles", "title")).map do |r|
    if r.is_a?(String)
      sanitize(r)
    else
      { "title_type" => r["titleType"], "lang" => r["lang"], "text" => sanitize(r["__content__"]) }.compact
    end
  end.unwrap

  container_title = Array.wrap(meta.dig("descriptions", "description")).find { |r| r["descriptionType"] == "SeriesInformation" }.to_h.fetch("__content__", nil)

  alternate_identifier = Array.wrap(meta.dig("alternateIdentifiers", "alternateIdentifier")).map do |r|
    { "type" => r["alternateIdentifierType"], "name" => r["__content__"] }
  end.unwrap
  description = Array.wrap(meta.dig("descriptions", "description")).select { |r| r["descriptionType"] != "SeriesInformation" }.map do |r|
    { "type" => r["descriptionType"], "text" => sanitize(r["__content__"]) }.compact
  end.unwrap
  license = Array.wrap(meta.dig("rightsList", "rights")).map do |r|
    { "id" => normalize_url(r["rightsURI"]), "name" => r["__content__"] }.compact
  end.unwrap
  keywords = Array.wrap(meta.dig("subjects", "subject")).map do |k|
    if k.nil?
      nil
    elsif k.is_a?(String)
      sanitize(k)
    else
      { "subject_scheme" => k["subjectScheme"], "scheme_uri" => k["schemeURI"], "text" => sanitize(k["__content__"]) }.compact
    end
  end.compact
  dates = Array.wrap(meta.dig("dates", "date"))
  sizes = Array.wrap(meta.dig("sizes", "size")).unwrap
  formats = Array.wrap(meta.dig("formats", "format")).unwrap
  funding = begin
    f = datacite_funder_contributor(meta) + datacite_funding_reference(meta)
    f.length > 1 ? f : f.first
  end
  state = doi.present? ? "findable" : "not_found"

  { "id" => id,
    "type" => type,
    "additional_type" => additional_type,
    "citeproc_type" => Bolognese::Utils::CR_TO_CP_TRANSLATIONS[additional_type.to_s.underscore.camelcase] || Bolognese::Utils::SO_TO_CP_TRANSLATIONS[type] || "article",
    "bibtex_type" => Bolognese::Utils::CR_TO_BIB_TRANSLATIONS[additional_type.to_s.underscore.camelcase] || Bolognese::Utils::SO_TO_BIB_TRANSLATIONS[type] || "misc",
    "ris_type" => Bolognese::Utils::CR_TO_RIS_TRANSLATIONS[additional_type.to_s.underscore.camelcase] || Bolognese::Utils::DC_TO_RIS_TRANSLATIONS[resource_type_general.to_s.dasherize] || "GEN",
    "resource_type_general" => resource_type_general,
    "doi" => doi,
    "alternate_identifier" => alternate_identifier,
    "url" => options.fetch(:url, nil),
    "title" => title,
    "author" => get_authors(Array.wrap(meta.dig("creators", "creator"))),
    "editor" => get_authors(Array.wrap(meta.dig("contributors", "contributor")).select { |r| r["contributorType"] == "Editor" }),
    "container_title" => container_title,
    "publisher" => meta.fetch("publisher", nil),
    "service_provider" => "DataCite",
    "funding" => funding,
    "is_identical_to" => datacite_is_identical_to(meta),
    "is_part_of" => datacite_is_part_of(meta),
    "has_part" => datacite_has_part(meta),
    "references" => datacite_references(meta),
    "is_referenced_by" => datacite_is_referenced_by(meta),
    "is_supplement_to" => datacite_is_supplement_to(meta),
    "is_supplemented_by" => datacite_is_supplemented_by(meta),
    "date_created" => datacite_date(dates, "Created"),
    "date_accepted" => datacite_date(dates, "Accepted"),
    "date_available" => datacite_date(dates, "Available"),
    "date_copyrighted" => datacite_date(dates, "Copyrights"),
    "date_collected" => datacite_date(dates, "Collected"),
    "date_submitted" => datacite_date(dates, "Submitted"),
    "date_valid" => datacite_date(dates, "Valid"),
    "date_published" => datacite_date(dates, "Issued") || meta.fetch("publicationYear", nil),
    "date_modified" => datacite_date(dates, "Updated"),
    "description" => description,
    "license" => license,
    "b_version" => meta.fetch("version", nil),
    "keywords" => keywords,
    "language" => meta.fetch("language", nil),
    "content_format" => formats,
    "content_size" => sizes,
    "schema_version" => schema_version,
    "state" => state
  }
end