Module: Bolognese::Readers::DataciteReader

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

Instance Method Summary collapse

Instance Method Details

#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:#{doi}",
             fl: "doi,url,xml,state,allocator_symbol,datacentre_symbol,media,minted,updated",
             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,
    "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 51

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")
  resource_type = meta.dig("resourceType", "__content__")
  schema_org = Bolognese::Utils::CR_TO_SO_TRANSLATIONS[resource_type.to_s.underscore.camelcase] || Bolognese::Utils::DC_TO_SO_TRANSLATIONS[resource_type_general.to_s.dasherize] || "CreativeWork"
  types = {
    "resourceTypeGeneral" => resource_type_general,
    "resourceType" => resource_type,
    "schemaOrg" => schema_org,
    "citeproc" => Bolognese::Utils::CR_TO_CP_TRANSLATIONS[resource_type.to_s.underscore.camelcase] || Bolognese::Utils::SO_TO_CP_TRANSLATIONS[schema_org] || "article",
    "bibtex" => Bolognese::Utils::CR_TO_BIB_TRANSLATIONS[resource_type.to_s.underscore.camelcase] || Bolognese::Utils::SO_TO_BIB_TRANSLATIONS[schema_org] || "misc",
    "ris" => Bolognese::Utils::CR_TO_RIS_TRANSLATIONS[resource_type.to_s.underscore.camelcase] || Bolognese::Utils::DC_TO_RIS_TRANSLATIONS[resource_type_general.to_s.dasherize] || "GEN"
  }.compact
  
  titles = Array.wrap(meta.dig("titles", "title")).map do |r|
    if r.is_a?(String)
      { "title" => sanitize(r) }
    else
      { "title" => sanitize(r["__content__"]), "titleType" => r["titleType"], "lang" => r["lang"] }.compact
    end
  end

  alternate_identifiers = Array.wrap(meta.dig("alternateIdentifiers", "alternateIdentifier")).map do |r|
    { "alternateIdentifierType" => r["alternateIdentifierType"], "alternateIdentifier" => r["__content__"] }
  end
  descriptions = Array.wrap(meta.dig("descriptions", "description")).select { |r| r["descriptionType"] != "SeriesInformation" }.map do |r|
    { "description" => sanitize(r["__content__"]), "descriptionType" => r["descriptionType"], "lang" => r["lang"] }.compact
  end
  rights_list = Array.wrap(meta.dig("rightsList", "rights")).map do |r|
    { "rights" => r["__content__"], "rightsUri" => normalize_url(r["rightsURI"]), "lang" => r["lang"] }.compact
  end
  subjects = Array.wrap(meta.dig("subjects", "subject")).map do |k|
    if k.nil?
      nil
    elsif k.is_a?(String)
      { "subject" => sanitize(k) }
    else
      { "subject" => sanitize(k["__content__"]), "subjectScheme" => k["subjectScheme"], "schemeUri" => k["schemeURI"], "valueUri" => k["valueURI"], "lang" => k["lang"] }.compact
    end
  end.compact
  dates = Array.wrap(meta.dig("dates", "date")).map do |d|
    {
      "date" => parse_attributes(d),
      "dateType" => parse_attributes(d, content: "dateType"),
      "dateInformation" => parse_attributes(d, content: "dateInformation")
    }.compact
  end
  dates << { "date" => meta.fetch("publicationYear", nil), "dateType" => "Issued" } if meta.fetch("publicationYear", nil).present? && get_date(dates, "Issued").blank?
  sizes = Array.wrap(meta.dig("sizes", "size"))
  formats = Array.wrap(meta.dig("formats", "format"))
  funding_references = Array.wrap(meta.dig("fundingReferences", "fundingReference")).compact.map do |fr|
    {
      "funderName" => fr["funderName"],
      "funderIdentifier" => normalize_id(parse_attributes(fr["funderIdentifier"])),
      "funderIdentifierType" => parse_attributes(fr["funderIdentifier"], content: "funderIdentifierType"),
      "awardNumber" => parse_attributes(fr["awardNumber"]),
      "awardUri" => parse_attributes(fr["awardNumber"], content: "awardURI"),
      "awardTitle" => fr["awardTitle"] }.compact
  end
  related_identifiers = Array.wrap(meta.dig("relatedIdentifiers", "relatedIdentifier")).map do |ri|
    if ri["relatedIdentifierType"] == "DOI"
      rid = ri["__content__"].to_s.downcase
    else
      rid = ri["__content__"]
    end

    { 
      "relatedIdentifier" => rid,
      "relatedIdentifierType" => ri["relatedIdentifierType"],
      "relationType" => ri["relationType"],
      "resourceTypeGeneral" => ri["resourceTypeGeneral"],
      "relatedMetadataScheme" => ri["relatedMetadataScheme"],
      "schemeUri" => ri["schemeURI"],
      "schemeType" => ri["schemeType"]
    }.compact
  end
  geo_locations = Array.wrap(meta.dig("geoLocations", "geoLocation")).map do |gl|
    if gl["geoLocationPoint"].is_a?(String) || gl["geoLocationBox"].is_a?(String)
      nil
    else
      {
        "geoLocationPoint" => {
          "pointLatitude" => gl.dig("geoLocationPoint", "pointLatitude"),
          "pointLongitude" => gl.dig("geoLocationPoint", "pointLongitude")
        }.compact.presence,
        "geoLocationBox" => {
          "westBoundLongitude" => gl.dig("geoLocationBox", "westBoundLongitude"),
          "eastBoundLongitude" => gl.dig("geoLocationBox", "eastBoundLongitude"),
          "southBoundLatitude" => gl.dig("geoLocationBox", "southBoundLatitude"),
          "northBoundLatitude" => gl.dig("geoLocationBox", "northBoundLatitude")
        }.compact.presence,
        "geoLocationPlace" => gl["geoLocationPlace"],
      }.compact
    end
  end
  periodical = set_periodical(meta)
  state = doi.present? ? "findable" : "not_found"

  { "id" => id,
    "types" => types,
    "doi" => doi,
    "alternate_identifiers" => alternate_identifiers,
    "url" => options.fetch(:url, nil),
    "titles" => titles,
    "creator" => get_authors(Array.wrap(meta.dig("creators", "creator"))),
    "contributor" => get_authors(Array.wrap(meta.dig("contributors", "contributor"))),
    "periodical" => periodical,
    "publisher" => meta.fetch("publisher", "").strip.presence,
    "source" => "DataCite",
    "funding_references" => funding_references,
    "dates" => dates,
    "publication_year" => meta.fetch("publicationYear", nil),
    "descriptions" => descriptions,
    "rights_list" => rights_list,
    "version" => meta.fetch("version", nil),
    "subjects" => subjects,
    "language" => meta.fetch("language", nil),
    "geo_locations" => geo_locations,
    "related_identifiers" => related_identifiers,
    "formats" => formats,
    "sizes" => sizes,
    "schema_version" => schema_version,
    "state" => state
  }
end

#set_periodical(meta) ⇒ Object 



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# File 'lib/bolognese/readers/datacite_reader.rb', line 199

def set_periodical(meta)
  container_title = Array.wrap(meta.dig("descriptions", "description")).find { |r| r["descriptionType"] == "SeriesInformation" }.to_h.fetch("__content__", nil)
  is_part_of = Array.wrap(meta.dig("relatedIdentifiers", "relatedIdentifier")).find { |ri| ri["relationType"] == "IsPartOf" }.to_h

  if container_title.present? || is_part_of.present?
    {
      "type" => meta.dig("resourceType", "resourceTypeGeneral") == "Dataset" ? "DataCatalog" : "Periodical",
      "id" => is_part_of["relatedIdentifierType"] == "DOI" ? normalize_doi(is_part_of["__content__"]) : is_part_of["__content__"],
      "title" => container_title,
      "issn" => is_part_of["relatedIdentifierType"] == "ISSN" ? is_part_of["__content__"] : nil
    }.compact
  end
end