# frozen_string_literal: true module Bolognese module Readers module DataciteReader 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 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__") type = 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 = { "type" => type, "resource_type_general" => resource_type_general, "resource_type" => resource_type, "citeproc" => Bolognese::Utils::CR_TO_CP_TRANSLATIONS[resource_type.to_s.underscore.camelcase] || Bolognese::Utils::SO_TO_CP_TRANSLATIONS[type] || "article", "bibtex" => Bolognese::Utils::CR_TO_BIB_TRANSLATIONS[resource_type.to_s.underscore.camelcase] || Bolognese::Utils::SO_TO_BIB_TRANSLATIONS[type] || "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 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 alternate_identifiers = 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 rights = 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")).map do |d| { "date" => parse_attributes(d), "date_type" => parse_attributes(d, content: "dateType") } end dates << { "date" => meta.fetch("publicationYear", nil), "date_type" => "Issued" } if meta.fetch("publicationYear", nil).present? && get_date(dates, "Issued").blank? sizes = Array.wrap(meta.dig("sizes", "size")).unwrap formats = Array.wrap(meta.dig("formats", "format")).unwrap funding_references = Array.wrap(meta.dig("fundingReferences", "fundingReference")).compact.map do |fr| { "funder_name" => fr["funderName"], "funder_identifier" => normalize_id(parse_attributes(fr["funderIdentifier"])), "funder_identifier_type" => parse_attributes(fr["funderIdentifier"], content: "funderIdentifierType"), "award_number" => parse_attributes(fr["awardNumber"]), "award_uri" => parse_attributes(fr["awardNumber"], content: "awardURI"), "award_title" => fr["awardTitle"] }.compact end related_identifiers = Array.wrap(meta.dig("relatedIdentifiers", "relatedIdentifier")).map do |ri| if ri["relatedIdentifierType"] == "DOI" rid = ri["__content__"].downcase else rid = ri["__content__"] end { "id" => rid, "related_identifier_type" => ri["relatedIdentifierType"], "relation_type" => ri["relationType"], "resource_type_general" => ri["resourceTypeGeneral"] }.compact end geo_location = Array.wrap(meta.dig("geoLocations", "geoLocation")).map do |gl| if gl["geoLocationPoint"].is_a?(String) || gl["geoLocationBox"].is_a?(String) nil else { "geo_location_place" => gl["geoLocationPlace"], "geo_location_point" => { "point_latitude" => gl.dig("geoLocationPoint", "pointLatitude"), "point_longitude" => gl.dig("geoLocationPoint", "pointLongitude") }.compact.presence, "geo_location_box" => { "west_bound_longitude" => gl.dig("geoLocationBox", "westBoundLongitude"), "east_bound_longitude" => gl.dig("geoLocationBox", "eastBoundLongitude"), "south_bound_latitude" => gl.dig("geoLocationBox", "southBoundLatitude"), "north_bound_latitude" => gl.dig("geoLocationBox", "northBoundLatitude") }.compact.presence }.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), "title" => title, "creator" => get_authors(Array.wrap(meta.dig("creators", "creator"))), "periodical" => periodical, "publisher" => meta.fetch("publisher", "").strip.presence, "service_provider" => "DataCite", "funding_references" => funding_references, "dates" => dates, "publication_year" => meta.fetch("publicationYear", nil), "description" => description, "rights" => rights, "version" => meta.fetch("version", nil), "keywords" => keywords, "language" => meta.fetch("language", nil), "geo_location" => geo_location, "related_identifiers" => related_identifiers, "formats" => formats, "size" => sizes, "schema_version" => schema_version, "state" => state } end 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 def datacite_funding_reference(meta) Array.wrap(meta.dig("fundingReferences", "fundingReference")).compact.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 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 end end end