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, 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 { "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) } end def read_datacite(string: nil, **options) meta = Maremma.from_xml(string).to_h.fetch("resource", {}) schema_version = meta.fetch("xmlns", nil) # 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["xml: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_name = Array.wrap(meta.dig("alternateIdentifiers", "alternateIdentifier")).map do |r| { "type" => r["alternateIdentifierType"], "name" => r["__content__"] }.compact 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")) 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, "url" => options.fetch(:url, nil), "title" => title, "alternate_name" => alternate_name, "author" => get_authors(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, "Copyrightes"), "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_size" => meta.fetch("size", nil), "schema_version" => schema_version, "state" => state } end def datacite_date(dates, date_type) dd = dates.find { |d| d["dateType"] == date_type } || {} dd.fetch("__content__", nil) end 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 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 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 def datacite_is_identical_to(meta) datacite_related_identifier(meta, relation_type: "IsIdenticalTo") end def datacite_is_part_of(meta) datacite_related_identifier(meta, relation_type: "IsPartOf") end def datacite_has_part(meta) datacite_related_identifier(meta, relation_type: "HasPart") end def datacite_is_previous_version_of(meta) datacite_related_identifier(meta, relation_type: "IsPreviousVersionOf") end def datacite_is_new_version_of(meta) datacite_related_identifier(meta, relation_type: "IsNewVersionOf") end def datacite_is_variant_form_of(meta) datacite_related_identifier(meta, relation_type: "IsVariantFormOf") end def datacite_is_original_form_of(meta) datacite_related_identifier(meta, relation_type: "IsOriginalFormOf") end def datacite_references(meta) datacite_related_identifier(meta, relation_type: "References Cites").presence end def datacite_is_referenced_by(meta) datacite_related_identifier(meta, relation_type: "IsCitedBy IsReferencedBy").presence end def datacite_is_supplement_to(meta) datacite_related_identifier(meta, relation_type: "IsSupplementTo") end def datacite_is_supplemented_by(meta) datacite_related_identifier(meta, relation_type: "isSupplementedBy") end def datacite_reviews(meta) datacite_related_identifier(meta, relation_type: "Reviews").presence end def datacite_is_reviewed_by(meta) datacite_related_identifier(meta, relation_type: "IsReviewedBy").presence end end end end