Module: Bolognese::Utils

Included in:
CLI, Metadata, Orcid
Defined in:
lib/bolognese/utils.rb

Constant Summary collapse

LICENSE_NAMES = 
{
  "http://creativecommons.org/publicdomain/zero/1.0/" => "Public Domain (CC0 1.0)",
  "http://creativecommons.org/licenses/by/3.0/" => "Creative Commons Attribution 3.0 (CC-BY 3.0)",
  "http://creativecommons.org/licenses/by/4.0/" => "Creative Commons Attribution 4.0 (CC-BY 4.0)",
  "http://creativecommons.org/licenses/by-nc/4.0/" => "Creative Commons Attribution Noncommercial 4.0 (CC-BY-NC 4.0)",
  "http://creativecommons.org/licenses/by-sa/4.0/" => "Creative Commons Attribution Share Alike 4.0 (CC-BY-SA 4.0)",
  "http://creativecommons.org/licenses/by-nc-nd/4.0/" => "Creative Commons Attribution Noncommercial No Derivatives 4.0 (CC-BY-NC-ND 4.0)"
}
DC_TO_SO_TRANSLATIONS = 
{
  "Audiovisual" => "MediaObject",
  "Collection" => "Collection",
  "Dataset" => "Dataset",
  "Event" => "Event",
  "Image" => "ImageObject",
  "InteractiveResource" => nil,
  "Model" => nil,
  "PhysicalObject" => nil,
  "Service" => "Service",
  "Software" => "SoftwareSourceCode",
  "Sound" => "AudioObject",
  "Text" => "ScholarlyArticle",
  "Workflow" => nil,
  "Other" => "CreativeWork"
}
DC_TO_CP_TRANSLATIONS = 
{
  "Audiovisual" => "motion_picture",
  "Collection" => nil,
  "Dataset" => "dataset",
  "Event" => nil,
  "Image" => "graphic",
  "InteractiveResource" => nil,
  "Model" => nil,
  "PhysicalObject" => nil,
  "Service" => nil,
  "Sound" => "song",
  "Text" => "report",
  "Workflow" => nil,
  "Other" => nil
}
CR_TO_CP_TRANSLATIONS = 
{
  "Proceedings" => nil,
  "ReferenceBook" => nil,
  "JournalIssue" => nil,
  "ProceedingsArticle" => "paper-conference",
  "Other" => nil,
  "Dissertation" => "thesis",
  "Dataset" => "dataset",
  "EditedBook" => "book",
  "JournalArticle" => "article-journal",
  "Journal" => nil,
  "Report" => "report",
  "BookSeries" => nil,
  "ReportSeries" => nil,
  "BookTrack" => nil,
  "Standard" => nil,
  "BookSection" => "chapter",
  "BookPart" => nil,
  "Book" => "book",
  "BookChapter" => "chapter",
  "StandardSeries" => nil,
  "Monograph" => "book",
  "Component" => nil,
  "ReferenceEntry" => "entry-dictionary",
  "JournalVolume" => nil,
  "BookSet" => nil
}
CR_TO_JATS_TRANSLATIONS = 
{
  "Proceedings" => "working-paper",
  "ReferenceBook" => "book",
  "JournalIssue" => "journal",
  "ProceedingsArticle" => "working-paper",
  "Other" => nil,
  "Dissertation" => nil,
  "Dataset" => "data",
  "EditedBook" => "book",
  "JournalArticle" => "journal",
  "Journal" => "journal",
  "Report" => "report",
  "BookSeries" => "book",
  "ReportSeries" => "report",
  "BookTrack" => "book",
  "Standard" => "standard",
  "BookSection" => "chapter",
  "BookPart" => "chapter",
  "Book" => "book",
  "BookChapter" => "chapter",
  "StandardSeries" => "standard",
  "Monograph" => "book",
  "Component" => nil,
  "ReferenceEntry" => nil,
  "JournalVolume" => "journal",
  "BookSet" => "book"
}
SO_TO_DC_TRANSLATIONS = 
{
  "Article" => "Text",
  "AudioObject" => "Sound",
  "Blog" => "Text",
  "BlogPosting" => "Text",
  "Chapter" => "Text",
  "Collection" => "Collection",
  "CreativeWork" => "Other",
  "DataCatalog" => "Dataset",
  "Dataset" => "Dataset",
  "Event" => "Event",
  "ImageObject" => "Image",
  "Movie" => "Audiovisual",
  "PublicationIssue" => "Text",
  "ScholarlyArticle" => "Text",
  "Service" => "Service",
  "SoftwareSourceCode" => "Software",
  "VideoObject" => "Audiovisual",
  "WebPage" => "Text",
  "WebSite" => "Text"
}
SO_TO_JATS_TRANSLATIONS = 
{
  "Article" => "journal",
  "AudioObject" => nil,
  "Blog" => nil,
  "BlogPosting" => nil,
  "Book" => "book",
  "Collection" => nil,
  "CreativeWork" => nil,
  "DataCatalog" => "data",
  "Dataset" => "data",
  "Event" => nil,
  "ImageObject" => nil,
  "Movie" => nil,
  "PublicationIssue" => "journal",
  "ScholarlyArticle" => "journal",
  "Service" => nil,
  "SoftwareSourceCode" => "software",
  "VideoObject" => nil,
  "WebPage" => nil,
  "WebSite" => "website"
}
SO_TO_CP_TRANSLATIONS = 
{
  "Article" => "",
  "AudioObject" => "song",
  "Blog" => "report",
  "BlogPosting" => "post-weblog",
  "Collection" => nil,
  "CreativeWork" => nil,
  "DataCatalog" => "dataset",
  "Dataset" => "dataset",
  "Event" => nil,
  "ImageObject" => "graphic",
  "Movie" => "motion_picture",
  "PublicationIssue" => nil,
  "ScholarlyArticle" => "article-journal",
  "Service" => nil,
  "VideoObject" => "broadcast",
  "WebPage" => "webpage",
  "WebSite" => "webpage"
}
SO_TO_RIS_TRANSLATIONS = 
{
  "Article" => nil,
  "AudioObject" => nil,
  "Blog" => nil,
  "BlogPosting" => "BLOG",
  "Collection" => nil,
  "CreativeWork" => "GEN",
  "DataCatalog" => "CTLG",
  "Dataset" => "DATA",
  "Event" => nil,
  "ImageObject" => "FIGURE",
  "Movie" => "MPCT",
  "PublicationIssue" => nil,
  "ScholarlyArticle" => "JOUR",
  "Service" => nil,
  "SoftwareSourceCode" => "COMP",
  "VideoObject" => "VIDEO",
  "WebPage" => "ELEC",
  "WebSite" => nil
}
CR_TO_RIS_TRANSLATIONS = 
{
  "Proceedings" => "CONF",
  "ReferenceBook" => "BOOK",
  "JournalIssue" => nil,
  "ProceedingsArticle" => "CPAPER",
  "Other" => "GEN",
  "Dissertation" => "THES",
  "Dataset" => "DATA",
  "EditedBook" => "BOOK",
  "JournalArticle" => "JOUR",
  "Journal" => nil,
  "Report" => nil,
  "BookSeries" => nil,
  "ReportSeries" => nil,
  "BookTrack" => nil,
  "Standard" => nil,
  "BookSection" => "CHAP",
  "BookPart" => "CHAP",
  "Book" => "BOOK",
  "BookChapter" => "CHAP",
  "StandardSeries" => nil,
  "Monograph" => "BOOK",
  "Component" => nil,
  "ReferenceEntry" => "DICT",
  "JournalVolume" => nil,
  "BookSet" => nil
}
DC_TO_RIS_TRANSLATIONS = 
{
  "Audiovisual" => "MPCT",
  "Collection" => nil,
  "Dataset" => "DATA",
  "Event" => nil,
  "Image" => "FIGURE",
  "InteractiveResource" => nil,
  "Model" => nil,
  "PhysicalObject" => nil,
  "Service" => nil,
  "Software" => "COMP",
  "Sound" => "SOUND",
  "Text" => "RPRT",
  "Workflow" => nil,
  "Other" => nil
}
SO_TO_BIB_TRANSLATIONS = 
{
  "Article" => "article",
  "AudioObject" => "misc",
  "Blog" => "misc",
  "BlogPosting" => "article",
  "Collection" => "misc",
  "CreativeWork" => "misc",
  "DataCatalog" => "misc",
  "Dataset" => "misc",
  "Event" => "misc",
  "ImageObject" => "misc",
  "Movie" => "misc",
  "PublicationIssue" => "misc",
  "ScholarlyArticle" => "article",
  "Service" => "misc",
  "SoftwareSourceCode" => "misc",
  "VideoObject" => "misc",
  "WebPage" => "misc",
  "WebSite" => "misc"
}

Instance Method Summary collapse

Instance Method Details

#find_from_format(id: nil, string: nil, ext: nil) ⇒ Object 



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# File 'lib/bolognese/utils.rb', line 252

def find_from_format(id: nil, string: nil, ext: nil)
  if id.present?
    find_from_format_by_id(id)
  elsif ext.present?
    find_from_format_by_ext(string, ext: ext)
  elsif string.present?
    find_from_format_by_string(string)
  end
end

#find_from_format_by_ext(string, options = {}) ⇒ Object 



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# File 'lib/bolognese/utils.rb', line 277

def find_from_format_by_ext(string, options={})
  if options[:ext] == ".bib"
    "bibtex"
  elsif options[:ext] == ".ris"
    "ris"
  elsif options[:ext] == ".xml" && Maremma.from_xml(string).to_h.dig("doi_records", "doi_record", "crossref")
    "crossref"
  elsif options[:ext] == ".xml" && Maremma.from_xml(string).to_h.dig("resource", "xmlns").to_s.start_with?("http://datacite.org/schema/kernel")
    "datacite"
  elsif options[:ext] == ".json" && Maremma.from_json(string).to_h.dig("ris_type")
    "crosscite"
  elsif options[:ext] == ".json" && Maremma.from_json(string).to_h.dig("schemaVersion").to_s.start_with?("http://datacite.org/schema/kernel")
    "datacite_json"
  elsif options[:ext] == ".json" && Maremma.from_json(string).to_h.dig("issued", "date-parts").present?
    "citeproc"
  elsif options[:ext] == ".json" && Maremma.from_json(string).to_h.dig("@context").to_s.start_with?("http://schema.org")
    "schema_org"
  elsif options[:ext] == ".json" && Maremma.from_json(string).to_h.dig("@context") == ("https://raw.githubusercontent.com/codemeta/codemeta/master/codemeta.jsonld")
    "codemeta"
  end
end

#find_from_format_by_id(id) ⇒ Object 



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# File 'lib/bolognese/utils.rb', line 262

def find_from_format_by_id(id)
  id = normalize_id(id)

  if /\A(?:(http|https):\/(\/)?(dx\.)?(doi.org|handle.test.datacite.org)\/)?(doi:)?(10\.\d{4,5}\/.+)\z/.match(id)
    ra = get_doi_ra(id)
    %w(DataCite Crossref).include?(ra) ? ra.downcase : nil
  elsif /\A(?:(http|https):\/(\/)?orcid\.org\/)?(\d{4}-\d{4}-\d{4}-\d{3}[0-9X]+)\z/.match(id)
    "orcid"
  elsif /\A(http|https):\/(\/)?github\.com\/(.+)\z/.match(id)
    "codemeta"
  else
    "schema_org"
  end
end

#find_from_format_by_string(string) ⇒ Object 



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# File 'lib/bolognese/utils.rb', line 299

def find_from_format_by_string(string)
  if Maremma.from_xml(string).to_h.dig("doi_records", "doi_record", "crossref").present?
    "crossref"
  elsif Maremma.from_xml(string).to_h.dig("resource", "xmlns").to_s.start_with?("http://datacite.org/schema/kernel")
    "datacite"
  elsif Maremma.from_json(string).to_h.dig("ris_type").present?
    "crosscite"
  elsif Maremma.from_json(string).to_h.dig("schemaVersion").to_s.start_with?("http://datacite.org/schema/kernel")
    "datacite_json"
  elsif Maremma.from_json(string).to_h.dig("issued", "date-parts").present?
    "citeproc"
  elsif Maremma.from_json(string).to_h.dig("@context").to_s.start_with?("http://schema.org")
    "schema_org"
  elsif Maremma.from_json(string).to_h.dig("@context") == ("https://raw.githubusercontent.com/codemeta/codemeta/master/codemeta.jsonld")
    "codemeta"
  end
end

#from_citeproc(element) ⇒ Object 



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# File 'lib/bolognese/utils.rb', line 468

def from_citeproc(element)
  Array.wrap(element).map do |a|
    if a["literal"].present?
      a["@type"] = "Organization"
      a["name"] = a["literal"]
    else
      a["@type"] = "Person"
      a["name"] = [a["given"], a["family"]].compact.join(" ")
    end
    a["givenName"] = a["given"]
    a["familyName"] = a["family"]
    a.except("given", "family", "literal").compact
  end.unwrap
end

#from_schema_org(element) ⇒ Object 



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# File 'lib/bolognese/utils.rb', line 448

def from_schema_org(element)
  mapping = { "@type" => "type", "@id" => "id" }

  map_hash_keys(element: element, mapping: mapping)
end

#get_date_from_date_parts(date_as_parts) ⇒ Object 



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# File 'lib/bolognese/utils.rb', line 569

def get_date_from_date_parts(date_as_parts)
  date_parts = date_as_parts.fetch("date-parts", []).first
  year, month, day = date_parts[0], date_parts[1], date_parts[2]
  get_date_from_parts(year, month, day)
end

#get_date_from_parts(year, month = nil, day = nil) ⇒ Object 



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# File 'lib/bolognese/utils.rb', line 575

def get_date_from_parts(year, month = nil, day = nil)
  [year.to_s.rjust(4, '0'), month.to_s.rjust(2, '0'), day.to_s.rjust(2, '0')].reject { |part| part == "00" }.join("-")
end

#get_date_parts(iso8601_time) ⇒ Object 



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# File 'lib/bolognese/utils.rb', line 560

def get_date_parts(iso8601_time)
  return nil if iso8601_time.nil?

  year = iso8601_time[0..3].to_i
  month = iso8601_time[5..6].to_i
  day = iso8601_time[8..9].to_i
  { 'date-parts' => [[year, month, day].reject { |part| part == 0 }] }
end

#github_as_codemeta_url(url) ⇒ Object 



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# File 'lib/bolognese/utils.rb', line 555

def github_as_codemeta_url(url)
  github_hash = github_from_url(url)
  "https://raw.githubusercontent.com/#{github_hash[:owner]}/#{github_hash[:repo]}/master/codemeta.json" if github_hash[:owner].present?
end

#github_as_owner_url(url) ⇒ Object 



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# File 'lib/bolognese/utils.rb', line 540

def github_as_owner_url(url)
  github_hash = github_from_url(url)
  "https://github.com/#{github_hash[:owner]}" if github_hash[:owner].present?
end

#github_as_release_url(url) ⇒ Object 



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# File 'lib/bolognese/utils.rb', line 550

def github_as_release_url(url)
  github_hash = github_from_url(url)
  "https://github.com/#{github_hash[:owner]}/#{github_hash[:repo]}/tree/#{github_hash[:release]}" if github_hash[:release].present?
end

#github_as_repo_url(url) ⇒ Object 



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# File 'lib/bolognese/utils.rb', line 545

def github_as_repo_url(url)
  github_hash = github_from_url(url)
  "https://github.com/#{github_hash[:owner]}/#{github_hash[:repo]}" if github_hash[:repo].present?
end

#github_from_url(url) ⇒ Object 



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# File 'lib/bolognese/utils.rb', line 519

def github_from_url(url)
  return {} unless /\Ahttps:\/\/github\.com\/(.+)(?:\/)?(.+)?(?:\/tree\/)?(.*)\z/.match(url)
  words = URI.parse(url).path[1..-1].split('/')

  { owner: words[0],
    repo: words[1],
    release: words[3] }.compact
end

#github_owner_from_url(url) ⇒ Object 



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# File 'lib/bolognese/utils.rb', line 536

def github_owner_from_url(url)
  github_from_url(url).fetch(:owner, nil)
end

#github_release_from_url(url) ⇒ Object 



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# File 'lib/bolognese/utils.rb', line 532

def github_release_from_url(url)
  github_from_url(url).fetch(:release, nil)
end

#github_repo_from_url(url) ⇒ Object 



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# File 'lib/bolognese/utils.rb', line 528

def github_repo_from_url(url)
  github_from_url(url).fetch(:repo, nil)
end

#jsonlint(json) ⇒ Object 



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# File 'lib/bolognese/utils.rb', line 579

def jsonlint(json)
  return ["No JSON provided"] unless json.present?

  error_array = []
  linter = JsonLint::Linter.new
  linter.send(:check_data, json, error_array)
  error_array
end

#map_hash_keys(element: nil, mapping: nil) ⇒ Object 



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# File 'lib/bolognese/utils.rb', line 454

def map_hash_keys(element: nil, mapping: nil)
  Array.wrap(element).map do |a|
    a.map {|k, v| [mapping.fetch(k, k), v] }.reduce({}) do |hsh, (k, v)|
      if v.is_a?(Hash)
        hsh[k] = to_schema_org(v)
        hsh
      else
        hsh[k] = v
        hsh
      end
    end
  end.unwrap
end

#normalize_id(id, options = {}) ⇒ Object 



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# File 'lib/bolognese/utils.rb', line 359

def normalize_id(id, options={})
  return nil unless id.present?

  # check for valid DOI
  doi = normalize_doi(id, options)
  return doi if doi.present?

  # check for valid HTTP uri
  uri = Addressable::URI.parse(id)
  return nil unless uri && uri.host && %w(http https).include?(uri.scheme)

  # clean up URL
  PostRank::URI.clean(id)
rescue Addressable::URI::InvalidURIError
  nil
end

#normalize_ids(ids: nil) ⇒ Object 



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# File 'lib/bolognese/utils.rb', line 397

def normalize_ids(ids: nil)
  Array.wrap(ids).map do |id|
    { "id" => normalize_id(id["@id"]),
      "type" => id["@type"] || Metadata::DC_TO_SO_TRANSLATIONS[id["resourceTypeGeneral"]] || "CreativeWork",
      "title" => id["title"] || id["name"] }.compact
  end.unwrap
end

#normalize_licenses(licenses) ⇒ Object

find Creative Commons or OSI license in licenses array, normalize url and name



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# File 'lib/bolognese/utils.rb', line 406

def normalize_licenses(licenses)
  standard_licenses = Array.wrap(licenses).map { |l| URI.parse(l["url"]) }.select { |li| li.host && li.host[/(creativecommons.org|opensource.org)$/] }
  return licenses unless standard_licenses.present?

  # use HTTPS
  uri.scheme = "https"

  # use host name without subdomain
  uri.host = Array(/(creativecommons.org|opensource.org)/.match uri.host).last

  # normalize URLs
  if uri.host == "creativecommons.org"
    uri.path = uri.path.split('/')[0..-2].join("/") if uri.path.split('/').last == "legalcode"
    uri.path << '/' unless uri.path.end_with?('/')
  else
    uri.path = uri.path.gsub(/(-license|\.php|\.html)/, '')
    uri.path = uri.path.sub(/(mit|afl|apl|osl|gpl|ecl)/) { |match| match.upcase }
    uri.path = uri.path.sub(/(artistic|apache)/) { |match| match.titleize }
    uri.path = uri.path.sub(/([^0-9\-]+)(-)?([1-9])?(\.)?([0-9])?$/) do
      m = Regexp.last_match
      text = m[1]

      if m[3].present?
        version = [m[3], m[5].presence || "0"].join(".")
        [text, version].join("-")
      else
        text
      end
    end
  end

  uri.to_s
rescue URI::InvalidURIError
  nil
end

#normalize_orcid(orcid) ⇒ Object 



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# File 'lib/bolognese/utils.rb', line 389

def normalize_orcid(orcid)
  orcid = validate_orcid(orcid)
  return nil unless orcid.present?

  # turn ORCID ID into URL
  "http://orcid.org/" + Addressable::URI.encode(orcid)
end

#normalize_url(id) ⇒ Object 



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# File 'lib/bolognese/utils.rb', line 376

def normalize_url(id)
  return nil unless id.present?

  # check for valid HTTP uri
  uri = Addressable::URI.parse(id)
  return nil unless uri && uri.host && %w(http https).include?(uri.scheme)

  # clean up URL
  PostRank::URI.clean(id)
rescue Addressable::URI::InvalidURIError
  nil
end

#orcid_as_url(orcid) ⇒ Object 



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# File 'lib/bolognese/utils.rb', line 321

def orcid_as_url(orcid)
  "https://orcid.org/#{orcid}" if orcid.present?
end

#orcid_from_url(url) ⇒ Object 



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# File 'lib/bolognese/utils.rb', line 317

def orcid_from_url(url)
  Array(/\A:(http|https):\/\/orcid\.org\/(.+)/.match(url)).last
end

#parse_attributes(element, options = {}) ⇒ Object 



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# File 'lib/bolognese/utils.rb', line 344

def parse_attributes(element, options={})
  content = options[:content] || "__content__"

  if element.is_a?(String)
    element
  elsif element.is_a?(Hash)
    element.fetch(content, nil)
  elsif element.is_a?(Array)
    a = element.map { |e| e.is_a?(Hash) ? e.fetch(content, nil) : e }.uniq
    a = options[:first] ? a.first : a.unwrap
  else
    nil
  end
end

#sanitize(text, options = {}) ⇒ Object 



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# File 'lib/bolognese/utils.rb', line 502

def sanitize(text, options={})
  options[:tags] ||= Set.new(%w(strong em b i code pre sub sup br))
  content = options[:content] || "__content__"
  custom_scrubber = Bolognese::WhitelistScrubber.new(options)

  if text.is_a?(String)
    Loofah.scrub_fragment(text, custom_scrubber).to_s.gsub(/\u00a0/, ' ').strip
  elsif text.is_a?(Hash)
    sanitize(text.fetch(content, nil))
  elsif text.is_a?(Array)
    a = text.map { |e| e.is_a?(Hash) ? sanitize(e.fetch(content, nil)) : sanitize(e) }.uniq
    a = options[:first] ? a.first : a.unwrap
  else
    nil
  end
end

#to_citeproc(element) ⇒ Object 



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# File 'lib/bolognese/utils.rb', line 483

def to_citeproc(element)
  Array.wrap(element).map do |a|
    a["family"] = a["familyName"]
    a["given"] = a["givenName"]
    a["literal"] = a["name"] unless a["familyName"].present?
    a.except("type", "@type", "id", "@id", "name", "familyName", "givenName").compact
  end.presence
end

#to_ris(element) ⇒ Object 



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# File 'lib/bolognese/utils.rb', line 492

def to_ris(element)
  Array.wrap(element).map do |a|
    if a["familyName"].present?
      [a["familyName"], a["givenName"]].join(", ")
    else
      a["name"]
    end
  end.unwrap
end

#to_schema_org(element) ⇒ Object 



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# File 'lib/bolognese/utils.rb', line 442

def to_schema_org(element)
  mapping = { "type" => "@type", "id" => "@id", "title" => "name" }

  map_hash_keys(element: element, mapping: mapping)
end

#validate_orcid(orcid) ⇒ Object 



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# File 'lib/bolognese/utils.rb', line 325

def validate_orcid(orcid)
  orcid = Array(/\A(?:(http|https):\/\/(www\.)?orcid\.org\/)?(\d{4}[[:space:]-]\d{4}[[:space:]-]\d{4}[[:space:]-]\d{3}[0-9X]+)\z/.match(orcid)).last
  orcid.gsub(/[[:space:]]/, "-") if orcid.present?
end

#validate_orcid_scheme(orcid_scheme) ⇒ Object 



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# File 'lib/bolognese/utils.rb', line 330

def validate_orcid_scheme(orcid_scheme)
  Array(/\A(http|https):\/\/(www\.)?(orcid\.org)/.match(orcid_scheme)).last
end

#validate_url(str) ⇒ Object 



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# File 'lib/bolognese/utils.rb', line 334

def validate_url(str)
  if /\A(?:(http|https):\/\/(dx\.)?doi.org\/)?(doi:)?(10\.\d{4,5}\/.+)\z/.match(str)
    "DOI"
  elsif /\A(http|https):\/\//.match(str)
    "URL"
  elsif /\A(ISSN|eISSN) (\d{4}-\d{3}[0-9X]+)\z/.match(str)
    "ISSN"
  end
end