Module: Bolognese::Utils

Included in:
CLI, MetadataUtils
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",
  # not part of DataCite schema, but used internally
  "Periodical" => "Periodical",
  "DataCatalog" => "DataCatalog"
}
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_SO_TRANSLATIONS = 
{
  "Proceedings" => nil,
  "ReferenceBook" => "Book",
  "JournalIssue" => "PublicationIssue",
  "ProceedingsArticle" => nil,
  "Other" => "CreativeWork",
  "Dissertation" => "Thesis",
  "Dataset" => "Dataset",
  "EditedBook" => "Book",
  "JournalArticle" => "ScholarlyArticle",
  "Journal" => nil,
  "Report" => nil,
  "BookSeries" => nil,
  "ReportSeries" => nil,
  "BookTrack" => nil,
  "Standard" => nil,
  "BookSection" => nil,
  "BookPart" => nil,
  "Book" => "Book",
  "BookChapter" => "Chapter",
  "StandardSeries" => nil,
  "Monograph" => "Book",
  "Component" => "CreativeWork",
  "ReferenceEntry" => nil,
  "JournalVolume" => "PublicationVolume",
  "BookSet" => nil,
  "PostedContent" => "ScholarlyArticle"
}
CR_TO_BIB_TRANSLATIONS = 
{
  "Proceedings" => "proceedings",
  "ReferenceBook" => "book",
  "JournalIssue" => nil,
  "ProceedingsArticle" => nil,
  "Other" => nil,
  "Dissertation" => "phdthesis",
  "Dataset" => nil,
  "EditedBook" => "book",
  "JournalArticle" => "article",
  "Journal" => nil,
  "Report" => nil,
  "BookSeries" => nil,
  "ReportSeries" => nil,
  "BookTrack" => nil,
  "Standard" => nil,
  "BookSection" => "inbook",
  "BookPart" => nil,
  "Book" => "book",
  "BookChapter" => "inbook",
  "StandardSeries" => nil,
  "Monograph" => "book",
  "Component" => nil,
  "ReferenceEntry" => nil,
  "JournalVolume" => nil,
  "BookSet" => nil,
  "PostedContent" => "article"
}
BIB_TO_CR_TRANSLATIONS = 
{
  "proceedings" => "Proceedings",
  "phdthesis" => "Dissertation",
  "article" => "JournalArticle",
  "book" => "Book",
  "inbook" => "BookChapter"
}
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",
  "DataCatalog" => "Dataset",
  "Dataset" => "Dataset",
  "Event" => "Event",
  "ImageObject" => "Image",
  "Movie" => "Audiovisual",
  "PublicationIssue" => "Text",
  "ScholarlyArticle" => "Text",
  "Thesis" => "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,
  "Thesis" => "thesis",
  "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",
  "Thesis" => "phdthesis",
  "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 



325
326
327
328
329
330
331
332
333
334
335
 
# File 'lib/bolognese/utils.rb', line 325

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)
  else
    "datacite"
  end
end

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



352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
 
# File 'lib/bolognese/utils.rb', line 352

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" && Nokogiri::XML(string, nil, 'UTF-8', &:noblanks).collect_namespaces.find { |k, v| v.start_with?("http://datacite.org/schema/kernel") }      
    "datacite"
  elsif options[:ext] == ".json" && Maremma.from_json(string).to_h.dig("@context").to_s.start_with?("http://schema.org", "https://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"
  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("types")
    "crosscite"
  elsif options[:ext] == ".json" && Maremma.from_json(string).to_h.dig("issued", "date-parts").present?
    "citeproc"
  end
end

#find_from_format_by_id(id) ⇒ Object 



337
338
339
340
341
342
343
344
345
346
347
348
349
350
 
# File 'lib/bolognese/utils.rb', line 337

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 



374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
 
# File 'lib/bolognese/utils.rb', line 374

def find_from_format_by_string(string)
  if Maremma.from_xml(string).to_h.dig("doi_records", "doi_record", "crossref").present?
    "crossref"
  elsif Nokogiri::XML(string, nil, 'UTF-8', &:noblanks).collect_namespaces.find { |k, v| v.start_with?("http://datacite.org/schema/kernel") }  
    "datacite"
  elsif Maremma.from_json(string).to_h.dig("@context").to_s.start_with?("http://schema.org", "https://schema.org")
    "schema_org"
  elsif Maremma.from_json(string).to_h.dig("@context") == ("https://raw.githubusercontent.com/codemeta/codemeta/master/codemeta.jsonld")
    "codemeta"
  elsif Maremma.from_json(string).to_h.dig("schema-version").to_s.start_with?("http://datacite.org/schema/kernel")
    "datacite_json"
  elsif Maremma.from_json(string).to_h.dig("types").present?
    "crosscite"
  elsif Maremma.from_json(string).to_h.dig("issued", "date-parts").present?
    "citeproc"
  elsif string.start_with?("TY  - ")
    "ris"
  elsif BibTeX.parse(string).first
    "bibtex"
  end
rescue BibTeX::ParseError => error
  nil
end

#from_citeproc(element) ⇒ Object 



668
669
670
671
672
673
674
675
676
677
678
679
680
681
 
# File 'lib/bolognese/utils.rb', line 668

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_datacite_json(element) ⇒ Object 



539
540
541
542
543
 
# File 'lib/bolognese/utils.rb', line 539

def from_datacite_json(element)
  Array.wrap(element).map do |e|
    e.inject({}) {|h, (k,v)| h[k.underscore] = v; h }
  end
end

#from_schema_org(element) ⇒ Object 



641
642
643
644
645
 
# File 'lib/bolognese/utils.rb', line 641

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

  map_hash_keys(element: element, mapping: mapping)
end

#get_contributor(contributor, contributor_type) ⇒ Object 



823
824
825
 
# File 'lib/bolognese/utils.rb', line 823

def get_contributor(contributor, contributor_type)
  contributor.select { |c| c["contributorType"] == contributor_type }
end

#get_date(dates, date_type) ⇒ Object 



818
819
820
821
 
# File 'lib/bolognese/utils.rb', line 818

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

#get_date_from_date_parts(date_as_parts) ⇒ Object 



776
777
778
779
780
 
# File 'lib/bolognese/utils.rb', line 776

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 



782
783
784
 
# File 'lib/bolognese/utils.rb', line 782

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 



767
768
769
770
771
772
773
774
 
# File 'lib/bolognese/utils.rb', line 767

def get_date_parts(iso8601_time)
  return { 'date-parts' => [[]] } 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

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



786
787
788
 
# File 'lib/bolognese/utils.rb', line 786

def get_date_parts_from_parts(year, month = nil, day = nil)
  { 'date-parts' => [[year.to_i, month.to_i, day.to_i].reject { |part| part == 0 }] }
end

#get_datetime_from_iso8601(iso8601_time) ⇒ Object

parsing of incomplete iso8601 timestamps such as 2015-04 is broken in standard library return nil if invalid iso8601 timestamp



812
813
814
815
816
 
# File 'lib/bolognese/utils.rb', line 812

def get_datetime_from_iso8601(iso8601_time)
  ISO8601::DateTime.new(iso8601_time).to_time.utc
rescue
  nil
end

#get_year_month(iso8601_time) ⇒ Object 



790
791
792
793
794
795
796
797
 
# File 'lib/bolognese/utils.rb', line 790

def get_year_month(iso8601_time)
  return [] if iso8601_time.nil?

  year = iso8601_time[0..3]
  month = iso8601_time[5..6]

  [year.to_i, month.to_i].reject { |part| part == 0 }
end

#get_year_month_day(iso8601_time) ⇒ Object 



799
800
801
802
803
804
805
806
807
 
# File 'lib/bolognese/utils.rb', line 799

def get_year_month_day(iso8601_time)
  return [] if iso8601_time.nil?

  year = iso8601_time[0..3]
  month = iso8601_time[5..6]
  day = iso8601_time[8..9]

  [year.to_i, month.to_i, day.to_i].reject { |part| part == 0 }
end

#github_as_codemeta_url(url) ⇒ Object 



757
758
759
760
761
762
763
764
765
 
# File 'lib/bolognese/utils.rb', line 757

def github_as_codemeta_url(url)
  github_hash = github_from_url(url)

  if github_hash[:path].to_s.end_with?("codemeta.json")
    "https://raw.githubusercontent.com/#{github_hash[:owner]}/#{github_hash[:repo]}/#{github_hash[:release]}/#{github_hash[:path]}"
  elsif github_hash[:owner].present?
    "https://raw.githubusercontent.com/#{github_hash[:owner]}/#{github_hash[:repo]}/master/codemeta.json"
  end
end

#github_as_owner_url(url) ⇒ Object 



742
743
744
745
 
# File 'lib/bolognese/utils.rb', line 742

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 



752
753
754
755
 
# File 'lib/bolognese/utils.rb', line 752

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 



747
748
749
750
 
# File 'lib/bolognese/utils.rb', line 747

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 



719
720
721
722
723
724
725
726
727
728
 
# File 'lib/bolognese/utils.rb', line 719

def github_from_url(url)
  return {} unless /\Ahttps:\/\/github\.com\/(.+)(?:\/)?(.+)?(?:\/tree\/)?(.*)\z/.match(url)
  words = URI.parse(url).path[1..-1].split('/')
  path = words.length > 3 ? words[4...words.length].join("/") : nil

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

#github_owner_from_url(url) ⇒ Object 



738
739
740
 
# File 'lib/bolognese/utils.rb', line 738

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

#github_release_from_url(url) ⇒ Object 



734
735
736
 
# File 'lib/bolognese/utils.rb', line 734

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

#github_repo_from_url(url) ⇒ Object 



730
731
732
 
# File 'lib/bolognese/utils.rb', line 730

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

#jsonlint(json) ⇒ Object 



827
828
829
830
831
832
833
834
 
# File 'lib/bolognese/utils.rb', line 827

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 



647
648
649
650
651
652
653
654
655
656
657
658
659
 
# File 'lib/bolognese/utils.rb', line 647

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 



440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
 
# File 'lib/bolognese/utils.rb', line 440

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, relation_type: nil) ⇒ Object 



482
483
484
485
486
487
488
489
490
491
492
493
 
# File 'lib/bolognese/utils.rb', line 482

def normalize_ids(ids: nil, relation_type: nil)
  Array.wrap(ids).select { |idx| idx["@id"].present? }.map do |idx|
    id = normalize_id(idx["@id"])
    related_identifier_type = doi_from_url(id).present? ? "DOI" : "URL"
    id = doi_from_url(id) || id

    { "relatedIdentifier" => id,
      "relationType" => relation_type,
      "relatedIdentifierType" => related_identifier_type,
      "resourceTypeGeneral" => Metadata::SO_TO_DC_TRANSLATIONS[idx["@type"]] }.compact
  end.unwrap
end

#normalize_licenses(licenses) ⇒ Object

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



496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
 
# File 'lib/bolognese/utils.rb', line 496

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 



474
475
476
477
478
479
480
 
# File 'lib/bolognese/utils.rb', line 474

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 



457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
 
# File 'lib/bolognese/utils.rb', line 457

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

  # handle info URIs
  return id if id.to_s.start_with?("info")

  # check for valid HTTP uri
  uri = Addressable::URI.parse(id)

  return nil unless uri && uri.host && %w(http https ftp).include?(uri.scheme)

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

#orcid_as_url(orcid) ⇒ Object 



402
403
404
 
# File 'lib/bolognese/utils.rb', line 402

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

#orcid_from_url(url) ⇒ Object 



398
399
400
 
# File 'lib/bolognese/utils.rb', line 398

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

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



425
426
427
428
429
430
431
432
433
434
435
436
437
438
 
# File 'lib/bolognese/utils.rb', line 425

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 



702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
 
# File 'lib/bolognese/utils.rb', line 702

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 



683
684
685
686
687
688
689
690
 
# File 'lib/bolognese/utils.rb', line 683

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_datacite_json(element, options = {}) ⇒ Object 



532
533
534
535
536
537
 
# File 'lib/bolognese/utils.rb', line 532

def to_datacite_json(element, options={})
  a = Array.wrap(element).map do |e|
    e.inject({}) {|h, (k,v)| h[k.dasherize] = v; h }
  end
  options[:first] ? a.unwrap : a.presence
end

#to_identifier(identifier) ⇒ Object 



661
662
663
664
665
666
 
# File 'lib/bolognese/utils.rb', line 661

def to_identifier(identifier)
  {
    "@type" => "PropertyValue",
    "propertyID" => identifier["relatedIdentifierType"],
    "value" => identifier["relatedIdentifier"] }
end

#to_ris(element) ⇒ Object 



692
693
694
695
696
697
698
699
700
 
# File 'lib/bolognese/utils.rb', line 692

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 



545
546
547
548
549
 
# File 'lib/bolognese/utils.rb', line 545

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

  map_hash_keys(element: element, mapping: mapping)
end

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



551
552
553
554
555
556
557
558
 
# File 'lib/bolognese/utils.rb', line 551

def to_schema_org_container(element, options={})
  return nil unless (element.is_a?(Hash) || (element.nil? && options[:container_title].present?))

  { 
    "@id" => element["relatedIdentifier"],
    "@type" => (options[:type] == "Dataset") ? "DataCatalog" : "Periodical",
    "name" => element["title"] || options[:container_title] }
end

#to_schema_org_funder(funding_references) ⇒ Object 



600
601
602
603
604
605
606
607
608
609
 
# File 'lib/bolognese/utils.rb', line 600

def to_schema_org_funder(funding_references)
  return nil unless funding_references.present?

  Array.wrap(funding_references).map do |fr|
    {
      "@id" => fr["funderIdentifier"],
      "@type" => "Organization",
      "name" => fr["funderName"] }.compact
  end.unwrap
end

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



560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
 
# File 'lib/bolognese/utils.rb', line 560

def to_schema_org_identifier(element, options={})
  ident = { 
    "@type" => "PropertyValue",
    "propertyID" => normalize_doi(element) ? "doi" : "url",
    "value" => element }

  if options[:alternate_identifiers].present?
    [ident] + Array.wrap(options[:alternate_identifiers]).map do |ai|
                if ai["alternateIdentifierType"].to_s.downcase == "url"
                  ai["alternateIdentifier"]
                else
                  { 
                    "@type" => "PropertyValue",
                    "propertyID" => ai["alternateIdentifierType"],
                    "value" => ai["alternateIdentifier"] }
                end
              end
  else
    ident
  end
end

#to_schema_org_relation(related_identifiers: nil, relation_type: nil) ⇒ Object 



582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
 
# File 'lib/bolognese/utils.rb', line 582

def to_schema_org_relation(related_identifiers: nil, relation_type: nil)
  return nil unless related_identifiers.present? && relation_type.present?

  relation_type = relation_type == "References" ? ["References", "Cites", "Documents"] : [relation_type] 

  Array.wrap(related_identifiers).select { |ri| relation_type.include?(ri["relationType"]) }.map do |r|
    if r["relatedIdentifierType"] == "ISSN" && r["relationType"] == "IsPartOf"
      {
        "@type" => "Periodical",
        "issn" => r["relatedIdentifier"] }.compact
    else
    {
      "@id" => normalize_id(r["relatedIdentifier"]),
      "@type" => DC_TO_SO_TRANSLATIONS[r["resourceTypeGeneral"]] || "CreativeWork" }.compact
    end
  end.unwrap
end

#to_schema_org_spatial_coverage(geo_location) ⇒ Object 



611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
 
# File 'lib/bolognese/utils.rb', line 611

def to_schema_org_spatial_coverage(geo_location)
  return nil unless geo_location.present?

  Array.wrap(geo_location).map do |gl|
    if gl.fetch("geoLocationPoint", nil)
      { 
        "@type" => "Place",
        "geo" => {
          "@type" => "GeoCoordinates",
          "address" => gl["geoLocationPlace"],
          "latitude" => gl.dig("geoLocationPoint", "pointLatitude"),
          "longitude" => gl.dig("geoLocationPoint", "pointLongitude")
        }.compact
      }
    elsif gl.fetch("geoLocationBox", nil)
      { 
        "@type" => "Place",
        "geo" => {
          "@type" => "GeoShape",
          "address" => gl["geoLocationPlace"],
          "box" => [gl.dig("geoLocationBox", "southBoundLatitude"),
                    gl.dig("geoLocationBox", "westBoundLongitude"),
                    gl.dig("geoLocationBox", "northBoundLatitude"),
                    gl.dig("geoLocationBox", "eastBoundLongitude")].join(" ")
        }.compact
      }
    end
  end.compact.unwrap
end

#validate_orcid(orcid) ⇒ Object 



406
407
408
409
 
# File 'lib/bolognese/utils.rb', line 406

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 



411
412
413
 
# File 'lib/bolognese/utils.rb', line 411

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

#validate_url(str) ⇒ Object 



415
416
417
418
419
420
421
422
423
 
# File 'lib/bolognese/utils.rb', line 415

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