Module: TaxonWorks::Vendor::Serrano

Defined in:
lib/vendor/serrano.rb

Overview

A middle-layer wrapper between Serrano and TaxonWorks

Defined Under Namespace

Classes: CrossRefLaTeX

Constant Summary collapse

CUTOFF = 
50.0

Class Method Summary collapse

Class Method Details

.bibtex_from_citproc(c, b) ⇒ Object 



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# File 'lib/vendor/serrano.rb', line 93

def self.bibtex_from_citproc(c, b)
  return nil unless c.present? && b.present?
  c = JSON.parse(c)

  b[:address] = ::Utilities::Strings.encode_with_utf8(c['address']) unless c['address'].blank?
  #b[:author]
  b[:booktitle] = ::Utilities::Strings.encode_with_utf8(c['booktitle']) unless c['booktitle'].blank?
  b[:chapter] = c['chapter'] unless c['chapter'].blank?
  b[:edition] = c['edition'] unless c['edition'].blank?
  #b[:editor]
  b[:howpublished] = ::Utilities::Strings.encode_with_utf8(c['how-published']) unless c['how-published'].blank?
  b[:institution] = ::Utilities::Strings.encode_with_utf8(c['institution']) unless c['institution'].blank?
  b[:journal] = ::Utilities::Strings.encode_with_utf8(c['container-title']) unless c['container-title'].blank?
  #b[:month]
  b[:note] = ::Utilities::Strings.encode_with_utf8(c['note']) unless c['note'].blank?
  #b[:number] = c['number'] unless c['volume'].blank?
  b[:organization] = ::Utilities::Strings.encode_with_utf8(c['organization']) unless c['organization'].blank?
  b[:pages] = c['page'] unless c['page'].blank?
  b[:publisher] = ::Utilities::Strings.encode_with_utf8(c['publisher']) unless c['publisher'].blank?
  b[:school] = ::Utilities::Strings.encode_with_utf8(c['school']) unless c['school'].blank?
  b[:series] = c['series'] unless c['series'].blank?
  #b[:title] = c['title']
  # b[:typeb]  # "Source::Bibtex"
  #b[:volume] = c['volume'] unless c['volume'].blank?
  #b[:doi] = c['DOI']
  unless c['abstract'].blank?
    b[:abstract] = ::Utilities::Strings.encode_with_utf8(c['abstract']).
      gsub('</jats:p>', '').
      gsub('<jats:p>', '').
      gsub('</jats:sec>', '').
      gsub('<jats:sec>', '').
      gsub('</jats:title>', '</b>').
      gsub('<jats:title>', '<b>').
      gsub('</jats:italic>', '</i>').
      gsub('<jats:italic>', '<i>').
      gsub('</jats:bold>', '</b>').
      gsub('<jats:bold>', '<b>')
  end
  b[:copyright] = c['copyright'] unless c['copyright'].blank?
  #b[:bibtex_type] = c['type'] unless c['type'].blank?
  b[:day]  = c['issued']['date-parts'][0][2] if c['issued'] && c['issued']['date-parts'] && c['issued']['date-parts'][0] && c['issued']['date-parts'][0][2]
  b[:year] = c['issued']['date-parts'][0][0] if c['issued'] && c['issued']['date-parts'] && c['issued']['date-parts'][0] && c['issued']['date-parts'][0][0]
  b[:isbn] = c['ISBN'].first unless c['ISBN'].blank?
  b[:issn] = c['ISSN'].first unless c['ISSN'].blank?
  #b[:translator]
  #b[:url]
  b[:serial_id] = Serial.where(name: b[:journal]).first.try(:id) unless b[:journal].blank?
  b
end

.citation_is_valid_doi?(citation) ⇒ Boolean

Returns Boolean use our global identifier class to determined if value is DOI this isn’t super robust, but maybe OK.

Returns:

  • (Boolean) —

    Boolean use our global identifier class to determined if value is DOI this isn’t super robust, but maybe OK



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# File 'lib/vendor/serrano.rb', line 157

def self.citation_is_valid_doi?(citation)
  doi = Identifier::Global::Doi.new(identifier: citation)
  doi.valid?
  !doi.errors.has_key?(:identifier)
end

.cutoff ⇒ Float

Returns:

  • (Float) 


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# File 'lib/vendor/serrano.rb', line 9

def self.cutoff
  CUTOFF
end

.get_bibtex_string(citation, format = 'bibtex') ⇒ String?

Returns ; format == ‘bibtex’ or ‘citeproc’.

Returns:

  • (String, nil) —

    ; format == ‘bibtex’ or ‘citeproc’



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# File 'lib/vendor/serrano.rb', line 67

def self.get_bibtex_string(citation, format = 'bibtex')
  begin
    # Convert citation to DOI if it isn't already
    if !citation_is_valid_doi?(citation)
      # First item should be the one with highest score/relevance: https://github.com/CrossRef/rest-api-doc#sort-order
      res = ::Serrano.works(query: citation, limit: 1)&.dig("message", "items")&.first
      # citation = Serrano.works(query: citation)&.dig("message", "items")&.max_by { |i| i["score"] }&.dig("DOI") unless citation_is_valid_doi?(citation)

      score = res&.dig("score") || -1.0
      citation = (score >= CUTOFF) ? res&.dig("DOI") : nil
    end

    if format == 'bibtex'
      bibtex = ::Serrano.content_negotiation(ids: unurize_doi(citation), format: "bibtex") unless citation.nil?
      return bibtex =~ /^\s*@/ ? bibtex : nil
    elsif format == 'citeproc'
      citeproc = ::Serrano.content_negotiation(ids: unurize_doi(citation), format: "citeproc-json") unless citation.nil?
      return citeproc
    else
      return nil
    end
  rescue
    return nil
  end
end

.new_from_citation(citation: nil) ⇒ Source::BibTex.new, ...

TODO: attempt to extract DOI from full string

Four possible paths: 1) citation. 2) citation which includes a doi. 3) naked doi, e.g., ‘10.3897/zookeys.20.205’. 4) doi with preamble, e.g., ‘dx.doi.org/10.3897/zookeys.20.205’ or

'https://doi.org/10.3897/zookeys.20.205'.

Returns:

  • (Source::BibTex.new) —

    a new instance

  • (Source::Verbatim.new) —

    a new instance

  • (false) 


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# File 'lib/vendor/serrano.rb', line 50

def self.new_from_citation(citation: nil)
  citation&.strip!
  return false if citation.length < 6
  # check string encoding, if not UTF-8, check if compatible with UTF-8,
  # if so convert to UTF-8 and parse with latex, else use type verbatim
  a = get_bibtex_string(citation, 'bibtex')
  b = ::Utilities::Strings.encode_with_utf8(a) if a
  if b
    bibtex = Source::Bibtex.new_from_bibtex(BibTeX::Bibliography.parse(b, filter: CrossRefLaTeX.instance).first)
    citeproc = get_bibtex_string(citation, 'citeproc')
    bibtex_from_citproc(citeproc, bibtex)
  else
    Source::Verbatim.new(verbatim: a ? a : citation)
  end
end

.unurize_doi(doi) ⇒ String

Returns:

  • (String) 


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# File 'lib/vendor/serrano.rb', line 144

def self.unurize_doi(doi)
  doi = doi.strip

  if matches = doi.match(/https?:\/\/[^\/]+\/(.*)/)
    matches[1]
  else
    doi
  end
end