Ruby 4.0 compatibility, contributor handling, and citation output fixes

lib/bolognese.rb

@@ -16,6 +16,7 @@
 require 'csl/styles'
 require 'edtf'
 
+require "bolognese/citeproc_extensions"
 require "bolognese/version"
 require "bolognese/metadata"
 require "bolognese/cli"

lib/bolognese/citeproc_extensions.rb

@@ -0,0 +1,48 @@
+# frozen_string_literal: true
+
+# Minimal patch for csl-ruby and citeproc-ruby compatibility
+# Root cause: 'contributor' is not recognized as a names variable in citeproc gem
+# https://github.com/inukshuk/citeproc/blob/121fa4a950b9bd71960e42d20db96bcea1165201/lib/citeproc/variable.rb#L20-L24
+
+module CiteProc
+  class Variable
+    # Unfreeze, modify, and refreeze the fields to add 'contributor' and 'accepted-date'
+    if @fields
+      # Unfreeze the fields hash temporarily
+      fields_dup = @fields.dup
+
+      # Add contributor to names (make a new unfrozen array)
+      fields_dup[:names] = (@fields[:names] + [:contributor]).uniq
+
+      # Add accepted-date to dates (make a new unfrozen array)
+      fields_dup[:date] = (@fields[:date] + [:'accepted-date']).uniq
+
+      # Rebuild the types mapping - only use actual type keys, not aliases like :all, :any, etc.
+      types_hash = Hash[*[:date, :names, :number, :text].map { |k| fields_dup[k].map { |n| [n, k] } }.flatten]
+
+      # Update the class instance variables
+      @fields = fields_dup
+      @types = Hash.new { |h,k| h.fetch(k.to_sym, nil) }.merge(types_hash).freeze
+
+      # Rebuild @factories from the new @types
+      # This maps each field name to its Variable subclass (Names, Date, Text, Number)
+      @factories = Hash.new { |h,k| h.fetch(k.to_s.intern, CiteProc::Variable) }.merge(
+        Hash[*@types.map { |field_name, type|
+          [field_name, CiteProc.const_get(type.to_s.capitalize)]
+        }.flatten]
+      ).freeze
+
+      # Recreate the aliases
+      @fields[:name] = @fields[:names]
+      @fields[:dates] = @fields[:date]
+      @fields[:numbers] = @fields[:number]
+
+      # Recreate :all and :any
+      @fields[:all] = @fields[:any] =
+        [:date, :names, :text, :number].reduce([]) { |s,a| s.concat(@fields[a]) }.sort
+
+      # Refreeze fields
+      @fields.freeze
+    end
+  end
+end

lib/bolognese/metadata_utils.rb

@@ -139,19 +139,28 @@ def citeproc_hsh
         author = to_citeproc(creators)
       end
 
-      if types["resourceTypeGeneral"] == "Software" && version_info.present?
-        type = "book"
+      if types["resourceTypeGeneral"] == "Software"
+        type = "software"
       else
         type = types["citeproc"]
       end
 
+      # Filter out contributors who are already creators, editors, or translators to avoid duplication
+      creator_names = Array.wrap(creators).map { |c| c["name"] || [c["givenName"], c["familyName"]].compact.join(" ") }.compact
+      unique_contributors = Array.wrap(contributors).reject do |c|
+        contributor_name = c["name"] || [c["givenName"], c["familyName"]].compact.join(" ")
+        creator_names.include?(contributor_name) ||
+        c["contributorType"] == "Editor" ||
+        c["contributorType"] == "Translator"
+      end
+
       {
         "type" => type,
         "id" => normalize_doi(doi),
         "categories" => Array.wrap(subjects).map { |k| parse_attributes(k, content: "subject", first: true) }.presence,
         "language" => language,
         "author" => author,
-        "contributor" => to_citeproc(contributors),
+        "contributor" => unique_contributors.presence ? to_citeproc(unique_contributors) : nil,
         "editor" => contributors ? to_citeproc(contributors.select { |c| c["contributorType"] == "Editor" }) : nil,
         "translator" => contributors ? to_citeproc(contributors.select { |c| c["contributorType"] == "Translator" }) : nil,
         "issued" => get_date(dates, "Issued") ? get_date_parts(get_date(dates, "Issued")) : get_date_parts(publication_year.to_s),

spec/fixtures/datacite_xml_csl_with_contributors_and_available.xml

@@ -0,0 +1,58 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<resource xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://datacite.org/schema/kernel-4" xsi:schemaLocation="http://datacite.org/schema/kernel-4 http://schema.datacite.org/meta/kernel-4/metadata.xsd">
+  <identifier identifierType="DOI">10.81360/BIFURCATED</identifier>
+  <creators>
+    <creator>
+      <creatorName>Toon, Geoffrey C.</creatorName>
+      <affiliation>Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA</affiliation>
+    </creator>
+    <creator>
+      <creatorName>Wunch, Debra</creatorName>
+      <nameIdentifier nameIdentifierScheme="ORCID">0000-0002-4924-0377</nameIdentifier>
+      <affiliation>California Institute of Technology, Pasadena, CA, U.S.A.</affiliation>
+    </creator>
+  </creators>
+  <titles>
+    <title>A stand-alone a priori profile generation tool for GGG2014 release</title>
+  </titles>
+  <publisher>CaltechDATA</publisher>
+  <publicationYear>2015</publicationYear>
+  <subjects>
+    <subject>TCCON</subject>
+  </subjects>
+  <contributors>
+    <contributor contributorType="ContactPerson">
+      <contributorName>Toon, Geoffrey C.</contributorName>
+      <affiliation>Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA</affiliation>
+    </contributor>
+    <contributor contributorType="ContactPerson">
+      <contributorName>Wunch, Debra</contributorName>
+      <affiliation>California Institute of Technology, Pasadena, CA, USA</affiliation>
+    </contributor>
+    <contributor contributorType="ResearchGroup">
+      <contributorName>TCCON</contributorName>
+    </contributor>
+  </contributors>
+  <dates>
+    <date dateType="Submitted">2017-07-24</date>
+    <date dateType="Available">2015-10-14</date>
+  </dates>
+  <language>eng</language>
+  <resourceType resourceTypeGeneral="Software"/>
+  <alternateIdentifiers>
+    <alternateIdentifier alternateIdentifierType="CaltechDATA_Identifier">250</alternateIdentifier>
+    <alternateIdentifier alternateIdentifierType="CaltechDATA_Identifier">250</alternateIdentifier>
+  </alternateIdentifiers>
+  <relatedIdentifiers>
+    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsDocumentedBy">10.14291/tccon.ggg2014.documentation.R0/1221662</relatedIdentifier>
+    <relatedIdentifier relatedIdentifierType="URL" relationType="IsDocumentedBy">https://tccon-wiki.caltech.edu/</relatedIdentifier>
+  </relatedIdentifiers>
+  <version>GGG2014.R0</version>
+  <rightsList>
+    <rights rightsURI="https://data.caltech.edu/tindfiles/serve/8ff8bc09-cecd-468d-b219-3ea372f2ea95/">TCCON Data Use Policy</rights>
+  </rightsList>
+  <descriptions>
+    <description descriptionType="Other">The Total Carbon Column Observing Network (TCCON) is a network of ground-based Fourier Transform Spectrometers that record direct solar absorption spectra of the atmosphere in the near-infrared. From these spectra, accurate and precise column-averaged abundances of atmospheric constituents including CO2, CH4, N2O, HF, CO, H2O, and HDO, are retrieved.  This is a stand-alone a priori profile generation tool for the GGG2014 data release.</description>
+    <description descriptionType="Other">&lt;br&gt;Cite this record as:&lt;br&gt;Toon, G. C., &amp;amp; Wunch, D. (2017). A stand-alone a priori profile generation tool for GGG2014 release. CaltechDATA. &lt;a href="https://doi.org/10.14291/tccon.ggg2014.priors.r0/1221661"&gt;https://doi.org/10.14291/tccon.ggg2014.priors.r0/1221661&lt;/a&gt;&lt;br&gt; or choose a &lt;a href="https://crosscite.org/?doi=10.14291/TCCON.GGG2014.PRIORS.R0/1221661"&gt; different citation style.&lt;/a&gt;&lt;br&gt;&lt;a href="https://data.datacite.org/application/x-bibtex/10.14291/TCCON.GGG2014.PRIORS.R0/1221661"&gt;Download Citation&lt;/a&gt;&lt;br&gt;</description>
+  </descriptions>
+</resource>

spec/writers/citation_writer_spec.rb

@@ -38,7 +38,7 @@
       subject = Bolognese::Metadata.new(input: input, from: "datacite")
       expect(subject.style).to eq("apa")
       expect(subject.locale).to eq("en-US")
-      expect(subject.citation).to eq("Lab for Exosphere and Near Space Environment Studies. (2019). <i>lenses-lab/LYAO_RT-2018JA026426: Original Release</i> (Version 1.0.0). Zenodo. https://doi.org/10.5281/zenodo.2598836")
+      expect(subject.citation).to eq("Lab for Exosphere and Near Space Environment Studies. (2019). <i>lenses-lab/LYAO_RT-2018JA026426: Original Release</i> (Version 1.0.0) [Computer software]. Zenodo. https://doi.org/10.5281/zenodo.2598836")
     end
 
     it "interactive resource without dates" do
@@ -112,5 +112,11 @@
       expect(subject.locale).to eq("en-US")
       expect(subject.citation).to eq("M. Fenner, “Eating your own Dog Food,” <i>Understanding the fictional John Smith</i>, vol. 776, no. 1. DataCite, pp. 50–60, Dec. 20, 2016. doi: 10.5438/4k3m-nyvg.")
     end
+
+    it "with contributors and available date" do
+      input = fixture_path + "datacite_xml_csl_with_contributors_and_available.xml"
+      subject = Bolognese::Metadata.new(input: input, from: "datacite")
+      expect(subject.citation).to eq("Toon, G. C., &amp; Wunch, D. (2015). <i>A stand-alone a priori profile generation tool for GGG2014 release</i> (Version GGG2014.R0) [Computer software]. CaltechDATA. https://doi.org/10.81360/bifurcated")
+    end
   end
 end

spec/writers/citeproc_writer_spec.rb

@@ -105,7 +105,7 @@
       input = "https://doi.org/10.6084/m9.figshare.4906367.v1"
       subject = Bolognese::Metadata.new(input: input, from: "datacite")
       json = JSON.parse(subject.citeproc)
-      expect(json["type"]).to eq("article")
+      expect(json["type"]).to eq("software")
       expect(json["DOI"]).to eq("10.6084/m9.figshare.4906367.v1")
       expect(json["title"]).to eq("Scimag catalogue of LibGen as of January 1st, 2014")
       expect(json["copyright"]).to eq("Creative Commons Zero v1.0 Universal")
@@ -115,7 +115,7 @@
       input = "https://doi.org/10.5281/zenodo.2598836"
       subject = Bolognese::Metadata.new(input: input, from: "datacite")
       json = JSON.parse(subject.citeproc)
-      expect(json["type"]).to eq("book")
+      expect(json["type"]).to eq("software")
       expect(json["DOI"]).to eq("10.5281/zenodo.2598836")
       expect(json["version"]).to eq("1.0.0")
       expect(json["copyright"]).to eq("Open Access")
@@ -125,7 +125,7 @@
       input = fixture_path + "datacite_software_version.json"
       subject = Bolognese::Metadata.new(input: input, from: "datacite_json")
       json = JSON.parse(subject.citeproc)
-      expect(json["type"]).to eq("book")
+      expect(json["type"]).to eq("software")
       expect(json["DOI"]).to eq("10.5281/ZENODO.2598836")
       expect(json["version"]).to eq("1.0.0")
       expect(json["copyright"]).to eq("Open Access")
@@ -241,7 +241,7 @@
       input = "https://github.com/datacite/maremma"
       subject = Bolognese::Metadata.new(input: input, from: "codemeta")
       json = JSON.parse(subject.citeproc)
-      expect(json["type"]).to eq("article-journal")
+      expect(json["type"]).to eq("software")
       expect(json["id"]).to eq("https://doi.org/10.5438/qeg0-3gm3")
       expect(json["DOI"]).to eq("10.5438/qeg0-3gm3")
       expect(json["title"]).to eq("Maremma: a Ruby library for simplified network calls")