minor tweaks to cff reader and writer. #4

Gemfile.lock

@@ -1,7 +1,7 @@
 PATH
   remote: .
   specs:
-    briard (2.2)
+    briard (2.2.1)
       activesupport (>= 4.2.5)
       benchmark_methods (~> 0.7)
       bibtex-ruby (>= 5.1.0)

lib/briard/readers/cff_reader.rb

@@ -49,7 +49,8 @@ def read_cff(string: nil, **options)
           sum
         end
 
-        titles =  meta.fetch("title", nil).present? ?  [{ "title" => meta.fetch("title", nil) }] : [] 
+        titles =  meta.fetch("title", nil).present? ?  [{ "title" => meta.fetch("title", nil) }] : []
+        related_identifiers = Array.wrap(cff_references(meta.fetch("references", nil)))
         rights_list = meta.fetch("license", nil).present? ? [hsh_to_spdx("rightsIdentifier" => meta.fetch("license"))] : nil
 
         { "id" => id,
@@ -60,6 +61,7 @@ def read_cff(string: nil, **options)
           "titles" => titles,
           "creators" => creators,
           "publisher" => publisher,
+          "related_identifiers" => related_identifiers,
           "dates" => dates,
           "publication_year" => publication_year,
           "descriptions" => meta.fetch("abstract", nil).present? ? [{ "description" => sanitize(meta.fetch("abstract")), "descriptionType" => "Abstract" }] : nil,
@@ -73,7 +75,7 @@ def read_cff(string: nil, **options)
       def cff_creators(creators)
         Array.wrap(creators).map do |a|
           name_identifiers = normalize_orcid(parse_attributes(a["orcid"])).present? ? [{ "nameIdentifier" => normalize_orcid(parse_attributes(a["orcid"])), "nameIdentifierScheme" => "ORCID", "schemeUri"=>"https://orcid.org" }] : nil
-          if a["given-names"].present? || name_identifiers.present?
+          if a["given-names"].present? || a["family-names"].present? || name_identifiers.present?
             given_name = parse_attributes(a["given-names"])
             family_name = parse_attributes(a["family-names"])
             affiliation = Array.wrap(a["affiliation"]).map do |a|
@@ -102,6 +104,20 @@ def cff_creators(creators)
           end
         end
       end
+
+      def cff_references(references)
+        Array.wrap(references).map do |r|
+          identifier = Array.wrap(r["identifiers"]).find { |i| i["type"] == "doi" }
+
+          if identifier.present?
+            { "relatedIdentifier" => normalize_id(parse_attributes(identifier["value"])),
+              "relationType" => "References",
+              "relatedIdentifierType" => "DOI" }.compact
+          else
+            nil
+          end
+        end.compact.unwrap
+      end
     end
   end
 end

lib/briard/version.rb

@@ -1,3 +1,3 @@
 module Briard
-  VERSION = "2.2"
+  VERSION = "2.2.1"
 end

lib/briard/writers/cff_writer.rb

@@ -8,20 +8,47 @@ def cff
 
         # only use CFF for software
         return nil unless types["resourceTypeGeneral"] == "Software"
+
+        title = parse_attributes(titles, content: "title", first: true)
 
         hsh = {
+          "cff-version" => "1.2.0",
+          "message" => "If you use #{title} in your work, please cite it using the following metadata",
           "doi" => normalize_doi(doi),
           "repository-code" => url,
           "title" => parse_attributes(titles, content: "title", first: true),
-          "authors" => creators,
+          "authors" => write_cff_creators(creators),
           "abstract" => parse_attributes(descriptions, content: "description", first: true),
           "version" => version_info,
           "keywords" => subjects.present? ? Array.wrap(subjects).map { |k| parse_attributes(k, content: "subject", first: true) } : nil,
           "date-released" => get_date(dates, "Issued") || publication_year,
-          "license" => Array.wrap(rights_list).map { |l| l["rightsUri"] }.compact.unwrap,
+          "license" => Array.wrap(rights_list).map { |l| l["rightsIdentifier"] }.compact.unwrap,
+          "references" => write_references(related_identifiers)
         }.compact
         hsh.to_yaml
       end
+
+      def write_cff_creators(creators)
+        Array.wrap(creators).map do |a|
+          if a["givenName"].present? || a["nameIdentifiers"].present?
+            { "given-names" => a["givenName"],
+              "family-names" => a["familyName"],
+              "orcid" => parse_attributes(a["nameIdentifiers"], content: "nameIdentifier", first: true),
+              "affiliation" => parse_attributes(a["affiliation"], content: "name", first: true) }.compact
+          else
+            { "name" => a["name"] }
+          end
+        end
+      end
+
+      def write_references(related_identifiers)
+        { "identifiers" => 
+        Array.wrap(related_identifiers).map do |r|
+          { 
+            "type" => r["relatedIdentifierType"].downcase,
+            "value" => r["relatedIdentifierType"] == "DOI" ? doi_from_url(r["relatedIdentifier"]) : r["relatedIdentifier"] }
+        end }
+      end
     end
   end
 end

spec/readers/cff_reader_spec.rb

@@ -36,6 +36,7 @@
         "rightsIdentifierScheme"=>"SPDX",
         "rightsUri"=>"http://www.apache.org/licenses/LICENSE-2.0",
         "schemeUri"=>"https://spdx.org/licenses/"}])
+      expect(subject.related_identifiers).to eq([{"relatedIdentifier"=>"https://doi.org/10.5281/zenodo.1003149", "relatedIdentifierType"=>"DOI", "relationType"=>"References"}])
     end
 
     it "cff-converter-python" do
@@ -101,6 +102,7 @@
         "rightsIdentifierScheme"=>"SPDX",
         "rightsUri"=>"http://www.apache.org/licenses/LICENSE-2.0",
         "schemeUri"=>"https://spdx.org/licenses/"}])
+      expect(subject.related_identifiers).to eq([{"relatedIdentifier"=>"https://doi.org/10.5281/zenodo.1310751", "relatedIdentifierType"=>"DOI", "relationType"=>"References"}])
     end
 
     it "ruby-cff" do
@@ -131,6 +133,7 @@
         "rightsIdentifierScheme"=>"SPDX",
         "rightsUri"=>"http://www.apache.org/licenses/LICENSE-2.0",
         "schemeUri"=>"https://spdx.org/licenses/"}])
+      expect(subject.related_identifiers).to eq([{"relatedIdentifier"=>"https://doi.org/10.5281/zenodo.1003149", "relatedIdentifierType"=>"DOI", "relationType"=>"References"}])
     end
 
     it "ruby-cff repository url" do
@@ -163,6 +166,7 @@
         "rightsIdentifierScheme"=>"SPDX",
         "rightsUri"=>"http://www.apache.org/licenses/LICENSE-2.0",
         "schemeUri"=>"https://spdx.org/licenses/"}])
+      expect(subject.related_identifiers).to eq([{"relatedIdentifier"=>"https://doi.org/10.5281/zenodo.1003149", "relatedIdentifierType"=>"DOI", "relationType"=>"References"}])
     end
   end
 end

spec/writers/cff_writer_spec.rb

@@ -10,24 +10,22 @@
       expect(subject.valid?).to be true
       json = Psych.safe_load(subject.cff, permitted_classes: [Date])
       expect(json["doi"]).to eq("https://doi.org/10.5281/zenodo.10164")
-      expect(json["authors"]).to eq([{"affiliation"=>[{"name"=>"Juelich Supercomputing Centre, Jülich, Germany"}],
-        "familyName"=>"Klatt",
-        "givenName"=>"Torbjörn",
-        "name"=>"Klatt, Torbjörn"},
-       {"affiliation"=>[{"name"=>"Juelich Supercomputing Centre, Jülich, Germany"}],
-        "familyName"=>"Moser",
-        "givenName"=>"Dieter",
-        "name"=>"Moser, Dieter"},
-       {"affiliation"=>[{"name"=>"Juelich Supercomputing Centre, Jülich, Germany"}],
-        "familyName"=>"Speck",
-        "givenName"=>"Robert",
-        "name"=>"Speck, Robert"}])
+      expect(json["authors"]).to eq([{"affiliation"=>"Juelich Supercomputing Centre, Jülich, Germany",
+        "family-names"=>"Klatt",
+        "given-names"=>"Torbjörn"},
+       {"affiliation"=>"Juelich Supercomputing Centre, Jülich, Germany",
+        "family-names"=>"Moser",
+        "given-names"=>"Dieter"},
+       {"affiliation"=>"Juelich Supercomputing Centre, Jülich, Germany",
+        "family-names"=>"Speck",
+        "given-names"=>"Robert"}])
       expect(json["title"]).to eq("Pypint -- Python Framework For Parallel-In-Time Methods")
       expect(json["abstract"]).to eq("<em>PyPinT</em> is a framework for Parallel-in-Time integration routines. The main purpose of <em>PyPinT</em> is to provide a framework for educational use and prototyping new parallel-in-time algorithms. As well it will aid in developing a high-performance C++ implementation for massively parallel computers providing the benefits of parallel-in-time routines to a zoo of time integrators in various applications.")
       expect(json["date-released"]).to eq("2014-05-27")
       expect(json["repository-code"]).to eq("https://zenodo.org/record/10164")
       expect(json["keywords"]).to eq(["Parallel-in-Time Integration", "Spectral Deferred Corrections", "Multigrid", "Multi-Level Spectral Deferred Corrections", "Python Framework"])
-      expect(json["license"]).to eq(["http://www.opensource.org/licenses/MIT", "info:eu-repo/semantics/openAccess"])
+      expect(json["license"]).to be_nil
+      expect(json["references"]).to eq("identifiers"=>[{"type"=>"url", "value"=>"https://github.com/Parallel-in-Time/PyPinT/tree/release-v0.0.4"}])
     end
 
     it "SoftwareSourceCode also Zenodo" do
@@ -37,29 +35,44 @@
       json = Psych.safe_load(subject.cff, permitted_classes: [Date])
       expect(json["doi"]).to eq("https://doi.org/10.5281/zenodo.15497")
       expect(json["authors"]).to eq([{"affiliation"=>
-        [{"name"=>
-          "Instituut voor Kern- en Stralingsfysica, KU Leuven, 3001 Leuven, België"}],
-          "familyName"=>"Gins",
-          "givenName"=>"Wouter",
-          "name"=>"Gins, Wouter"},
-         {"affiliation"=>
-        [{"name"=>
-          "Instituut voor Kern- en Stralingsfysica, KU Leuven, 3001 Leuven, België"}],
-          "familyName"=>"de Groote",
-          "givenName"=>"Ruben",
-          "name"=>"de Groote, Ruben"},
-         {"affiliation"=>
-        [{"name"=>
-          "Instituut voor Kern- en Stralingsfysica, KU Leuven, 3001 Leuven, België"}],
-          "familyName"=>"Heylen",
-          "givenName"=>"Hanne",
-          "name"=>"Heylen, Hanne"}])
+        "Instituut voor Kern- en Stralingsfysica, KU Leuven, 3001 Leuven, België",
+        "family-names"=>"Gins",
+        "given-names"=>"Wouter"},
+       {"affiliation"=>
+        "Instituut voor Kern- en Stralingsfysica, KU Leuven, 3001 Leuven, België",
+        "family-names"=>"de Groote",
+        "given-names"=>"Ruben"},
+       {"affiliation"=>
+        "Instituut voor Kern- en Stralingsfysica, KU Leuven, 3001 Leuven, België",
+        "family-names"=>"Heylen",
+        "given-names"=>"Hanne"}])
       expect(json["title"]).to eq("Satlas: Simulation And Analysis Toolbox For Laser Spectroscopy And Nmr Experiments")
       expect(json["abstract"]).to eq("Initial release of the satlas Python package for the analysis and simulation for laser spectroscopy experiments. For the documentation, see http://woutergins.github.io/satlas/")
       expect(json["date-released"]).to eq("2015-02-18")
       expect(json["repository-code"]).to eq("https://zenodo.org/record/15497")
       expect(json["keywords"]).to be_nil
-      expect(json["license"]).to eq(["http://www.opensource.org/licenses/MIT", "info:eu-repo/semantics/openAccess"])
+      expect(json["license"]).to be_nil
+      expect(json["references"]).to eq("identifiers"=>[{"type"=>"url", "value"=>"https://github.com/woutergins/satlas/tree/v1.0.0"}])
+    end
+
+    it "ruby-cff" do
+      input = "https://github.com/citation-file-format/ruby-cff"
+      subject = Briard::Metadata.new(input: input)
+      expect(subject.valid?).to be true
+      json = Psych.safe_load(subject.cff, permitted_classes: [Date])
+      expect(json["doi"]).to eq("https://doi.org/10.5281/zenodo.1184077")
+      expect(json["authors"]).to eq([{"affiliation"=>"The University of Manchester, UK",
+        "family-names"=>"Haines",
+        "given-names"=>"Robert",
+        "orcid"=>"https://orcid.org/0000-0002-9538-7919"},
+       {"name"=>"The Ruby Citation File Format Developers"}])
+      expect(json["title"]).to eq("Ruby CFF Library")
+      expect(json["abstract"]).to eq("This library provides a Ruby interface to manipulate Citation File Format files")
+      expect(json["date-released"]).to eq("2021-08-18")
+      expect(json["repository-code"]).to eq("https://github.com/citation-file-format/ruby-cff")
+      expect(json["keywords"]).to eq(["ruby", "credit", "software citation", "research software", "software sustainability", "metadata", "citation file format", "CFF"])
+      expect(json["license"]).to eq("apache-2.0")
+      expect(json["references"]).to eq("identifiers"=>[{"type"=>"doi", "value"=>"10.5281/zenodo.1003149"}])
     end
   end
 end