bolognese 2.0.0 → 2.2.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 23ccf372b59b7d9c8919ec7ad7137eef6e99512eed488977e847f938f389aa2f
-  data.tar.gz: 390e56023d57e637a52776a98dcd0bea4fa0acd8b8459ced05cbc6785f69fe0a
+  metadata.gz: ce52f2eb08396d0e56bdccf06702901fe7c04f1925cacafc71f315a1edda91c3
+  data.tar.gz: 29fb5a1d987a95220bbc7a3912aa24735f54924f47c8a74d61d1f51e25b75314
 SHA512:
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-  data.tar.gz: 6281527f6b312d398a96b9f1df9be55de991f6ac939417131633b24ddaa24741c3b86c3b2e4e73408ca1350e0b17addf9439ae30dff998bc6dda07e8c4459db7
+  metadata.gz: 4d528d2597900dfb90410504833a83e79b1bda1974d9f77102071cecd3f71c3e1f899d8e59abe24cf1110469807cc0c6382c50a5a62571ceceb9278e7cfa37b7
+  data.tar.gz: 341d76ed37284899ea1e74e331026ba6d042d92037a260d7591b9a48b38b7c8a0b06a6908e97917b2c345c5be8b3ac6475cc63a5478891589d624f248137b315

data/.github/workflows/ci.yml

@@ -7,7 +7,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        ruby: ["2.6", "2.7", "3.0", "3.1"]
+        ruby: ["3.0", "3.1", "3.2", "3.3"]
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v3

data/.github/workflows/release.yml

@@ -11,10 +11,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v3
-    - name: Set up Ruby 2.6
+    - name: Set up Ruby 3.1.4
       uses: ruby/setup-ruby@v1
       with:
-        ruby-version: "2.6"
+        ruby-version: "3.1.4"
 
     - name: Build
       run: |

data/Gemfile.lock

@@ -1,7 +1,7 @@
 PATH
   remote: .
   specs:
-    bolognese (2.0.0)
+    bolognese (2.2.0)
       activesupport (>= 4.2.5)
       benchmark_methods (~> 0.7)
       bibtex-ruby (>= 5.1.0)
@@ -16,9 +16,9 @@ PATH
       json-ld-preloaded (~> 3.1, >= 3.1.3)
       jsonlint (~> 0.3.0)
       loofah (~> 2.0, >= 2.0.3)
-      maremma (>= 4.9.4, < 5)
+      maremma (~> 5.0)
       namae (~> 1.0)
-      nokogiri (>= 1.13.2, < 1.14)
+      nokogiri (~> 1.16, >= 1.16.2)
       oj (~> 3.10)
       oj_mimic_json (~> 1.0, >= 1.0.1)
       postrank-uri (~> 1.0, >= 1.0.18)
@@ -95,10 +95,10 @@ GEM
       concurrent-ruby (~> 1.0)
     iso8601 (0.9.1)
     json (2.6.2)
-    json-canonicalization (0.3.2)
-    json-ld (3.2.5)
+    json-canonicalization (0.3.1)
+    json-ld (3.2.4)
       htmlentities (~> 4.3)
-      json-canonicalization (~> 0.3, >= 0.3.2)
+      json-canonicalization (~> 0.3)
       link_header (~> 0.0, >= 0.0.8)
       multi_json (~> 1.15)
       rack (>= 2.2, < 4)
@@ -114,7 +114,7 @@ GEM
     loofah (2.21.3)
       crass (~> 1.0.2)
       nokogiri (>= 1.12.0)
-    maremma (4.9.9)
+    maremma (5.0.0)
       activesupport (>= 4.2.5)
       addressable (>= 2.3.6)
       builder (~> 3.2, >= 3.2.2)
@@ -125,17 +125,17 @@ GEM
       faraday-follow_redirects (~> 0.3.0)
       faraday-gzip (~> 0.1.0)
       faraday-multipart (~> 1.0.4)
-      nokogiri (>= 1.13.1, < 1.14.0)
+      nokogiri (~> 1.16, >= 1.16.2)
       oj (>= 2.8.3)
       oj_mimic_json (~> 1.0, >= 1.0.1)
     matrix (0.4.2)
-    mini_portile2 (2.8.0)
+    mini_portile2 (2.8.5)
     minitest (5.18.0)
     multi_json (1.15.0)
     multipart-post (2.3.0)
     namae (1.1.1)
-    nokogiri (1.13.9)
-      mini_portile2 (~> 2.8.0)
+    nokogiri (1.16.2)
+      mini_portile2 (~> 2.8.2)
       racc (~> 1.4)
     oj (3.14.2)
     oj_mimic_json (1.0.1)
@@ -225,6 +225,7 @@ DEPENDENCIES
   bundler (>= 1.0)
   byebug
   hashdiff (>= 1.0.0.beta1, < 2.0.0)
+  json-canonicalization (= 0.3.1)
   rack-test (~> 0)
   rake (~> 12.0)
   rspec (~> 3.4)
@@ -234,4 +235,4 @@ DEPENDENCIES
   webmock (~> 3.0, >= 3.0.1)
 
 BUNDLED WITH
-   2.4.20
+   2.5.5

data/bolognese.gemspec

@@ -13,12 +13,12 @@ Gem::Specification.new do |s|
   s.version       = Bolognese::VERSION
   s.extra_rdoc_files = ["README.md"]
   s.license       = 'MIT'
-  s.required_ruby_version = ['>=2.3']
+  s.required_ruby_version = ['>=3.0']
 
   # Declare dependencies here, rather than in the Gemfile
-  s.add_dependency 'maremma', '>= 4.9.4', '< 5'
+  s.add_dependency 'maremma', '~> 5.0'
   #s.add_dependency 'faraday', '~> 0.17.3'
-  s.add_dependency 'nokogiri', '>= 1.13.2', '< 1.14'
+  s.add_dependency 'nokogiri', '~> 1.16', '>= 1.16.2'
   s.add_dependency 'loofah', '~> 2.0', '>= 2.0.3'
   s.add_dependency 'builder', '~> 3.2', '>= 3.2.2'
   s.add_dependency 'activesupport', '>= 4.2.5'
@@ -50,6 +50,7 @@ Gem::Specification.new do |s|
   s.add_development_dependency 'simplecov', '0.17.1'
   s.add_development_dependency 'hashdiff', ['>= 1.0.0.beta1', '< 2.0.0']
   s.add_development_dependency 'byebug'
+  s.add_development_dependency 'json-canonicalization', '0.3.1'
 
   s.require_paths = ["lib"]
   s.files       = `git ls-files`.split($/)

data/lib/bolognese/author_utils.rb

@@ -30,20 +30,20 @@ module Bolognese
       name_type = parse_attributes(author.fetch("creatorName", nil), content: "nameType", first: true) || parse_attributes(author.fetch("contributorName", nil), content: "nameType", first: true)
 
       name_identifiers = Array.wrap(author.fetch("nameIdentifier", nil)).map do |ni|
-        ni["__content__"] = ni["__content__"].strip
+        name_identifier = ni["__content__"].strip if ni["__content__"].present?
         if ni["nameIdentifierScheme"] == "ORCID"
           {
-            "nameIdentifier" => normalize_orcid(ni["__content__"]),
+            "nameIdentifier" => normalize_orcid(name_identifier),
             "schemeUri" => "https://orcid.org",
             "nameIdentifierScheme" => "ORCID" }.compact
         elsif ni["nameIdentifierScheme"] == "ROR"
           {
-            "nameIdentifier" => normalize_ror(ni["__content__"]),
+            "nameIdentifier" => normalize_ror(name_identifier),
             "schemeUri" => "https://ror.org",
             "nameIdentifierScheme" => "ROR" }.compact
         else
           {
-            "nameIdentifier" => ni["__content__"],
+            "nameIdentifier" => name_identifier,
             "schemeUri" => ni.fetch("schemeURI", nil),
             "nameIdentifierScheme" => ni["nameIdentifierScheme"] }.compact
         end

data/lib/bolognese/metadata_utils.rb

@@ -96,7 +96,7 @@ module Bolognese
       if container.present?
         container["title"]
       elsif types["citeproc"] == "article-journal"
-        publisher
+        publisher["name"] if publisher.present?
       else
         nil
       end

data/lib/bolognese/readers/datacite_reader.rb

@@ -101,7 +101,7 @@ module Bolognese
             { "name" => r.strip }
           elsif r.is_a?(Hash)
             {
-              "name" => r["__content__"].strip,
+              "name" => r["__content__"].present? ? r["__content__"].strip : nil,
               "publisherIdentifier" => r["publisherIdentifierScheme"] == "ROR" ? normalize_ror(r["publisherIdentifier"]) : r["publisherIdentifier"],
               "publisherIdentifierScheme" => r["publisherIdentifierScheme"],
               "schemeUri" => r["schemeURI"],

data/lib/bolognese/readers/schema_org_reader.rb

@@ -74,8 +74,11 @@ module Bolognese
           creators = get_authors(from_schema_org_creators(Array.wrap(authors)))
         end
         contributors = get_authors(from_schema_org_contributors(Array.wrap(meta.fetch("editor", nil))))
-        publisher_name = parse_attributes(meta.fetch("publisher", nil), content: "name", first: true)
-        publisher = { "name" => publisher_name } if publisher_name.present?
+
+        publisher = {
+          "name" => parse_attributes(meta.fetch("publisher", nil), content: "name", first: true),
+          "publisherIdentifier" => parse_attributes(meta.fetch("publisher", nil), content: "@id", first: true),
+        }.compact if meta.fetch("publisher", nil).present?
 
         ct = (schema_org == "Dataset") ? "includedInDataCatalog" : "Periodical"
         container = if meta.fetch(ct, nil).present?

data/lib/bolognese/utils.rb

@@ -600,12 +600,12 @@ module Bolognese
     end
 
     def validate_orcid(orcid)
-      orcid = Array(/\A(?:(?:http|https):\/\/(?:(?:www|sandbox)?\.)?orcid\.org\/)?(\d{4}[[:space:]-]\d{4}[[:space:]-]\d{4}[[:space:]-]\d{3}[0-9X]+)\z/.match(orcid)).last
+      orcid = Array(/\A(?:(?:http|https):\/\/(?:(?:www|sandbox)?\.)?orcid\.org\/)?(\d{4}[[:space:]-]\d{4}[[:space:]-]\d{4}[[:space:]-]\d{3}[0-9X]+)\/{0,1}\z/.match(orcid)).last
       orcid.gsub(/[[:space:]]/, "-") if orcid.present?
     end
 
     def validate_ror(ror)
-      Array(/^(?:(?:(?:http|https):\/\/)?ror\.org\/)?(0\w{6}\d{2})$/.match(ror)).last
+      Array(/^(?:(?:(?:http|https):\/\/)?ror\.org\/)?(0\w{6}\d{2})\/{0,1}$/.match(ror)).last
     end
 
     def validate_orcid_scheme(orcid_scheme)

data/lib/bolognese/version.rb

@@ -1,3 +1,3 @@
 module Bolognese
-  VERSION = "2.0.0"
+  VERSION = "2.2.0"
 end

data/lib/bolognese/writers/datacite_json_writer.rb

@@ -4,11 +4,8 @@ module Bolognese
   module Writers
     module DataciteJsonWriter
       def datacite_json
-        # Remove the following change for the schema 4.5 release
         if crosscite_hsh.present?
-          datacite_json_hsh = crosscite_hsh
-          datacite_json_hsh['publisher'] = self.publisher['name'] if self.publisher&.respond_to?(:to_hash) && self.publisher.has_key?('name') && !self.publisher['name'].blank?
-          JSON.pretty_generate datacite_json_hsh.transform_keys! { |key| key.camelcase(uppercase_first_letter = :lower) }
+          JSON.pretty_generate crosscite_hsh.transform_keys! { |key| key.camelcase(uppercase_first_letter = :lower) }
         end
       end
     end

data/lib/bolognese/writers/jats_writer.rb

@@ -86,7 +86,10 @@ module Bolognese
       end
 
       def insert_publisher_name(xml)
-        xml.send("publisher-name", publisher["name"])
+        attributes = {
+          "xml:lang" => publisher["lang"]
+        }.compact
+        xml.send("publisher-name", attributes, publisher["name"])
       end
 
       def insert_publication_date(xml)

data/lib/bolognese/writers/schema_org_writer.rb

@@ -37,7 +37,7 @@ module Bolognese
           "schemaVersion" => schema_version,
           "periodical" => types.present? ? ((types["schemaOrg"] != "Dataset") && container.present? ? to_schema_org(container) : nil) : nil,
           "includedInDataCatalog" => types.present? ? ((types["schemaOrg"] == "Dataset") && container.present? ? to_schema_org_container(container, type: "Dataset") : nil) : nil,
-          "publisher" => publisher.present? ? { "@type" => "Organization", "name" => publisher["name"] } : nil,
+          "publisher" => publisher.present? ? { "@type" => "Organization", "@id" => publisher["publisherIdentifier"], "name" => publisher["name"] }.compact : nil,
           "funder" => to_schema_org_funder(funding_references),
           "provider" => agency.present? ? { "@type" => "Organization", "name" => agency } : nil
         }.compact.presence

data/spec/author_utils_spec.rb

@@ -168,11 +168,12 @@ describe Bolognese::Metadata, vcr: true do
     expect(subject.creators[4]).to eq("nameType"=>"Organizational", "name"=>"University Of Kivu", "nameIdentifiers"=> [{"nameIdentifier"=>"https://ror.org/01qfhxr31", "schemeUri"=>"https://ror.org", "nameIdentifierScheme"=>"ROR"}], "affiliation"=>[])
     expect(subject.creators[5]).to eq("nameType"=>"Organizational", "name"=>"សាកលវិទ្យាល័យកម្ពុជា", "nameIdentifiers"=> [{"nameIdentifier"=>"http://ror.org/025e3rc84", "nameIdentifierScheme"=>"RORS"}], "affiliation"=>[])
     expect(subject.creators[6]).to eq("nameType"=>"Organizational", "name"=>"جامعة زاخۆ", "nameIdentifiers"=> [{"nameIdentifier"=>"05sd1pz50", "schemeUri"=>"https://ror.org", "nameIdentifierScheme"=>"RORS"}], "affiliation"=>[])
+    expect(subject.creators[9]).to eq("nameType"=>"Organizational", "name"=>"Gump South Pacific Research Station", "nameIdentifiers"=> [{"nameIdentifier"=>"https://ror.org/04sk0et52", "schemeUri"=>"https://ror.org", "nameIdentifierScheme"=>"ROR"}], "affiliation"=>[])
     expect(subject.contributors.first).to eq("nameType"=>"Organizational", "name"=>" Nawroz University ", "nameIdentifiers"=> [{"nameIdentifier"=>"https://ror.org/04gp75d48", "schemeUri"=>"https://ror.org", "nameIdentifierScheme"=>"ROR"}], "affiliation"=>[], "contributorType"=>"Producer")
     expect(subject.contributors.last).to eq("nameType"=>"Organizational", "name"=>"University Of Greenland (Https://Www.Uni.Gl/)", "nameIdentifiers"=> [{"nameIdentifier"=>"https://ror.org/00t5j6b61", "schemeUri"=>"https://ror.org", "nameIdentifierScheme"=>"ROR"}],"affiliation"=>[], "contributorType"=>"Sponsor")
   end
 
-  context "affiliationIdentifier" do
+  context "affiliationIdentifier/nameIdentifier" do
     let(:input) { fixture_path + 'datacite-example-ROR-nameIdentifiers.xml' }
     subject { Bolognese::Metadata.new(input: input, from: "datacite") }
 
@@ -207,6 +208,11 @@ describe Bolognese::Metadata, vcr: true do
       expect(subject.creators[8]["nameIdentifiers"]).to eq([{"nameIdentifier"=>"https://orcid.org/0000-0001-9998-0118", "schemeUri"=>"https://orcid.org", "nameIdentifierScheme"=>"ORCID"}])
     end
 
+    it "should normalize valid ORCID nameIdentifier with trailing slash" do
+      #"  0000-0001-9998-0118  ",  # Valid ORCID with leading/trailing spaces
+      expect(subject.creators[10]["nameIdentifiers"]).to eq([{"nameIdentifier"=>"https://orcid.org/0000-0001-9998-0117", "schemeUri"=>"https://orcid.org", "nameIdentifierScheme"=>"ORCID"}])
+    end
+
     it "should parse non ROR schema's without normalizing them" do
       input = fixture_path + 'datacite-example-ROR-nameIdentifiers.xml'
       subject = Bolognese::Metadata.new(input: input, from: "datacite")
@@ -250,4 +256,4 @@ describe Bolognese::Metadata, vcr: true do
       expect(response).to eq("Matt Jones and Peter Slaughter and {University of California, Santa Barbara}")
     end
   end
-end
+end

data/spec/fixtures/datacite-example-ROR-nameIdentifiers.xml

@@ -43,6 +43,14 @@
             <creatorName nameType="Personal">Mike B</creatorName>
             <nameIdentifier nameIdentifierScheme="ORCID"> 0000-0001-9998-0118 </nameIdentifier>
         </creator>
+        <creator>
+            <creatorName nameType="Organizational">Gump South Pacific Research Station</creatorName>
+            <nameIdentifier nameIdentifierScheme="ROR" schemeURI="https://ror.org/">https://ror.org/04sk0et52/</nameIdentifier>
+        </creator>
+        <creator>
+            <creatorName nameType="Personal">Ashwini Sukale</creatorName>
+            <nameIdentifier schemeURI="https://orcid.org/" nameIdentifierScheme="ORCID">https://orcid.org/0000-0001-9998-0117/</nameIdentifier>
+        </creator>
     </creators>
     <titles>
         <title xml:lang="en-US">Genomic Standards Consortium (GSC) Island Sampling Day: Moorea Reef to Ridges Genomic Transect</title>

data/spec/fixtures/datacite-xml-lang.xml

@@ -15,7 +15,7 @@
         <title xml:lang="en">DOI Test 2 title content</title>
         <title xml:lang="en">AAPP</title>
     </titles>
-    <publisher>OSI SAF</publisher>
+    <publisher xml:lang="en">OSI SAF</publisher>
     <publicationYear>2004</publicationYear>
     <resourceType resourceTypeGeneral="Collection">Climate Data Record</resourceType>
     <dates>

data/spec/fixtures/datacite_blank_name_identifier.xml

@@ -0,0 +1,22 @@
+<?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://schema.datacite.org/meta/kernel-4.3/metadata.xsd">
+  <identifier identifierType="DOI">10.15148/3b68dac4-7688-4fbb-ba64-5f9b3bbab954</identifier>
+  <creators>
+    <creator>
+      <creatorName>SNO KARST</creatorName>
+      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="https://orcid.org"/>
+    </creator>
+  </creators>
+  <publisher>OSU OREME</publisher>
+  <titles>
+    <title>Time series of type chemistry in Le Tarn basin - PARC NATIONAL CEVENNES observatory - KARST observatory network -  OZCAR Critical Zone network Research Infrastructure</title>
+  </titles>
+  <publicationYear>2023</publicationYear>
+  <contributors>
+    <contributor contributorType="ProjectMember">
+      <contributorName>Manche, Yannick</contributorName>
+      <nameIdentifier schemeURI="http://orcid.org/" nameIdentifierScheme="ORCID"></nameIdentifier>
+    </contributor>
+  </contributors>
+  <resourceType resourceTypeGeneral="Dataset">Dataset</resourceType>
+</resource>

data/spec/fixtures/datacite_blank_publisher.xml

@@ -0,0 +1,18 @@
+<?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">10.81360/4DVP-KR57</identifier>
+  <creators>
+    <creator>
+      <creatorName nameType="Personal">Møller, Jørgen</creatorName>
+      <givenName>Jørgen</givenName>
+      <familyName>Møller</familyName>
+    </creator>
+  </creators>
+  <titles>
+    <title xml:lang="en">Economic Crisis and Democratic Breakdown in the Interwar Years: A Reassessment</title>
+    <title xml:lang="de">Wirtschaftskrise und demokratischer Zusammenbruch in der Zwischenkriegszeit: Eine Neubewertung</title>
+  </titles>
+  <publisher publisherIdentifier="https://ror.org/04wxnsj81"></publisher>
+  <publicationYear>2015</publicationYear>
+  <resourceType resourceTypeGeneral="JournalArticle"/>
+</resource>

data/spec/fixtures/datacite_journal_article.xml

@@ -0,0 +1,64 @@
+<?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">10.60843/5EGY-VC42</identifier>
+    <creators>
+        <creator>
+            <creatorName nameType="Personal">Feldman, Heidi Li</creatorName>
+            <givenName>Heidi Li</givenName>
+            <familyName>Feldman</familyName>
+            <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="https://orcid.org">https://orcid.org/0000-0003-1905-2698</nameIdentifier>
+        </creator>
+    </creators>
+    <titles>
+        <title xml:lang="en">Science and Uncertainty in Mass Exposure Litigation</title>
+        <title xml:lang="en">Science and Uncertainty in Mass Exposure Litigation, 74 Tex. L. Rev. 1 (1995)</title>
+    </titles>
+    <publisher>Texas Law Review</publisher>
+    <publicationYear>1995</publicationYear>
+    <resourceType resourceTypeGeneral="JournalArticle">Article</resourceType>
+    <subjects>
+        <subject subjectScheme="Fields of Science and Technology (FOS)" schemeURI="http://www.oecd.org/science/inno/38235147.pdf" classificationCode="5.5">FOS: Law</subject>
+    </subjects>
+    <contributors>
+        <contributor contributorType="HostingInstitution">
+            <contributorName nameType="Organizational">Georgetown Law Library</contributorName>
+            <nameIdentifier nameIdentifierScheme="" schemeURI=""/>
+            <affiliation affiliationIdentifier="https://ror.org/05vzafd60" affiliationIdentifierScheme="ROR" schemeURI="https://ror.org">Georgetown University</affiliation>
+        </contributor>
+    </contributors>
+    <dates>
+        <date dateType="Issued">1995-11</date>
+        <date dateType="Collected">2016-04-25</date>
+    </dates>
+    <language>en</language>
+    <relatedIdentifiers>
+        <relatedIdentifier relatedIdentifierType="ISSN" relationType="IsPublishedIn" resourceTypeGeneral="Journal">0040-4411</relatedIdentifier>
+    </relatedIdentifiers>
+    <relatedItems>
+        <relatedItem relatedItemType="Journal" relationType="IsSourceOf">
+            <relatedItemIdentifier relatedItemIdentifierType="ISSN">0040-4411</relatedItemIdentifier>
+            <creators>
+                <creator>
+                    <creatorName>University of Texas School of Law</creatorName>
+                </creator>
+            </creators>
+            <titles>
+                <title>Texas Law Review</title>
+            </titles>
+            <publicationYear>1995</publicationYear>
+            <volume>74</volume>
+            <issue>1</issue>
+        </relatedItem>
+    </relatedItems>
+    <sizes/>
+    <formats>
+        <format>text/html</format>
+        <format>application/pdf</format>
+    </formats>
+    <version/>
+    <descriptions>
+        <description xml:lang="en" descriptionType="Abstract">Critics of the tort system have condemned courts for their alleged leniency in admitting scientific expert testimony, especially in mass exposure litigation. Claiming that this has resulted in an epidemic of "junk science" in the courtroom, these commentators have urged a more scientific approach to admissibility, intimating that employing more scientific standards would exclude scientific evidence favorable to plaintiffs, thereby demonstrating to factfinders that litigated substances are in fact safe or at least not unsafe.</description>
+    </descriptions>
+</resource>

data/spec/fixtures/schema_org.json

@@ -14,6 +14,7 @@
     }],
     "publisher": {
         "@type": "Organization",
+        "@id": "https://ror.org/04wxnsj81",
         "name": "DataCite"
     },
     "dateCreated": "2016-12-20",

data/spec/readers/datacite_reader_spec.rb

@@ -1759,4 +1759,54 @@ describe Bolognese::Metadata, vcr: true do
       )
     end
   end
+
+  it "blank nameIdentifier" do
+    input = fixture_path + "datacite_blank_name_identifier.xml"
+    subject = Bolognese::Metadata.new(input: input)
+    expect(subject.creators).to eq(
+      [
+        {
+          "nameType" => "Personal",
+          "name" => "KARST, SNO",
+          "givenName" => "SNO",
+          "familyName" => "KARST",
+          "nameIdentifiers" =>
+            [
+              {
+                "schemeUri" => "https://orcid.org",
+                "nameIdentifierScheme" => "ORCID"
+              }
+            ],
+          "affiliation" => []
+        }
+      ]
+    )
+    expect(subject.contributors).to eq(
+      [
+        {
+          "nameType" => "Personal",
+          "name" => "Manche, Yannick",
+          "givenName" => "Yannick",
+          "familyName" => "Manche",
+          "nameIdentifiers" =>
+            [
+              {
+                "schemeUri" => "https://orcid.org",
+                "nameIdentifierScheme" => "ORCID"
+              }
+            ],
+          "affiliation" => [],
+          "contributorType" => "ProjectMember"
+        }
+      ]
+    )
+  end
+
+  it "blank publisher" do
+    input = fixture_path + "datacite_blank_publisher.xml"
+    subject = Bolognese::Metadata.new(input: input)
+    expect(subject.publisher).to eq(
+      { "publisherIdentifier" => "https://ror.org/04wxnsj81" }
+    )
+  end
 end

data/spec/readers/schema_org_reader_spec.rb

@@ -169,7 +169,7 @@ describe Bolognese::Metadata, vcr: true do
       expect(subject.publication_year).to eq("2016")
       expect(subject.related_identifiers.length).to eq(3)
       expect(subject.related_identifiers.last).to eq("relatedIdentifier"=>"10.5438/55e5-t5c0", "relatedIdentifierType"=>"DOI", "relationType"=>"References")
-      expect(subject.publisher).to eq({"name"=>"DataCite"})
+      expect(subject.publisher).to eq({"name"=>"DataCite", "publisherIdentifier"=>"https://ror.org/04wxnsj81"})
     end
 
     it "GTEx dataset" do

data/spec/writers/citation_writer_spec.rb

@@ -48,5 +48,14 @@ describe Bolognese::Metadata, vcr: true do
       expect(subject.locale).to eq("en-US")
       expect(subject.citation).to eq("Clark, D. (2019). <i>Exploring the \"Many analysts, one dataset\" project from COS</i>. Gigantum, Inc. https://doi.org/10.34747/g6yb-3412")
     end
+
+    it "journal article with container title" do
+      input = fixture_path + "datacite_journal_article.xml"
+      subject = Bolognese::Metadata.new(input: input, from: "datacite")
+      expect(subject.types["citeproc"]).to eq("article-journal")
+      expect(subject.style).to eq("apa")
+      expect(subject.locale).to eq("en-US")
+      expect(subject.citation).to eq('Feldman, H. L. (1995). Science and Uncertainty in Mass Exposure Litigation. <i>Texas Law Review</i>. https://doi.org/10.60843/5egy-vc42')
+    end
   end
 end

data/spec/writers/datacite_json_writer_spec.rb

@@ -18,9 +18,7 @@ describe Bolognese::Metadata, vcr: true do
         "rightsIdentifierScheme"=>"SPDX",
         "rightsUri"=>"https://creativecommons.org/licenses/by/3.0/legalcode",
         "schemeUri"=>"https://spdx.org/licenses/"}])
-      # REVERT the publisher line to the commented line for the schema 4.5 release
-      # expect(datacite.fetch("publisher")).to eq({"name"=>"eLife Sciences Publications, Ltd"})
-      expect(datacite.fetch("publisher")).to eq("eLife Sciences Publications, Ltd")
+      expect(datacite.fetch("publisher")).to eq({"name"=>"eLife Sciences Publications, Ltd"})
     end
 
     it "with ORCID ID" do
@@ -31,9 +29,7 @@ describe Bolognese::Metadata, vcr: true do
       expect(datacite.fetch("types")).to eq("bibtex"=>"article", "citeproc"=>"article-journal", "resourceType"=>"JournalArticle", "resourceTypeGeneral"=>"JournalArticle", "ris"=>"JOUR", "schemaOrg"=>"ScholarlyArticle")
       expect(datacite.fetch("creators").length).to eq(7)
       expect(datacite.fetch("creators").first).to eq("nameType"=>"Personal", "name"=>"Thanassi, Wendy", "givenName"=>"Wendy", "familyName"=>"Thanassi", "affiliation" => [{"name"=>"Department of Medicine, Veterans Affairs Palo Alto Health Care System, 3801 Miranda Avenue MC-, Palo Alto, CA 94304-1207, USA"}, {"name"=>"Occupational Health Strategic Health Care Group, Office of Public Health, Veterans Health Administration, Washington, DC 20006, USA"}, {"name"=>"Division of Emergency Medicine, Stanford University School of Medicine, Stanford, CA 94304, USA"}, {"name"=>"War Related Illness and Injury Study Center (WRIISC) and Mental Illness Research Education and Clinical Center (MIRECC), Department of Veterans Affairs, Palo Alto, CA 94304, USA"}])
-      # REVERT the publisher line to the commented line for the schema 4.5 release
-      # expect(datacite.fetch("publisher")).to eq({"name"=>"Hindawi Limited"})
-      expect(datacite.fetch("publisher")).to eq("Hindawi Limited")
+      expect(datacite.fetch("publisher")).to eq({"name"=>"Hindawi Limited"})
     end
 
     it "Crossref DOI" do
@@ -45,9 +41,7 @@ describe Bolognese::Metadata, vcr: true do
       expect(datacite.dig("descriptions", 0, "description")).to start_with("Among various advantages, their small size makes model organisms preferred subjects of investigation.")
       expect(datacite.fetch("creators").length).to eq(5)
       expect(datacite.fetch("creators").first).to eq("nameType"=>"Personal", "name"=>"Sankar, Martial", "givenName"=>"Martial", "familyName"=>"Sankar")
-      # REVERT the publisher line to the commented line for the schema 4.5 release
-      # expect(datacite.fetch("publisher")).to eq({"name"=>"{eLife} Sciences Organisation, Ltd."})
-      expect(datacite.fetch("publisher")).to eq("{eLife} Sciences Organisation, Ltd.")
+      expect(datacite.fetch("publisher")).to eq({"name"=>"{eLife} Sciences Organisation, Ltd."})
     end
 
     it "BlogPosting Citeproc JSON" do
@@ -58,9 +52,7 @@ describe Bolognese::Metadata, vcr: true do
       expect(datacite.fetch("titles")).to eq([{"title"=>"Eating your own Dog Food"}])
       expect(datacite.dig("descriptions", 0, "description")).to start_with("Eating your own dog food")
       expect(datacite.fetch("creators")).to eq([{"familyName"=>"Fenner", "givenName"=>"Martin", "name"=>"Fenner, Martin"}])
-      # REVERT the publisher line to the commented line for the schema 4.5 release
-      # expect(datacite.fetch("publisher")).to eq({"name"=>"DataCite"})
-      expect(datacite.fetch("publisher")).to eq("DataCite")
+      expect(datacite.fetch("publisher")).to eq({"name"=>"DataCite"})
     end
 
     it "rdataone" do
@@ -72,9 +64,7 @@ describe Bolognese::Metadata, vcr: true do
       expect(datacite.fetch("creators").first).to eq("affiliation"=>[{"name"=>"NCEAS"}], "nameType"=>"Personal", "name" => "Jones, Matt",
         "nameIdentifiers" => [{"nameIdentifier"=>"https://orcid.org/0000-0003-0077-4738", "nameIdentifierScheme"=>"ORCID", "schemeUri"=>"https://orcid.org"}], "givenName"=>"Matt", "familyName"=>"Jones")
       expect(datacite.fetch("version")).to eq("2.0.0")
-      # REVERT the publisher line to the commented line for the schema 4.5 release
-      # expect(datacite.fetch("publisher")).to eq({"name"=>"https://cran.r-project.org"})
-      expect(datacite.fetch("publisher")).to eq("https://cran.r-project.org")
+      expect(datacite.fetch("publisher")).to eq({"name"=>"https://cran.r-project.org"})
     end
 
     it "maremma" do
@@ -90,9 +80,7 @@ describe Bolognese::Metadata, vcr: true do
          [{"nameIdentifier"=>"https://orcid.org/0000-0003-0077-4738",
            "nameIdentifierScheme"=>"ORCID", "schemeUri"=>"https://orcid.org"}],
         "nameType"=>"Personal"}])
-      # REVERT the publisher line to the commented line for the schema 4.5 release
-      # expect(datacite.fetch("publisher")).to eq({"name"=>"DataCite"})
-      expect(datacite.fetch("publisher")).to eq("DataCite")
+      expect(datacite.fetch("publisher")).to eq({"name"=>"DataCite"})
     end
 
     it "with data citation schema.org" do
@@ -103,26 +91,22 @@ describe Bolognese::Metadata, vcr: true do
       expect(datacite.fetch("titles")).to eq([{"title"=>"Eating your own Dog Food"}])
       expect(datacite.fetch("relatedIdentifiers").count).to eq(3)
       expect(datacite.fetch("relatedIdentifiers").first).to eq("relatedIdentifier"=>"10.5438/0000-00ss", "relatedIdentifierType"=>"DOI", "relationType"=>"IsPartOf", "resourceTypeGeneral"=>"Text")
-      # REVERT the publisher line to the commented line for the schema 4.5 release
-      # expect(datacite.fetch("publisher")).to eq({"name"=>"DataCite"})
-      expect(datacite.fetch("publisher")).to eq("DataCite")
+      expect(datacite.fetch("publisher")).to eq({"name"=>"DataCite"})
     end
 
     it "DataCite DOI with Schema 4.5 publisher attributes" do
       input = fixture_path + "datacite-example-full-v4.5.xml"
       subject = Bolognese::Metadata.new(input: input, from: "datacite")
       datacite = JSON.parse(subject.datacite_json)
-      # REVERT the publisher line to the commented lines for the schema 4.5 release
-      # expect(datacite.fetch("publisher")).to eq(
-      #   {
-      #     "name" => "Example Publisher",
-      #     "publisherIdentifier" => "https://ror.org/04z8jg394",
-      #     "publisherIdentifierScheme" => "ROR",
-      #     "schemeUri" => "https://ror.org/",
-      #     "lang" => "en",
-      #   },
-      # )
-      expect(datacite.fetch("publisher")).to eq("Example Publisher")
+      expect(datacite.fetch("publisher")).to eq(
+        {
+          "name" => "Example Publisher",
+          "publisherIdentifier" => "https://ror.org/04z8jg394",
+          "publisherIdentifierScheme" => "ROR",
+          "schemeUri" => "https://ror.org/",
+          "lang" => "en",
+        },
+      )
     end
   end
 end

data/spec/writers/jats_writer_spec.rb

@@ -179,6 +179,13 @@ describe Bolognese::Metadata, vcr: true do
       expect(jats.dig("day")).to be_nil
       expect(jats.dig("pub_id")).to eq("pub_id_type"=>"doi", "__content__"=>"10.34747/g6yb-3412")
     end
+
+    it "with publisher with language" do
+      input = fixture_path + 'datacite-xml-lang.xml'
+      subject = Bolognese::Metadata.new(input: input)
+      jats = Maremma.from_xml(subject.jats).fetch("element_citation", {})
+      expect(jats.dig("publisher_name")).to eq({"xml:lang"=>"en", "__content__"=>"OSI SAF"})
+    end
   end
 
   context "change metadata as datacite xml" do

data/spec/writers/schema_org_writer_spec.rb

@@ -365,5 +365,18 @@ describe Bolognese::Metadata, vcr: true do
       expect(json["@type"]).to eq("CreativeWork")
       expect(json["datePublished"]).to eq("2019")
     end
+
+    it "from Schema 4.5 with publisher attributes" do
+      input = fixture_path + 'datacite-example-full-v4.5.xml'
+      subject = Bolognese::Metadata.new(input: input)
+      json = JSON.parse(subject.schema_org)
+      expect(json["publisher"]).to eq(
+         {
+          "@type" => "Organization",
+          "@id" => "https://ror.org/04z8jg394",
+          "name" => "Example Publisher"
+         }
+      )
+    end
   end
 end

metadata

@@ -1,55 +1,49 @@
 --- !ruby/object:Gem::Specification
 name: bolognese
 version: !ruby/object:Gem::Version
-  version: 2.0.0
+  version: 2.2.0
 platform: ruby
 authors:
 - Martin Fenner
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2023-12-04 00:00:00.000000000 Z
+date: 2024-02-28 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: maremma
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: 4.9.4
-    - - "<"
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '5'
+        version: '5.0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: 4.9.4
-    - - "<"
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '5'
+        version: '5.0'
 - !ruby/object:Gem::Dependency
   name: nokogiri
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: 1.13.2
-    - - "<"
+        version: '1.16'
+    - - ">="
       - !ruby/object:Gem::Version
-        version: '1.14'
+        version: 1.16.2
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: 1.13.2
-    - - "<"
+        version: '1.16'
+    - - ">="
       - !ruby/object:Gem::Version
-        version: '1.14'
+        version: 1.16.2
 - !ruby/object:Gem::Dependency
   name: loofah
   requirement: !ruby/object:Gem::Requirement
@@ -556,6 +550,20 @@ dependencies:
     - - ">="
       - !ruby/object:Gem::Version
         version: '0'
+- !ruby/object:Gem::Dependency
+  name: json-canonicalization
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 0.3.1
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 0.3.1
 description: Ruby gem and command-line utility for conversion of DOI metadata from
   and to different metadata formats, including schema.org.
 email: mfenner@datacite.org
@@ -814,7 +822,10 @@ files:
 - spec/fixtures/datacite-xml-lang.xml
 - spec/fixtures/datacite.json
 - spec/fixtures/datacite.xml
+- spec/fixtures/datacite_blank_name_identifier.xml
+- spec/fixtures/datacite_blank_publisher.xml
 - spec/fixtures/datacite_dataset.xml
+- spec/fixtures/datacite_journal_article.xml
 - spec/fixtures/datacite_malformed_creator.xml
 - spec/fixtures/datacite_missing_creator.xml
 - spec/fixtures/datacite_schema_3.xml
@@ -1305,14 +1316,14 @@ required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
   - - ">="
     - !ruby/object:Gem::Version
-      version: '2.3'
+      version: '3.0'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
   - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.0.3.1
+rubygems_version: 3.3.26
 signing_key: 
 specification_version: 4
 summary: Ruby client library for conversion of DOI Metadata