bolognese 2.1.0 → 2.2.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: b97f37a5ebcbedcb33b6937353b9afe721084c52591033d04657c8ef1e3fa4b7
-  data.tar.gz: 119f596d499c6465304b91eb2ea4733a6d83be967d564bf0bc895e69312133d0
+  metadata.gz: ce52f2eb08396d0e56bdccf06702901fe7c04f1925cacafc71f315a1edda91c3
+  data.tar.gz: 29fb5a1d987a95220bbc7a3912aa24735f54924f47c8a74d61d1f51e25b75314
 SHA512:
-  metadata.gz: 77194ea5ab5fac3555fad930a642081f4cb146dc804baed87b35be72f9c91cf88a72e44a1b2a8ab760f15ce5d49843dd65f2c41b24aa3ce840a940093705d715
-  data.tar.gz: 504322b19079059e7946043c087408237e48e1266f76cc4cb9bbfaf980d47d0f628dda1e1b35d20d79a27b07e18fb220b5a22234ee572b82020a31d98f52c196
+  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 (2.1.0)
+    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)
@@ -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)
@@ -235,4 +235,4 @@ DEPENDENCIES
   webmock (~> 3.0, >= 3.0.1)
 
 BUNDLED WITH
-   2.4.22
+   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'

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 = "2.1.0"
+  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/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/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

metadata

@@ -1,55 +1,49 @@
 --- !ruby/object:Gem::Specification
 name: bolognese
 version: !ruby/object:Gem::Version
-  version: 2.1.0
+  version: 2.2.0
 platform: ruby
 authors:
 - Martin Fenner
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2024-01-08 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
@@ -1322,14 +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