bolognese 2.0.3 → 2.1.1

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: 997f406aa28447acf4507aad0c2ffb0f4e4e42da4028dbe2210d027b438dea09
+  metadata.gz: 71ee294125ac977b19c081b25a540d504bc78e932be89beb5d25e4754637166d
+  data.tar.gz: e95a2a6495a9ae0cf3014ba20024902da8ab1fd78d28472abfa0472ea3eb9b2b
 SHA512:
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-  data.tar.gz: d1a74bd310e4ad4a7e8f34c218685cf3d76183d063feffab36c926e4d449e46a0792b2d279d4aeb6540ad74c441cabda0d242053eb96a01f5c6598112a1848e2
+  metadata.gz: 02de737b6845e350022dff585da6c2c5ef564852ae41e569d27474aee996afb482fa7711e7a47ebe0d020df9d7a93e88dc889d2529896955306a784d0b4862b5
+  data.tar.gz: 78b6149f043f22700f638a8105e9242e98e9da9cb4329a427f35c0e4c51125044eedaf639994b0586296f1cb1e65c15694304b340a5b3dab9a36631490c45fd0

data/Gemfile.lock

@@ -1,7 +1,7 @@
 PATH
   remote: .
   specs:
-    bolognese (2.0.3)
+    bolognese (2.1.1)
       activesupport (>= 4.2.5)
       benchmark_methods (~> 0.7)
       bibtex-ruby (>= 5.1.0)
@@ -235,4 +235,4 @@ DEPENDENCIES
   webmock (~> 3.0, >= 3.0.1)
 
 BUNDLED WITH
-   2.4.20
+   2.4.22

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 = "2.0.3"
+  VERSION = "2.1.1"
 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/schema_org.json

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

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/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

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bolognese
 version: !ruby/object:Gem::Version
-  version: 2.0.3
+  version: 2.1.1
 platform: ruby
 authors:
 - Martin Fenner
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2023-12-11 00:00:00.000000000 Z
+date: 2024-02-26 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: maremma