bolognese 1.11.2 → 1.11.3

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 55d900e332741ad66b6b4bc1d0abd62fc7f2f8fff4e3800fa80c9745d5366cce
-  data.tar.gz: 8d646dcaa3e7224387b49bb76102d979e2e8cd89f07e390a4b5ab296b5cbe907
+  metadata.gz: 84e06f3ca24650902cd1d96f777b2103a242fc44346d9995667961f090c1e300
+  data.tar.gz: 047d14ab54b8a9aa0569bdaeb90806a8a835809f399693c2b29c0a97e9eb0658
 SHA512:
-  metadata.gz: 5b9b9e267bab3ffcbdd4b866867ca98e395b9222ce5bd396ac559a8133736562a31b382d2ddce0d75255ba6099ebcdd203f440a2c83ff20b86fd4072f0eda44e
-  data.tar.gz: 913398d14852b68b6e4c82cb373f288a8746bb39b80586cba43960657ab63dd367efeedb8bb8e507fa68ecd2bdbd4d0a54945e3765a1115bea7e1ea5fe63ee4c
+  metadata.gz: 2547f9e0c41915163269e3802c32c2f73abf6977987748eb70eec7d324585487585a3952a8874bb40e35e4d65d748e6968c0d1f7d92f76992ee3068b2cd718dd
+  data.tar.gz: 3beb48ca299e9b0a1ab95e7e74fabd99e127c374a513b9b775644695e12ac489f3d35851bc1553bc01a593c2ce3c84bc37e8f5e2bd452f6ac561d431edd4f669

data/.github/workflows/build.yml

@@ -7,17 +7,3 @@ on:
 jobs:
   ci:
     uses: ./.github/workflows/ci.yml
-  build:
-    needs: ci
-    runs-on: ubuntu-latest
-    env:
-      SLACK_WEBHOOK_URL: ${{ secrets.SLACK_WEBHOOK_URL }}
-    steps:
-    - name: Notify Slack
-      uses: adamkdean/simple-slack-notify@1.0.4
-      with:
-        channel: '#ops'
-        username: 'GitHub Actions'
-        color: 'good'
-        text: 'A new version of the bolognese gem is ready for release.'
-

data/.github/workflows/release.yml

@@ -9,8 +9,6 @@ jobs:
   build:
     needs: ci
     runs-on: ubuntu-latest
-    env:
-      SLACK_WEBHOOK_URL: ${{ secrets.SLACK_WEBHOOK_URL }}
     steps:
     - uses: actions/checkout@v3
     - name: Set up Ruby 2.6
@@ -32,11 +30,3 @@ jobs:
         gem push *.gem
       env:
         GEM_HOST_API_KEY: "${{secrets.RUBYGEMS_AUTH_TOKEN}}"
-
-    - name: Notify Slack
-      uses: adamkdean/simple-slack-notify@1.0.4
-      with:
-        channel: '#ops'
-        username: 'GitHub Actions'
-        color: 'good'
-        text: 'A new version of the bolognese gem has been released.'

data/Gemfile.lock

@@ -1,7 +1,7 @@
 PATH
   remote: .
   specs:
-    bolognese (1.11.2)
+    bolognese (1.11.3)
       activesupport (>= 4.2.5)
       benchmark_methods (~> 0.7)
       bibtex-ruby (>= 5.1.0)
@@ -232,4 +232,4 @@ DEPENDENCIES
   webmock (~> 3.0, >= 3.0.1)
 
 BUNDLED WITH
-   2.3.12
+   2.4.10

data/lib/bolognese/author_utils.rb

@@ -144,16 +144,28 @@ module Bolognese
           affiliation_identifier_scheme = nil
           scheme_uri = nil
         else
+          scheme_uri = a["schemeURI"]
           if a["affiliationIdentifier"].present?
             affiliation_identifier = a["affiliationIdentifier"]
             if a["schemeURI"].present?
               schemeURI = a["schemeURI"].end_with?("/") ? a["schemeURI"] : a["schemeURI"] + "/"
             end
             affiliation_identifier = !affiliation_identifier.to_s.start_with?("https://") && schemeURI.present? ? normalize_id(schemeURI + affiliation_identifier) : normalize_id(affiliation_identifier)
+            # The normalize_id(affiliation_identifier) method currently discards affiliation identifiers that don't start with a URL, 
+            # for example: affiliation_identifier = "05bp8ka05".
+            # To address this issue, we are introducing the following change to handle such affiliation identifiers.
+            # when `normalize_id` method could not normalize, it returns nil, hence we have following condition
+            if affiliation_identifier.nil?
+              if a["affiliationIdentifierScheme"] == "ROR"
+                scheme_uri = "https://ror.org"
+                affiliation_identifier = normalize_ror(a["affiliationIdentifier"])
+              else
+                affiliation_identifier = a["affiliationIdentifier"]
+              end
+            end
           end
           name = a["__content__"].to_s.squish.presence
           affiliation_identifier_scheme = a["affiliationIdentifierScheme"]
-          scheme_uri = a["SchemeURI"]
         end
 
         { "name" => name,

data/lib/bolognese/version.rb

@@ -1,3 +1,3 @@
 module Bolognese
-  VERSION = "1.11.2"
+  VERSION = "1.11.3"
 end

data/spec/author_utils_spec.rb

@@ -163,15 +163,39 @@ describe Bolognese::Metadata, vcr: true do
   it "has ROR nameIdentifiers" do
     input = fixture_path + 'datacite-example-ROR-nameIdentifiers.xml'
     subject = Bolognese::Metadata.new(input: input, from: "datacite")
-    expect(subject.creators[1]).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.creators[2]).to eq("nameType"=>"Organizational", "name"=>"University Of Vic", "nameIdentifiers"=> [{"nameIdentifier"=>"https://ror.org/006zjws59", "schemeUri"=>"https://ror.org", "nameIdentifierScheme"=>"ROR"}], "affiliation"=>[])
-    expect(subject.creators[3]).to eq("nameType"=>"Organizational", "name"=>"University Of Kivu", "nameIdentifiers"=> [{"nameIdentifier"=>"https://ror.org/01qfhxr31", "schemeUri"=>"https://ror.org", "nameIdentifierScheme"=>"ROR"}], "affiliation"=>[])
-    expect(subject.creators[4]).to eq("nameType"=>"Organizational", "name"=>"សាកលវិទ្យាល័យកម្ពុជា", "nameIdentifiers"=> [{"nameIdentifier"=>"http://ror.org/025e3rc84", "nameIdentifierScheme"=>"RORS"}], "affiliation"=>[])
-    expect(subject.creators[5]).to eq("nameType"=>"Organizational", "name"=>"جامعة زاخۆ", "nameIdentifiers"=> [{"nameIdentifier"=>"05sd1pz50", "schemeUri"=>"https://ror.org", "nameIdentifierScheme"=>"RORS"}], "affiliation"=>[])
+    expect(subject.creators[2]).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.creators[3]).to eq("nameType"=>"Organizational", "name"=>"University Of Vic", "nameIdentifiers"=> [{"nameIdentifier"=>"https://ror.org/006zjws59", "schemeUri"=>"https://ror.org", "nameIdentifierScheme"=>"ROR"}], "affiliation"=>[])
+    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.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
+    it "should normalize ROR affiliationIdentifier with and without URL" do
+      input = fixture_path + 'datacite-example-ROR-nameIdentifiers.xml'
+      subject = Bolognese::Metadata.new(input: input, from: "datacite")
+      # without URL inside affiliationIdentifier="05bp8ka77"
+      ror_affiliater0 = subject.creators[0]["affiliation"].select { |r| r["affiliationIdentifierScheme"] == "ROR" }
+      expect(ror_affiliater0[0]["affiliationIdentifier"]).to eq("https://ror.org/05bp8ka77")
+      # with URL "affiliationIdentifier"=>"https://ror.org/05bp8ka05"
+      ror_affiliater1 = subject.creators[1]["affiliation"].select { |r| r["affiliationIdentifierScheme"] == "ROR" }
+      expect(ror_affiliater1[0]["affiliationIdentifier"]).to eq("https://ror.org/05bp8ka05")
+    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")
+      # without "schemeURI"
+      grid_affiliater0 = subject.creators[0]["affiliation"].select { |r| r["affiliationIdentifierScheme"] == "GRID" }
+      expect(grid_affiliater0[0]["affiliationIdentifier"]).to eq("grid.268117.b")
+      # with "schemeURI"=>"https://grid.ac/institutes/"
+      grid_affiliater1 = subject.creators[1]["affiliation"].select { |r| r["affiliationIdentifierScheme"] == "GRID" }
+      expect(grid_affiliater1[0]["affiliationIdentifier"]).to eq("https://grid.ac/institutes/grid.268117.b")
+    end
+  end
+
   context "authors_as_string" do
     let(:author_with_organization) { [{"type"=>"Person",
                                        "id"=>"http://orcid.org/0000-0003-0077-4738",

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

@@ -3,10 +3,17 @@
     xmlns="http://datacite.org/schema/kernel-4" xsi:schemaLocation="http://datacite.org/schema/kernel-%s http://schema.datacite.org/meta/kernel-4/metadata.xsd">
     <identifier identifierType="DOI">10.48321/D1Z60Q</identifier>
     <creators>
+        <creator>
+            <creatorName nameType="Personal">Ashwini Sukale</creatorName>
+            <nameIdentifier schemeURI="https://orcid.org/" nameIdentifierScheme="ORCID"> https://orcid.org/0000-0001-9998-0117 </nameIdentifier>
+            <affiliation affiliationIdentifier="05bp8ka77" affiliationIdentifierScheme="ROR"> Metadata Game Changers </affiliation>
+            <affiliation affiliationIdentifier="grid.268117.b" affiliationIdentifierScheme="GRID">Wesleyan University</affiliation>
+        </creator>
         <creator>
             <creatorName nameType="Personal">Erin Robinson</creatorName>
             <nameIdentifier schemeURI="https://orcid.org/" nameIdentifierScheme="ORCID"> https://orcid.org/0000-0001-9998-0114 </nameIdentifier>
             <affiliation schemeURI="https://ror.org" affiliationIdentifier="https://ror.org/05bp8ka05" affiliationIdentifierScheme="ROR"> Metadata Game Changers </affiliation>
+            <affiliation affiliationIdentifier="grid.268117.b" affiliationIdentifierScheme="GRID" schemeURI="https://grid.ac/institutes/">Wesleyan University</affiliation>
         </creator>
         <creator>
             <creatorName nameType="Organizational">Gump South Pacific Research Station</creatorName>

data/spec/readers/datacite_reader_spec.rb

@@ -121,7 +121,7 @@ describe Bolognese::Metadata, vcr: true do
         "name"=>"Brown University"},
        {"affiliationIdentifier"=>"https://grid.ac/institutes/grid.268117.b",
         "affiliationIdentifierScheme"=>"GRID",
-        "name"=>"Wesleyan University"}])
+        "name"=>"Wesleyan University", "schemeUri"=>"https://grid.ac/institutes/"}])
       expect(subject.creators.dig(2, "affiliation")).to eq([{"affiliationIdentifier"=>"https://ror.org/05gq02987",
         "affiliationIdentifierScheme"=>"ROR", "name"=>"Brown University"}])
       expect(subject.titles).to eq([{"lang"=>"en-US", "title"=>"Full DataCite XML Example"}, {"lang"=>"en-US", "title"=>"Demonstration of DataCite Properties.", "titleType"=>"Subtitle"}])
@@ -950,7 +950,7 @@ describe Bolognese::Metadata, vcr: true do
       expect(subject.types["ris"]).to eq("DATA")
       expect(subject.types["bibtex"]).to eq("misc")
       expect(subject.creators.length).to eq(1)
-      expect(subject.creators.first).to eq("affiliation" => [{"affiliationIdentifier"=>"https://ror.org/04zt3wx35", "affiliationIdentifierScheme"=>"ROR", "name"=>"Canada Mortgage and Housing Corporation"}],
+      expect(subject.creators.first).to eq("affiliation" => [{"affiliationIdentifier"=>"https://ror.org/04zt3wx35", "affiliationIdentifierScheme"=>"ROR", "name"=>"Canada Mortgage and Housing Corporation", "schemeUri"=>"https://ror.org"}],
         "name" => "Statistique Canada",
          "nameIdentifiers" => [],
         "nameType" => "Organizational")

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bolognese
 version: !ruby/object:Gem::Version
-  version: 1.11.2
+  version: 1.11.3
 platform: ruby
 authors:
 - Martin Fenner
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2023-06-08 00:00:00.000000000 Z
+date: 2023-09-27 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: maremma