bolognese 2.0.0 → 2.3.2
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/.github/workflows/ci.yml +1 -1
- data/.github/workflows/release.yml +2 -2
- data/Gemfile.lock +13 -12
- data/bolognese.gemspec +4 -3
- data/lib/bolognese/author_utils.rb +4 -4
- data/lib/bolognese/metadata_utils.rb +2 -1
- data/lib/bolognese/readers/citeproc_reader.rb +6 -0
- data/lib/bolognese/readers/crossref_reader.rb +37 -3
- data/lib/bolognese/readers/datacite_reader.rb +1 -1
- data/lib/bolognese/readers/schema_org_reader.rb +26 -4
- data/lib/bolognese/utils.rb +14 -9
- data/lib/bolognese/version.rb +1 -1
- data/lib/bolognese/writers/datacite_json_writer.rb +1 -4
- data/lib/bolognese/writers/jats_writer.rb +4 -1
- data/lib/bolognese/writers/schema_org_writer.rb +5 -1
- data/resources/kernel-4/include/datacite-contributorType-v4.xsd +3 -1
- data/resources/kernel-4/include/datacite-dateType-v4.xsd +3 -1
- data/resources/kernel-4/include/datacite-relatedIdentifierType-v4.xsd +5 -2
- data/resources/kernel-4/include/datacite-relationType-v4.xsd +7 -3
- data/resources/kernel-4/include/datacite-resourceType-v4.xsd +5 -1
- data/resources/kernel-4/include/datacite-titleType-v4.xsd +1 -1
- data/resources/kernel-4/metadata.xsd +2 -1
- data/resources/kernel-4.6/include/datacite-contributorType-v4.xsd +37 -0
- data/resources/kernel-4.6/include/datacite-dateType-v4.xsd +27 -0
- data/resources/kernel-4.6/include/datacite-descriptionType-v4.xsd +19 -0
- data/resources/kernel-4.6/include/datacite-funderIdentifierType-v4.xsd +16 -0
- data/resources/kernel-4.6/include/datacite-nameType-v4.xsd +10 -0
- data/resources/kernel-4.6/include/datacite-numberType-v4.xsd +12 -0
- data/resources/kernel-4.6/include/datacite-relatedIdentifierType-v4.xsd +37 -0
- data/resources/kernel-4.6/include/datacite-relationType-v4.xsd +57 -0
- data/resources/kernel-4.6/include/datacite-resourceType-v4.xsd +49 -0
- data/resources/kernel-4.6/include/datacite-titleType-v4.xsd +14 -0
- data/resources/kernel-4.6/include/xml.xsd +286 -0
- data/resources/kernel-4.6/metadata.xsd +712 -0
- data/spec/author_utils_spec.rb +8 -2
- data/spec/datacite_utils_spec.rb +109 -1
- data/spec/fixtures/citeproc.json +6 -2
- data/spec/fixtures/crossref_schema_4.6_values.xml +183 -0
- data/spec/fixtures/datacite-example-ROR-nameIdentifiers.xml +8 -0
- data/spec/fixtures/datacite-example-full-v4.6.xml +114 -0
- data/spec/fixtures/datacite-xml-lang.xml +1 -1
- data/spec/fixtures/datacite_blank_name_identifier.xml +22 -0
- data/spec/fixtures/datacite_blank_publisher.xml +18 -0
- data/spec/fixtures/datacite_journal_article.xml +64 -0
- data/spec/fixtures/schema_org.json +1 -0
- data/spec/fixtures/schema_org_4.6_attributes.json +108 -0
- data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/insert_contributors_Translator/supports_Translator_contributorType.yml +71 -0
- data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/insert_dates_with_Coverage/inserts_date_with_dateType_Coverage.yml +71 -0
- data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/insert_related_identifiers_CSTR/supports_CSTR_relatedIdentifierType.yml +71 -0
- data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/insert_related_identifiers_HasTranslation/supports_HasTranslation_relationType.yml +71 -0
- data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/insert_related_identifiers_RRID/supports_RRID_relatedIdentifierType.yml +71 -0
- data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/insert_resource_type_with_Award/supports_Award_as_resourceTypeGeneral.yml +71 -0
- data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/insert_resource_type_with_Project/supports_Project_as_resourceTypeGeneral.yml +71 -0
- data/spec/readers/citeproc_reader_spec.rb +1 -0
- data/spec/readers/crossref_reader_spec.rb +31 -0
- data/spec/readers/datacite_reader_spec.rb +91 -0
- data/spec/readers/schema_org_reader_spec.rb +28 -1
- data/spec/writers/citation_writer_spec.rb +9 -0
- data/spec/writers/citeproc_writer_spec.rb +9 -0
- data/spec/writers/datacite_json_writer_spec.rb +16 -32
- data/spec/writers/datacite_writer_spec.rb +71 -0
- data/spec/writers/jats_writer_spec.rb +8 -1
- data/spec/writers/schema_org_writer_spec.rb +49 -0
- metadata +55 -22
data/spec/author_utils_spec.rb
CHANGED
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@@ -168,11 +168,12 @@ describe Bolognese::Metadata, vcr: true do
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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"=>[])
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expect(subject.creators[5]).to eq("nameType"=>"Organizational", "name"=>"សាកលវិទ្យាល័យកម្ពុជា", "nameIdentifiers"=> [{"nameIdentifier"=>"http://ror.org/025e3rc84", "nameIdentifierScheme"=>"RORS"}], "affiliation"=>[])
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expect(subject.creators[6]).to eq("nameType"=>"Organizational", "name"=>"جامعة زاخۆ", "nameIdentifiers"=> [{"nameIdentifier"=>"05sd1pz50", "schemeUri"=>"https://ror.org", "nameIdentifierScheme"=>"RORS"}], "affiliation"=>[])
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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"=>[])
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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")
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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")
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end
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-
context "affiliationIdentifier" do
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context "affiliationIdentifier/nameIdentifier" do
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let(:input) { fixture_path + 'datacite-example-ROR-nameIdentifiers.xml' }
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subject { Bolognese::Metadata.new(input: input, from: "datacite") }
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@@ -207,6 +208,11 @@ describe Bolognese::Metadata, vcr: true do
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expect(subject.creators[8]["nameIdentifiers"]).to eq([{"nameIdentifier"=>"https://orcid.org/0000-0001-9998-0118", "schemeUri"=>"https://orcid.org", "nameIdentifierScheme"=>"ORCID"}])
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end
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it "should normalize valid ORCID nameIdentifier with trailing slash" do
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#" 0000-0001-9998-0118 ", # Valid ORCID with leading/trailing spaces
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expect(subject.creators[10]["nameIdentifiers"]).to eq([{"nameIdentifier"=>"https://orcid.org/0000-0001-9998-0117", "schemeUri"=>"https://orcid.org", "nameIdentifierScheme"=>"ORCID"}])
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end
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it "should parse non ROR schema's without normalizing them" do
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input = fixture_path + 'datacite-example-ROR-nameIdentifiers.xml'
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subject = Bolognese::Metadata.new(input: input, from: "datacite")
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@@ -250,4 +256,4 @@ describe Bolognese::Metadata, vcr: true do
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expect(response).to eq("Matt Jones and Peter Slaughter and {University of California, Santa Barbara}")
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end
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end
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-
end
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end
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data/spec/datacite_utils_spec.rb
CHANGED
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@@ -204,4 +204,112 @@ describe Bolognese::Metadata, vcr: true do
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)
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end
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end
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-
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### New DataCite 4.6 Features Tests ###
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context "insert_resource_type with Project" do
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it "supports Project as resourceTypeGeneral" do
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# Mock the `types` hash to include Project
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subject.instance_variable_set(:@types, {
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"resourceTypeGeneral" => "Project",
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"resourceType" => "Research Project"
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})
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# Generate XML using the insert_resource_type method
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xml = Nokogiri::XML::Builder.new(:encoding => 'UTF-8') { |xml| subject.insert_resource_type(xml) }.to_xml
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response = Maremma.from_xml(xml)
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# Expect `Project` in resourceTypeGeneral and `Research Project` as the content
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expect(response["resourceType"]).to eq(
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"resourceTypeGeneral" => "Project",
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"__content__" => "Research Project"
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)
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end
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end
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context "insert_resource_type with Award" do
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it "supports Award as resourceTypeGeneral" do
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# Mock the `types` hash to include Award
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subject.instance_variable_set(:@types, {
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"resourceTypeGeneral" => "Award",
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"resourceType" => "Nobel Prize"
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})
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# Generate XML using the insert_resource_type method
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xml = Nokogiri::XML::Builder.new(:encoding => 'UTF-8') { |xml| subject.insert_resource_type(xml) }.to_xml
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response = Maremma.from_xml(xml)
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# Expect `Award` in resourceTypeGeneral and `Nobel Prize` as the content
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expect(response["resourceType"]).to eq(
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"resourceTypeGeneral" => "Award",
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"__content__" => "Nobel Prize"
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)
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end
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end
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# Test case to insert Coverage DateType (new dateType in DataCite 4.6).
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context "insert_dates with Coverage" do
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it "inserts date with dateType Coverage" do
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subject.dates = [{ "date" => "2021-01-01", "dateType" => "Coverage" }]
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xml = Nokogiri::XML::Builder.new(:encoding => 'UTF-8') { |xml| subject.insert_dates(xml) }.to_xml
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response = Maremma.from_xml(xml)
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dates = response.dig("dates", "date")
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expect(dates).to eq("__content__" => "2021-01-01", "dateType" => "Coverage")
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end
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end
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# Test case to insert Translator contributor (new contributorType in DataCite 4.6)
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context "insert_contributors Translator" do
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it "supports Translator contributorType" do
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subject.contributors = [
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{ "contributorName" => "John Translator", "contributorType" => "Translator" }
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]
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xml = Nokogiri::XML::Builder.new(:encoding => 'UTF-8') { |xml| subject.insert_contributors(xml) }.to_xml
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response = Maremma.from_xml(xml)
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expect(response.dig("contributors", "contributor", "contributorType")).to eq("Translator")
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end
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end
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# Test case for RRID (new relatedIdentifierType in DataCite 4.6)
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context "insert_related_identifiers RRID" do
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it "supports RRID relatedIdentifierType" do
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subject.related_identifiers = [
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{ "relatedIdentifier" => "RRID:AB_90755", "relatedIdentifierType" => "RRID", "relationType" => "References" }
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]
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xml = Nokogiri::XML::Builder.new(:encoding => 'UTF-8') { |xml| subject.insert_related_identifiers(xml) }.to_xml
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response = Maremma.from_xml(xml)
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expect(response.dig("relatedIdentifiers", "relatedIdentifier")).to eq("__content__" => "RRID:AB_90755", "relatedIdentifierType" => "RRID", "relationType" => "References")
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end
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end
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### Test case #2 for adding CSTR ###
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context "insert_related_identifiers CSTR" do
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it "supports CSTR relatedIdentifierType" do
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subject.related_identifiers = [
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{ "relatedIdentifier" => "CSTR:AB_12345", "relatedIdentifierType" => "CSTR", "relationType" => "References" }
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]
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xml = Nokogiri::XML::Builder.new(:encoding => 'UTF-8') { |xml| subject.insert_related_identifiers(xml) }.to_xml
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response = Maremma.from_xml(xml)
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expect(response.dig("relatedIdentifiers", "relatedIdentifier")).to eq("__content__" => "CSTR:AB_12345", "relatedIdentifierType" => "CSTR", "relationType" => "References")
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end
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end
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# Test case for HasTranslation (new relationType in DataCite 4.6)
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context "insert_related_identifiers HasTranslation" do
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it "supports HasTranslation relationType" do
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subject.related_identifiers = [
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{ "relatedIdentifier" => "10.1234/translated-version", "relatedIdentifierType" => "DOI", "relationType" => "HasTranslation" }
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]
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xml = Nokogiri::XML::Builder.new(:encoding => 'UTF-8') { |xml| subject.insert_related_identifiers(xml) }.to_xml
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response = Maremma.from_xml(xml)
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expect(response.dig("relatedIdentifiers", "relatedIdentifier")).to eq("__content__" => "10.1234/translated-version", "relatedIdentifierType" => "DOI", "relationType" => "HasTranslation")
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end
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end
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end
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data/spec/fixtures/citeproc.json
CHANGED
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@@ -0,0 +1,183 @@
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<?xml version="1.0" encoding="UTF-8"?>
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<crossref_result xmlns="http://www.crossref.org/qrschema/3.0" version="3.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.crossref.org/qrschema/3.0 http://www.crossref.org/schemas/crossref_query_output3.0.xsd">
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<query_result>
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<head>
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<doi_batch_id>none</doi_batch_id>
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</head>
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<body>
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<query status="resolved">
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<doi type="journal_article">10.7554/eLife.01567</doi>
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<crm-item name="publisher-name" type="string">eLife Sciences Publications, Ltd</crm-item>
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<crm-item name="prefix-name" type="string">eLife Sciences Publications, Ltd.</crm-item>
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<crm-item name="member-id" type="number">4374</crm-item>
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<crm-item name="citation-id" type="number">67124617</crm-item>
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<crm-item name="journal-id" type="number">189365</crm-item>
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<crm-item name="deposit-timestamp" type="number">20180823133646</crm-item>
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<crm-item name="owner-prefix" type="string">10.7554</crm-item>
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<crm-item name="last-update" type="date">2018-08-23T13:41:49Z</crm-item>
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<crm-item name="created" type="date">2014-02-11T16:29:04Z</crm-item>
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<crm-item name="citedby-count" type="number">13</crm-item>
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<doi_record>
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<crossref xmlns="http://www.crossref.org/xschema/1.1" xsi:schemaLocation="http://www.crossref.org/xschema/1.1 http://doi.crossref.org/schemas/unixref1.1.xsd">
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<journal>
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<journal_metadata language="en">
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<full_title>Journal of Metadata Perfection</full_title>
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<abbrev_title>JOMPer</abbrev_title>
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<doi_data>
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<doi>10.32013/487529</doi>
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<resource>https://www.crossref.org/jomper</resource>
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</doi_data>
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</journal_metadata>
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<journal_issue>
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<publication_date media_type="online">
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<month>08</month>
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<day>13</day>
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<year>2008</year>
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</publication_date>
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<publication_date media_type="print">
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<month>08</month>
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<day>14</day>
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<year>2008</year>
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</publication_date>
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<journal_volume>
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<volume>5</volume>
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</journal_volume>
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<issue>11</issue>
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</journal_issue>
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<journal_article publication_type="full_text">
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<titles>
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<title>Quand vos meilleures métadonnées ne suffisent pas: travailler avec une spécification imparfaite</title>
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<original_language_title language="en">When your best metadata isn't good enough: working with an imperfect specification </original_language_title>
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</titles>
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<contributors>
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Data Commons. Susanna-Assunta Sansone, Alejandra Gonzalez-Beltran,
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Philippe Rocca-Serra, PeterMcQuilton, Massimiliano Izzo, Allyson Lister,
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Milo Thurston. bioRxiv 144147</unstructured_citation>
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<doi>10.1515/jdis-2017-0012</doi>
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<unstructured_citation>Greenberg, J. (2017). Big Metadata, Smart Metadata,
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and Metadata Capital: Toward Greater Synergy Between Data Science and
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Metadata, Journal of Data and Information Science, 2(3), 19-36.
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<doi>10.1108/LHTN-12-2016-0059</doi>
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<unstructured_citation>Jung ran Park, Yuji Tosaka, (2017) “Emerging
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information standards and technologies: cataloging and metadata
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professionals’ perspectives", Library Hi Tech News, Vol. 34 Issue: 4,
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pp.22-26</unstructured_citation>
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<journal_title>Information Technology and Libraries</journal_title>
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<doi>10.6017/ital.v29i3.3136</doi>
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<article_title>Metadata creation practices in digital repositories and collections: Schemata, selection criteria, and interoperability</article_title>
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Bethesda,MD: NISO Press.</unstructured_citation>
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<creatorName nameType="Organizational">Gump South Pacific Research Station</creatorName>
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<identifier identifierType="DOI">10.82433/B09Z-4K37</identifier>
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<subject subjectScheme="Fields of Science and Technology (FOS)" schemeURI="http://www.oecd.org/science/inno" valueURI="http://www.oecd.org/science/inno/38235147.pdf">FOS: Computer and information sciences</subject>
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<subject subjectScheme="Australian and New Zealand Standard Research Classification (ANZSRC), 2020" schemeURI="https://www.abs.gov.au/statistics/classifications/australian-and-new-zealand-standard-research-classification-anzsrc" classificationCode="461001">Digital curation and preservation</subject>
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<date dateType="Coverage">2020-01-01</date> <!-- DataCite 4.6: Coverage DateType -->
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<date dateType="Created">2023-01-01</date>
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<date dateType="Issued">2023-01-01</date>
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<date dateType="Submitted">2023-01-01</date>
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<relatedIdentifier relatedIdentifierType="RRID" relationType="References">RRID:AB_90755</relatedIdentifier> <!-- DataCite 4.6: New RRID Identifier -->
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<relatedIdentifier relatedIdentifierType="CSTR" relationType="References">CSTR:AB_12345</relatedIdentifier> <!-- DataCite 4.6: New CSTR Identifier -->
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<relatedIdentifier relatedIdentifierType="DOI" relationType="HasTranslation">10.1234/translated-version</relatedIdentifier> <!-- DataCite 4.6: HasTranslation RelationType -->
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<relatedIdentifier relatedIdentifierType="DOI" relationType="IsTranslationOf">10.1234/other-version</relatedIdentifier> <!-- DataCite 4.6: HasTranslation RelationType -->
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<publisher>OSI SAF</publisher>
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<publicationYear>2004</publicationYear>
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<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">
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<identifier identifierType="DOI">10.15148/3b68dac4-7688-4fbb-ba64-5f9b3bbab954</identifier>
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<creators>
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<creator>
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<creatorName>SNO KARST</creatorName>
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</creator>
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<publisher>OSU OREME</publisher>
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<titles>
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<title>Time series of type chemistry in Le Tarn basin - PARC NATIONAL CEVENNES observatory - KARST observatory network - OZCAR Critical Zone network Research Infrastructure</title>
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</titles>
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<publicationYear>2023</publicationYear>
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<creatorName>University of Texas School of Law</creatorName>
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<title>Texas Law Review</title>
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<descriptions>
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<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>
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