bolognese 1.6.12 → 1.7.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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-  data.tar.gz: d9c6f41c15f6b4ef19c1867e8c325d1321d34fbf3458e0ebd76869424fdfb166
+  metadata.gz: 34f2f4c88f2a10491132ce386d931e83f5f84fed96bf4accf442e82d2c59889e
+  data.tar.gz: 5a8ec1c8fe1962d6531effeca7ca3d0e769506d9580d00b559ac0e8d2f11ed83
 SHA512:
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-  data.tar.gz: 76446fa76402b465a3538c258f0967a6a7dac7db96806dbf26e2e40fbe60fa5287106addc6490b0a8c48b28cfb1282f191dd8e49681459528cac92994536fff6
+  metadata.gz: 99c48d238c54eaf64003bacd6488c558d837c37405fc59acb46a17d9999f838f9bde197c966d3bef35e315febd789dc6f06c0732f46d8a53462433a38cd08cf1
+  data.tar.gz: 71240642a6069ef06e412ad4fc28b80fd84768021c21b770d9553aa85f09a440f66ffd7b982bc82a549970b2987bbc32627e2b2a593f565ccea0bc42e743ee0b

data/Gemfile.lock

@@ -1,15 +1,15 @@
 PATH
   remote: .
   specs:
-    bolognese (1.6.12)
+    bolognese (1.7.1)
       activesupport (>= 4.2.5)
       benchmark_methods (~> 0.7)
       bibtex-ruby (>= 5.1.0)
       builder (~> 3.2, >= 3.2.2)
-      citeproc-ruby (~> 1.1, >= 1.1.10)
+      citeproc-ruby (~> 1.1, >= 1.1.12)
       colorize (~> 0.8.1)
       concurrent-ruby (~> 1.1, >= 1.1.5)
-      csl-styles (~> 1.0, >= 1.0.1.8)
+      csl-styles (~> 1.0, >= 1.0.1.10)
       edtf (~> 3.0, >= 3.0.4)
       faraday (~> 0.17.3)
       gender_detector (~> 0.1.2)

data/bolognese.gemspec

@@ -27,8 +27,8 @@ Gem::Specification.new do |s|
   s.add_dependency 'colorize', '~> 0.8.1'
   s.add_dependency 'namae', '~> 1.0'
   s.add_dependency 'edtf', '~> 3.0', '>= 3.0.4'
-  s.add_dependency 'citeproc-ruby', '~> 1.1', '>= 1.1.10'
-  s.add_dependency 'csl-styles', '~> 1.0', '>= 1.0.1.8'
+  s.add_dependency 'citeproc-ruby', '~> 1.1', '>= 1.1.12'
+  s.add_dependency 'csl-styles', '~> 1.0', '>= 1.0.1.10'
   s.add_dependency 'iso8601', '~> 0.9.1'
   s.add_dependency 'postrank-uri', '~> 1.0', '>= 1.0.18'
   s.add_dependency 'json-ld', '~> 3.1', '>= 3.1.4'

data/lib/bolognese/datacite_utils.rb

@@ -116,11 +116,10 @@ module Bolognese
     end
 
     def insert_alternate_identifiers(xml)
-      alternate_identifiers = Array.wrap(identifiers).select { |r| r["identifierType"] != "DOI" }
-      return xml unless alternate_identifiers.present?
+      return xml unless identifiers.present?
 
       xml.alternateIdentifiers do
-        Array.wrap(alternate_identifiers).each do |alternate_identifier|
+        Array.wrap(identifiers).each do |alternate_identifier|
           xml.alternateIdentifier(alternate_identifier["identifier"], 'alternateIdentifierType' => alternate_identifier["identifierType"])
         end
       end

data/lib/bolognese/doi_utils.rb

@@ -28,7 +28,7 @@ module Bolognese
 
     def doi_api_url(doi, options = {})
       sandbox = Array(/handle.test.datacite.org/.match(doi)).last
-      sandbox.present? || options[:sandbox] ? "https://api.test.datacite.org/dois/" + doi_from_url(doi) : "https://api.datacite.org/dois/" + doi_from_url(doi)
+      sandbox.present? || options[:sandbox] ? "https://api.test.datacite.org/dois/#{doi_from_url(doi)}?include=media,client"  : "https://api.datacite.org/dois/#{doi_from_url(doi)}?include=media,client"
     end
 
     def normalize_doi(doi, options = {})

data/lib/bolognese/metadata.rb

@@ -8,7 +8,7 @@ module Bolognese
 
     attr_accessor :string, :from, :sandbox, :meta, :regenerate, :issue, :show_errors
     attr_reader :doc, :page_start, :page_end
-    attr_writer :id, :provider_id, :client_id, :doi, :identifiers, :creators, :contributors, :titles, :publisher, 
+    attr_writer :id, :provider_id, :client_id, :doi, :identifiers, :alternate_identifiers, :creators, :contributors, :titles, :publisher, 
                 :rights_list, :dates, :publication_year, :volume, :url, :version_info,
                 :subjects, :contributor, :descriptions, :language, :sizes,
                 :formats, :schema_version, :meta, :container, :agency,
@@ -99,6 +99,7 @@ module Bolognese
         :titles,
         :types,
         :identifiers,
+        :alternate_identifiers,
         :container,
         :publisher,
         :funding_references,
@@ -215,7 +216,11 @@ module Bolognese
     end
 
     def identifiers
-      @identifiers ||= meta.fetch("identifiers", nil)
+      @identifiers ||= Array.wrap(@alternate_identifiers).map { |a| { "identifierType" => a["alternateIdentifierType"], "identifier" => a["alternateIdentifier"] } }.presence || meta.fetch("identifiers", nil)
+      # (Array.wrap(@identifiers) +
+      # Array.wrap(@alternate_identifiers).select { |r| r["alternateIdentifierType"] != "DOI" }.map do |a|
+      #   { "identifierType" => a["alternateIdentifierType"], "identifier" => a["alternateIdentifier"] }
+      # end).uniq ||= meta.fetch("identifiers", nil)
     end
 
     def content_url

data/lib/bolognese/readers/bibtex_reader.rb

@@ -80,7 +80,6 @@ module Bolognese
 
         { "id" => normalize_doi(doi),
           "types" => types,
-          "identifiers" => [{ "identifier" => normalize_doi(doi), "identifierType" => "DOI" }],
           "doi" => doi,
           "url" => meta.try(:url).to_s.presence,
           "titles" => meta.try(:title).present? ? [{ "title" => meta.try(:title).to_s }] : [],

data/lib/bolognese/readers/citeproc_reader.rb

@@ -86,19 +86,8 @@ module Bolognese
           nil
         end
 
-        identifiers = [normalize_id(meta.fetch("id", nil)), normalize_doi(meta.fetch("DOI", nil))].compact.map do |r|
-          r = normalize_id(r)
+        id = normalize_id(meta.fetch("id", nil) || meta.fetch("DOI", nil))
 
-          if r.start_with?("https://doi.org")
-            { "identifierType" => "DOI", "identifier" => r }
-          else
-              { "identifierType" => "URL", "identifier" => r }
-          end
-        end.uniq
-
-        id = Array.wrap(identifiers).first.to_h.fetch("identifier", nil)
-        doi = Array.wrap(identifiers).find { |r| r["identifierType"] == "DOI" }.to_h.fetch("identifier", nil)
-          
         state = id.present? || read_options.present? ? "findable" : "not_found"
         subjects = Array.wrap(meta.fetch("categories", nil)).reduce([]) do |sum, subject|
           sum += name_to_fos(subject)
@@ -107,9 +96,8 @@ module Bolognese
         end
 
         { "id" => id,
-          "identifiers" => identifiers,
           "types" => types,
-          "doi" => doi_from_url(doi),
+          "doi" => doi_from_url(id),
           "url" => normalize_id(meta.fetch("URL", nil)),
           "titles" => [{ "title" => meta.fetch("title", nil) }],
           "creators" => creators,

data/lib/bolognese/readers/codemeta_reader.rb

@@ -22,19 +22,16 @@ module Bolognese
 
         meta = string.present? ? Maremma.from_json(string) : {}
 
-        identifiers = ([meta.fetch("@id", nil)] + Array.wrap(meta.fetch("identifier", nil))).map do |r|
+        identifiers = Array.wrap(meta.fetch("identifier", nil)).map do |r|
           r = normalize_id(r) if r.is_a?(String)
-          if r.is_a?(String) && r.start_with?("https://doi.org")
-            { "identifierType" => "DOI", "identifier" => r }
-          elsif r.is_a?(String)
+          if r.is_a?(String) && !r.start_with?("https://doi.org")
               { "identifierType" => "URL", "identifier" => r }
           elsif r.is_a?(Hash)
             { "identifierType" => get_identifier_type(r["propertyID"]), "identifier" => r["value"] }
           end
         end.compact.uniq
 
-        id = Array.wrap(identifiers).first.to_h.fetch("identifier", nil)
-        doi = Array.wrap(identifiers).find { |r| r["identifierType"] == "DOI" }.to_h.fetch("identifier", nil)
+        id = normalize_id(options[:doi] || meta.fetch("@id", nil) || meta.fetch("identifier", nil))
 
         has_agents = meta.fetch("agents", nil)
         authors =  has_agents.nil? ? meta.fetch("authors", nil) : has_agents
@@ -70,7 +67,7 @@ module Bolognese
         { "id" => id,
           "types" => types,
           "identifiers" => identifiers,
-          "doi" => doi_from_url(doi),
+          "doi" => doi_from_url(id),
           "url" => normalize_id(meta.fetch("codeRepository", nil)),
           "titles" => titles,
           "creators" => creators,

data/lib/bolognese/readers/crossref_reader.rb

@@ -150,14 +150,12 @@ module Bolognese
                         "volume" => bibliographic_metadata.fetch("volume", nil) }.compact
                     end
 
-        identifiers = [{ "identifierType" => "DOI", "identifier" => normalize_doi(options[:doi] || options[:id] || bibliographic_metadata.dig("doi_data", "doi")) }, crossref_alternate_identifiers(bibliographic_metadata)].compact
-
-        id = Array.wrap(identifiers).first.to_h.fetch("identifier", nil)
-        doi = Array.wrap(identifiers).find { |r| r["identifierType"] == "DOI" }.to_h.fetch("identifier", nil)
+        id = normalize_doi(options[:doi] || options[:id] || bibliographic_metadata.dig("doi_data", "doi"))
+        identifiers = [crossref_alternate_identifiers(bibliographic_metadata)].compact
 
         { "id" => id,
           "types" => types,
-          "doi" => doi_from_url(doi),
+          "doi" => doi_from_url(id),
           "url" => parse_attributes(bibliographic_metadata.dig("doi_data", "resource"), first: true),
           "titles" => titles,
           "identifiers" => identifiers,

data/lib/bolognese/readers/datacite_reader.rb

@@ -74,14 +74,12 @@ module Bolognese
           id = normalize_doi(meta.dig("identifier", "__content__") || options[:id], sandbox: options[:sandbox])
         end
 
-        identifiers = [{ "identifierType" => "DOI", "identifier" => id }] + Array.wrap(meta.dig("alternateIdentifiers", "alternateIdentifier")).map do |r|
+        identifiers = Array.wrap(meta.dig("alternateIdentifiers", "alternateIdentifier")).map do |r|
           if r["__content__"].present?
             { "identifierType" => get_identifier_type(r["alternateIdentifierType"]), "identifier" => r["__content__"] }
           end
         end.compact
 
-        doi = Array.wrap(identifiers).find { |r| r["identifierType"] == "DOI" }.to_h.fetch("identifier", nil)
-
         resource_type_general = meta.dig("resourceType", "resourceTypeGeneral")
         resource_type = meta.dig("resourceType", "__content__")
         schema_org = Bolognese::Utils::CR_TO_SO_TRANSLATIONS[resource_type.to_s.underscore.camelcase] || Bolognese::Utils::DC_TO_SO_TRANSLATIONS[resource_type_general.to_s.dasherize] || "CreativeWork"
@@ -217,11 +215,11 @@ module Bolognese
           end
         end.compact
 
-        state = doi.present? || read_options.present? ? "findable" : "not_found"
+        state = id.present? || read_options.present? ? "findable" : "not_found"
 
         { "id" => id,
           "types" => types,
-          "doi" => doi_from_url(doi),
+          "doi" => doi_from_url(id),
           "identifiers" => identifiers,
           "url" => options.fetch(:url, nil).to_s.strip.presence,
           "titles" => titles,

data/lib/bolognese/readers/ris_reader.rb

@@ -47,13 +47,8 @@ module Bolognese
           "ris" => ris_type
         }.compact
 
-        identifiers = [normalize_doi(options[:doi]) || normalize_doi(meta.fetch("DO", nil))].map do |r|
-          { "identifierType" => "DOI", "identifier" => normalize_id(r) }
-        end.compact
-
-        id = Array.wrap(identifiers).first.to_h.fetch("identifier", nil)
-        doi = Array.wrap(identifiers).find { |r| r["identifierType"] == "DOI" }.to_h.fetch("identifier", nil)
-
+        id = normalize_doi(options[:doi] || meta.fetch("DO", nil))
+        
         author = Array.wrap(meta.fetch("AU", nil)).map { |a| { "creatorName" => a } }
         date_parts = meta.fetch("PY", nil).to_s.split("/")
         created_date_parts = meta.fetch("Y1", nil).to_s.split("/")
@@ -90,8 +85,7 @@ module Bolognese
 
         { "id" => id,
           "types" => types,
-          "identifiers" => identifiers,
-          "doi" => doi_from_url(doi),
+          "doi" => doi_from_url(id),
           "url" => meta.fetch("UR", nil),
           "titles" => meta.fetch("T1", nil).present? ? [{ "title" => meta.fetch("T1", nil) }] : nil,
           "creators" => get_authors(author),

data/lib/bolognese/readers/schema_org_reader.rb

@@ -48,18 +48,16 @@ module Bolognese
 
         meta = string.present? ? Maremma.from_json(string) : {}
 
-        identifiers = ([options[:doi] || meta.fetch("@id", nil)] + Array.wrap(meta.fetch("identifier", nil))).map do |r|
+        identifiers = Array.wrap(meta.fetch("identifier", nil)).map do |r|
           r = normalize_id(r) if r.is_a?(String)
-          if r.is_a?(String) && r.start_with?("https://doi.org")
-            { "identifierType" => "DOI", "identifier" => r }
-          elsif r.is_a?(String)
+          if r.is_a?(String) && !r.start_with?("https://doi.org")
               { "identifierType" => "URL", "identifier" => r }
           elsif r.is_a?(Hash)
             { "identifierType" => get_identifier_type(r["propertyID"]), "identifier" => r["value"] }
           end
         end.compact.uniq
 
-        id = Array.wrap(identifiers).first.to_h.fetch("identifier", nil)
+        id = normalize_id(options[:doi] || meta.fetch("@id", nil) || meta.fetch("identifier", nil))
 
         schema_org = meta.fetch("@type", nil) && meta.fetch("@type").camelcase
         resource_type_general = Bolognese::Utils::SO_TO_DC_TRANSLATIONS[schema_org]

data/lib/bolognese/version.rb

@@ -1,3 +1,3 @@
 module Bolognese
-  VERSION = "1.6.12"
+  VERSION = "1.7.1"
 end

data/spec/author_utils_spec.rb

@@ -57,7 +57,7 @@ describe Bolognese::Metadata, vcr: true do
       subject = Bolognese::Metadata.new(input: input, from: "datacite")
       meta = Maremma.from_xml(subject.raw).fetch("resource", {})
       response = subject.get_one_author(meta.dig("creators", "creator").first)
-      expect(response).to eq("nameType"=>"Personal", "name"=>"Ollomo, Benjamin", "givenName"=>"Benjamin", "familyName"=>"Ollomo", "nameIdentifiers" => [], "affiliation" => [])
+      expect(response).to eq("nameType"=>"Personal", "name"=>"Ollomo, Benjamin", "givenName"=>"Benjamin", "familyName"=>"Ollomo", "nameIdentifiers" => [], "affiliation" => [{"affiliationIdentifier"=>"https://ror.org/01wyqb997", "affiliationIdentifierScheme"=>"ROR", "name"=>"Centre International de Recherches Médicales de Franceville"}])
     end
 
     it "has name in display-order" do

data/spec/cli_spec.rb

@@ -51,12 +51,12 @@ describe Bolognese::CLI do
       let(:input) { "10.5061/dryad.8515" }
 
       it 'default' do
-        expect { subject.convert input }.to output(/Phylogeny, Malaria, Parasites, Taxonomy, Mitochondrial genome, Africa, Plasmodium/).to_stdout
+        expect { subject.convert input }.to output(/Plasmodium, malaria, taxonomy, mitochondrial genome, phylogeny, Parasites/).to_stdout
       end
 
       it 'to schema_org' do
         subject.options = { to: "schema_org" }
-        expect { subject.convert input }.to output(/Phylogeny, Malaria, Parasites, Taxonomy, Mitochondrial genome, Africa, Plasmodium/).to_stdout
+        expect { subject.convert input }.to output(/Plasmodium, malaria, taxonomy, mitochondrial genome, phylogeny, Parasites/).to_stdout
       end
 
       it 'to bibtex' do

data/spec/datacite_utils_spec.rb

@@ -19,7 +19,7 @@ describe Bolognese::Metadata, vcr: true do
     it "insert" do
       xml = Nokogiri::XML::Builder.new(:encoding => 'UTF-8') { |xml| subject.insert_creators(xml) }.to_xml
       response = Maremma.from_xml(xml)
-      expect(response.dig("creators", "creator").first).to eq("creatorName"=>{"__content__"=>"Ollomo, Benjamin", "nameType"=>"Personal"}, "familyName"=>"Ollomo", "givenName"=>"Benjamin")
+      expect(response.dig("creators", "creator").first).to eq("affiliation" => {"__content__"=>"Centre International de Recherches Médicales de Franceville", "affiliationIdentifier"=>"https://ror.org/01wyqb997", "affiliationIdentifierScheme"=>"ROR"}, "creatorName"=>{"__content__"=>"Ollomo, Benjamin", "nameType"=>"Personal"}, "familyName"=>"Ollomo", "givenName"=>"Benjamin")
     end
   end
 
@@ -61,7 +61,7 @@ describe Bolognese::Metadata, vcr: true do
     it "insert" do
       xml = Nokogiri::XML::Builder.new(:encoding => 'UTF-8') { |xml| subject.insert_publisher(xml) }.to_xml
       response = Maremma.from_xml(xml)
-      expect(response["publisher"]).to eq("Dryad Digital Repository")
+      expect(response["publisher"]).to eq("Dryad")
     end
   end
 
@@ -77,17 +77,17 @@ describe Bolognese::Metadata, vcr: true do
     it "insert" do
       xml = Nokogiri::XML::Builder.new(:encoding => 'UTF-8') { |xml| subject.insert_resource_type(xml) }.to_xml
       response = Maremma.from_xml(xml)
-      expect(response["resourceType"]).to eq("resourceTypeGeneral"=>"Dataset", "__content__"=>"DataPackage")
+      expect(response["resourceType"]).to eq("resourceTypeGeneral"=>"Dataset", "__content__"=>"dataset")
     end
   end
 
-  context "insert_alternate_identifiers" do
-    it "insert" do
-      xml = Nokogiri::XML::Builder.new(:encoding => 'UTF-8') { |xml| subject.insert_alternate_identifiers(xml) }.to_xml
-      response = Maremma.from_xml(xml)
-      expect(response.dig("alternateIdentifiers", "alternateIdentifier")).to eq("alternateIdentifierType"=>"citation", "__content__"=>"Ollomo B, Durand P, Prugnolle F, Douzery EJP, Arnathau C, Nkoghe D, Leroy E, Renaud F (2009) A new malaria agent in African hominids. PLoS Pathogens 5(5): e1000446.")
-    end
-  end
+  # context "insert_alternate_identifiers" do
+  #   it "insert" do
+  #     xml = Nokogiri::XML::Builder.new(:encoding => 'UTF-8') { |xml| subject.insert_alternate_identifiers(xml) }.to_xml
+  #     response = Maremma.from_xml(xml)
+  #     expect(response.dig("alternateIdentifiers", "alternateIdentifier").to be_nil)
+  #   end
+  # end
 
   context "insert_dates" do
     it "insert" do
@@ -101,7 +101,7 @@ describe Bolognese::Metadata, vcr: true do
     it "insert" do
       xml = Nokogiri::XML::Builder.new(:encoding => 'UTF-8') { |xml| subject.insert_subjects(xml) }.to_xml
       response = Maremma.from_xml(xml)
-      expect(response.dig("subjects", "subject")).to eq(["Phylogeny", "Malaria", "Parasites", "Taxonomy", "Mitochondrial genome", "Africa", "Plasmodium"])
+      expect(response.dig("subjects", "subject")).to eq(["Plasmodium", "malaria", "taxonomy", "mitochondrial genome", "phylogeny", "Parasites"])
     end
   end
 
@@ -143,15 +143,14 @@ describe Bolognese::Metadata, vcr: true do
 
   context "insert_related_identifiers" do
     it "related_identifier" do
-      expect(subject.related_identifiers.length).to eq(6)
-      expect(subject.related_identifiers.first).to eq("relatedIdentifier"=>"10.5061/dryad.8515/1", "relatedIdentifierType"=>"DOI", "relationType"=>"HasPart")
+      expect(subject.related_identifiers.length).to eq(1)
+      expect(subject.related_identifiers.first).to eq("relatedIdentifier"=>"10.1371/journal.ppat.1000446", "relatedIdentifierType"=>"DOI", "relationType"=>"IsSupplementTo")
     end
 
     it "insert" do
       xml = Nokogiri::XML::Builder.new(:encoding => 'UTF-8') { |xml| subject.insert_related_identifiers(xml) }.to_xml
       response = Maremma.from_xml(xml)
-      expect(response.dig("relatedIdentifiers", "relatedIdentifier").length).to eq(6)
-      expect(response.dig("relatedIdentifiers", "relatedIdentifier").first).to eq("__content__"=>"10.5061/dryad.8515/1", "relatedIdentifierType"=>"DOI", "relationType"=>"HasPart")
+      expect(response.dig("relatedIdentifiers", "relatedIdentifier")).to eq("__content__"=>"10.1371/journal.ppat.1000446", "relatedIdentifierType"=>"DOI", "relationType"=>"IsSupplementTo")
     end
   end
 

data/spec/doi_utils_spec.rb

@@ -55,43 +55,43 @@ describe Bolognese::Metadata, vcr: true do
     it "doi" do
       doi = "10.5061/DRYAD.8515"
       response = subject.doi_api_url(doi)
-      expect(response).to eq("https://api.datacite.org/dois/10.5061/dryad.8515")
+      expect(response).to eq("https://api.datacite.org/dois/10.5061/dryad.8515?include=media,client")
     end
 
     it "doi with protocol" do
       doi = "doi:10.5061/DRYAD.8515"
       response = subject.doi_api_url(doi)
-      expect(response).to eq("https://api.datacite.org/dois/10.5061/dryad.8515")
+      expect(response).to eq("https://api.datacite.org/dois/10.5061/dryad.8515?include=media,client")
     end
 
     it "https url" do
       doi = "https://doi.org/10.5061/dryad.8515"
       response = subject.doi_api_url(doi)
-      expect(response).to eq("https://api.datacite.org/dois/10.5061/dryad.8515")
+      expect(response).to eq("https://api.datacite.org/dois/10.5061/dryad.8515?include=media,client")
     end
 
     it "dx.doi.org url" do
       doi = "http://dx.doi.org/10.5061/dryad.8515"
       response = subject.doi_api_url(doi)
-      expect(response).to eq("https://api.datacite.org/dois/10.5061/dryad.8515")
+      expect(response).to eq("https://api.datacite.org/dois/10.5061/dryad.8515?include=media,client")
     end
 
     it "test resolver" do
       doi = "https://handle.test.datacite.org/10.5061/dryad.8515"
       response = subject.doi_api_url(doi)
-      expect(response).to eq("https://api.test.datacite.org/dois/10.5061/dryad.8515")
+      expect(response).to eq("https://api.test.datacite.org/dois/10.5061/dryad.8515?include=media,client")
     end
 
     it "test resolver http" do
       doi = "http://handle.test.datacite.org/10.5061/dryad.8515"
       response = subject.doi_api_url(doi)
-      expect(response).to eq("https://api.test.datacite.org/dois/10.5061/dryad.8515")
+      expect(response).to eq("https://api.test.datacite.org/dois/10.5061/dryad.8515?include=media,client")
     end
 
     it "force test resolver" do
       doi = "https://doi.org/10.5061/dryad.8515"
       response = subject.doi_api_url(doi, sandbox: true)
-      expect(response).to eq("https://api.test.datacite.org/dois/10.5061/dryad.8515")
+      expect(response).to eq("https://api.test.datacite.org/dois/10.5061/dryad.8515?include=media,client")
     end
   end
 

data/spec/fixtures/schema_org_gtex.json

@@ -3,7 +3,6 @@
   "@type": "Dataset",
   "@id": "https://doi.org/10.25491/d50j-3083",
   "identifier": [
-    "https://doi.org/10.25491/d50j-3083",
     {
       "@type": "PropertyValue",
       "propertyID": "md5",

data/spec/fixtures/schema_org_list.json

@@ -4,11 +4,6 @@
     "@type": "Dataset",
     "@id": "https://doi.org/10.23725/7jg3-v803",
     "identifier": [
-      {
-        "@type": "PropertyValue",
-        "propertyID": "doi",
-        "value": "https://doi.org/10.23725/7jg3-v803"
-      },
       {
         "@type": "PropertyValue",
         "propertyID": "minid",

data/spec/fixtures/schema_org_topmed.json

@@ -3,7 +3,6 @@
   "@type": "Dataset",
   "@id": "https://doi.org/10.23725/8na3-9s47",
   "identifier": [
-    "https://doi.org/10.23725/8na3-9s47",
     {
       "@type": "PropertyValue",
       "propertyID": "md5",