bolognese 1.6.9 → 1.7.2

data/spec/readers/ris_reader_spec.rb

@@ -15,7 +15,7 @@ describe Bolognese::Metadata, vcr: true do
     it "string" do
       Bolognese::Metadata.new(input: IO.read(input).strip)
       expect(subject.valid?).to be true
-      expect(subject.identifiers).to eq([{"identifier"=>"https://doi.org/10.7554/elife.01567", "identifierType"=>"DOI"}])
+      expect(subject.id).to eq("https://doi.org/10.7554/elife.01567")
     end
   end
 
@@ -28,7 +28,7 @@ describe Bolognese::Metadata, vcr: true do
   context "get ris metadata" do
     it "Crossref DOI" do
       expect(subject.valid?).to be true
-      expect(subject.identifiers).to eq([{"identifier"=>"https://doi.org/10.7554/elife.01567", "identifierType"=>"DOI"}])
+      expect(subject.id).to eq("https://doi.org/10.7554/elife.01567")
       expect(subject.types).to eq("citeproc"=>"misc", "resourceTypeGeneral"=>"Text", "ris"=>"JOUR", "schemaOrg"=>"ScholarlyArticle")
       expect(subject.url).to eq("http://elifesciences.org/lookup/doi/10.7554/eLife.01567")
       expect(subject.creators.length).to eq(5)
@@ -52,7 +52,7 @@ describe Bolognese::Metadata, vcr: true do
       subject = Bolognese::Metadata.new(input: input, doi: doi)
       expect(subject.valid?).to be false
       expect(subject.state).to eq("not_found")
-      expect(subject.identifiers).to eq([{"identifier"=>"https://doi.org/10.7554/elife.01567", "identifierType"=>"DOI"}])
+      expect(subject.id).to eq("https://doi.org/10.7554/elife.01567")
       expect(subject.types).to eq("citeproc"=>"misc", "resourceTypeGeneral"=>"Text", "ris"=>"THES", "schemaOrg"=>"Thesis")
       expect(subject.creators).to eq([{"nameType"=>"Personal", "name"=>"Toparlar, Y.", "givenName"=>"Y.", "familyName"=>"Toparlar", "nameIdentifiers" => [], "affiliation" => []}])
       expect(subject.titles).to eq([{"title"=>"A multiscale analysis of the urban heat island effect"}])
@@ -67,7 +67,7 @@ describe Bolognese::Metadata, vcr: true do
       doi = "10.7554/elife.01567"
       subject = Bolognese::Metadata.new(input: input, doi: doi)
       expect(subject.valid?).to be true
-      expect(subject.identifiers).to eq([{"identifier"=>"https://doi.org/10.7554/elife.01567", "identifierType"=>"DOI"}])
+      expect(subject.id).to eq("https://doi.org/10.7554/elife.01567")
       expect(subject.titles).to eq([{"title"=>"Validation of an Image-based Subject-Specific Dynamic Model of the Ankle Joint Complex and its Applications to the Study of the Effect of Articular Surface Morphology on Ankle Joint Mechanics"}])
       expect(subject.descriptions.first["description"]).to eq(abs)
     end

data/spec/readers/schema_org_reader_spec.rb

@@ -19,7 +19,7 @@ describe Bolognese::Metadata, vcr: true do
   context "get schema_org metadata" do
     it "BlogPosting" do
       expect(subject.valid?).to be true
-      expect(subject.identifiers).to eq([{"identifier"=>"https://doi.org/10.5438/4k3m-nyvg", "identifierType"=>"DOI"}])
+      expect(subject.id).to eq("https://doi.org/10.5438/4k3m-nyvg")
       expect(subject.url).to eq("https://blog.datacite.org/eating-your-own-dog-food")
       expect(subject.types).to eq("bibtex"=>"article", "citeproc"=>"post-weblog", "resourceTypeGeneral"=>"Text", "ris"=>"GEN", "schemaOrg"=>"BlogPosting")
       expect(subject.creators).to eq([{"affiliation"=>[{"affiliationIdentifier"=>"https://ror.org/04wxnsj81",
@@ -38,7 +38,7 @@ describe Bolognese::Metadata, vcr: true do
     it "BlogPosting with new DOI" do
       subject = Bolognese::Metadata.new(input: input, doi: "10.5438/0000-00ss")
       expect(subject.valid?).to be true
-      expect(subject.identifiers).to eq([{"identifier"=>"https://doi.org/10.5438/0000-00ss", "identifierType"=>"DOI"}])
+      expect(subject.id).to eq("https://doi.org/10.5438/0000-00ss")
       expect(subject.doi).to eq("10.5438/0000-00ss")
       expect(subject.url).to eq("https://blog.datacite.org/eating-your-own-dog-food")
       expect(subject.types).to eq("bibtex"=>"article", "citeproc"=>"post-weblog", "resourceTypeGeneral"=>"Text", "ris"=>"GEN", "schemaOrg"=>"BlogPosting")
@@ -48,7 +48,7 @@ describe Bolognese::Metadata, vcr: true do
       input = fixture_path + 'schema_org_type_as_array.json'
       subject = Bolognese::Metadata.new(input: input)
       #expect(subject.valid?).to be true
-      expect(subject.identifiers).to eq([{"identifier"=>"https://doi.org/10.5438/4k3m-nyvg", "identifierType"=>"DOI"}])
+      expect(subject.id).to eq("https://doi.org/10.5438/4k3m-nyvg")
       expect(subject.url).to eq("https://blog.datacite.org/eating-your-own-dog-food")
       expect(subject.types).to eq("bibtex"=>"article", "citeproc"=>"post-weblog", "resourceTypeGeneral"=>"Text", "ris"=>"GEN", "schemaOrg"=>"BlogPosting")
       expect(subject.creators).to eq([{"affiliation"=>[{"name"=>"DataCite"}],"familyName"=>"Fenner", "givenName"=>"Martin", "name"=>"Fenner, Martin", "nameIdentifiers"=> [{"nameIdentifier"=>"https://orcid.org/0000-0003-1419-2405", "nameIdentifierScheme"=>"ORCID", "schemeUri"=>"https://orcid.org"}], "nameType"=>"Personal"}])
@@ -66,8 +66,10 @@ describe Bolognese::Metadata, vcr: true do
       input = "https://www.zenodo.org/record/1196821"
       subject = Bolognese::Metadata.new(input: input, from: "schema_org")
       expect(subject.valid?).to be false
+
+      expect(subject.language).to eq("eng")
       expect(subject.errors).to eq("49:0: ERROR: Element '{http://datacite.org/schema/kernel-4}publisher': [facet 'minLength'] The value has a length of '0'; this underruns the allowed minimum length of '1'.")
-      expect(subject.identifiers).to eq([{"identifier"=>"https://doi.org/10.5281/zenodo.1196821", "identifierType"=>"DOI"}])
+      expect(subject.id).to eq("https://doi.org/10.5281/zenodo.1196821")
       expect(subject.doi).to eq("10.5281/zenodo.1196821")
       expect(subject.url).to eq("https://zenodo.org/record/1196821")
       expect(subject.types).to eq("bibtex"=>"misc", "citeproc"=>"dataset", "resourceTypeGeneral"=>"Dataset", "ris"=>"DATA", "schemaOrg"=>"Dataset")
@@ -97,7 +99,7 @@ describe Bolognese::Metadata, vcr: true do
       subject = Bolognese::Metadata.new(input: input, from: "schema_org")
       
       expect(subject.valid?).to be true
-      expect(subject.identifiers).to eq([{"identifier"=>"https://doi.org/10.1594/pangaea.836178", "identifierType"=>"DOI"}])
+      expect(subject.id).to eq("https://doi.org/10.1594/pangaea.836178")
       expect(subject.doi).to eq("10.1594/pangaea.836178")
       expect(subject.url).to eq("https://doi.pangaea.de/10.1594/PANGAEA.836178")
       expect(subject.types).to eq("bibtex"=>"misc", "citeproc"=>"dataset", "resourceTypeGeneral"=>"Dataset", "ris"=>"DATA", "schemaOrg"=>"Dataset")
@@ -108,24 +110,25 @@ describe Bolognese::Metadata, vcr: true do
       expect(subject.publication_year).to eq("2014")
     end
 
-    it "ornl" do
-      input = "https://doi.org/10.3334/ornldaac/1339"
-      subject = Bolognese::Metadata.new(input: input, from: "schema_org")
-      expect(subject.valid?).to be true
-      expect(subject.identifiers).to eq([{"identifier"=>"https://doi.org/10.3334/ornldaac/1339", "identifierType"=>"DOI"}])
-      expect(subject.doi).to eq("10.3334/ornldaac/1339")
-      expect(subject.url).to eq("https://doi.org/10.3334/ornldaac/1339")
-      expect(subject.types).to eq("bibtex"=>"misc", "citeproc"=>"article-journal", "ris"=>"GEN", "schemaOrg"=>"DataSet")
-      expect(subject.titles).to eq([{"title"=>"Soil Moisture Profiles and Temperature Data from SoilSCAPE Sites, USA"}])
-      expect(subject.creators.size).to eq(12)
-      expect(subject.creators.first).to eq("familyName"=>"MOGHADDAM", "givenName"=>"M.", "name"=>"MOGHADDAM, M.", "nameType"=>"Personal", "nameIdentifiers"=>[], "affiliation" => [])
-    end
+    # TODO: check redirections
+    # it "ornl" do
+    #   input = "https://doi.org/10.3334/ornldaac/1339"
+    #   subject = Bolognese::Metadata.new(input: input, from: "schema_org")
+    #   expect(subject.valid?).to be true
+    #   expect(subject.id).to eq("https://doi.org/10.3334/ornldaac/1339")
+    #   expect(subject.doi).to eq("10.3334/ornldaac/1339")
+    #   expect(subject.url).to eq("https://doi.org/10.3334/ornldaac/1339")
+    #   expect(subject.types).to eq("bibtex"=>"misc", "citeproc"=>"article-journal", "ris"=>"GEN", "schemaOrg"=>"DataSet")
+    #   expect(subject.titles).to eq([{"title"=>"Soil Moisture Profiles and Temperature Data from SoilSCAPE Sites, USA"}])
+    #   expect(subject.creators.size).to eq(12)
+    #   expect(subject.creators.first).to eq("familyName"=>"MOGHADDAM", "givenName"=>"M.", "name"=>"MOGHADDAM, M.", "nameType"=>"Personal", "nameIdentifiers"=>[], "affiliation" => [])
+    # end
 
     it "harvard dataverse" do
       input = "https://dataverse.harvard.edu/dataset.xhtml?persistentId=doi:10.7910/DVN/NJ7XSO"
       subject = Bolognese::Metadata.new(input: input, from: "schema_org")
       expect(subject.valid?).to be true
-      expect(subject.identifiers).to eq([{"identifier"=>"https://doi.org/10.7910/dvn/nj7xso", "identifierType"=>"DOI"}])
+      expect(subject.id).to eq("https://doi.org/10.7910/dvn/nj7xso")
       expect(subject.doi).to eq("10.7910/dvn/nj7xso")
       expect(subject.types).to eq("bibtex"=>"misc", "citeproc"=>"dataset", "resourceTypeGeneral"=>"Dataset", "ris"=>"DATA", "schemaOrg"=>"Dataset")
       expect(subject.titles).to eq([{"title"=>"Summary data ankylosing spondylitis GWAS"}])
@@ -136,17 +139,18 @@ describe Bolognese::Metadata, vcr: true do
         {"subject"=>"Ankylosing spondylitis"}])
     end
 
-    it "harvard dataverse via identifiers.org" do
-      input = "https://identifiers.org/doi/10.7910/DVN/NJ7XSO"
-      subject = Bolognese::Metadata.new(input: input, from: "schema_org")
-      expect(subject.valid?).to be true
-      expect(subject.identifiers).to eq([{"identifier"=>"https://doi.org/10.7910/dvn/nj7xso", "identifierType"=>"DOI"}])
-      expect(subject.doi).to eq("10.7910/dvn/nj7xso")
-      expect(subject.types).to eq("bibtex"=>"misc", "citeproc"=>"dataset", "resourceTypeGeneral"=>"Dataset", "ris"=>"DATA", "schemaOrg"=>"Dataset")
-      expect(subject.titles).to eq([{"title"=>"Summary data ankylosing spondylitis GWAS"}])
-      expect(subject.container).to eq("identifier"=>"https://dataverse.harvard.edu", "identifierType"=>"URL", "title"=>"Harvard Dataverse", "type"=>"DataRepository")
-      expect(subject.creators).to eq([{"name" => "International Genetics Of Ankylosing Spondylitis Consortium (IGAS)", "nameIdentifiers"=>[], "affiliation" => []}])
-    end
+    # TODO check 403 status in DOI resolver
+    # it "harvard dataverse via identifiers.org" do
+    #   input = "https://identifiers.org/doi/10.7910/DVN/NJ7XSO"
+    #   subject = Bolognese::Metadata.new(input: input, from: "schema_org")
+    #   expect(subject.valid?).to be true
+    #   expect(subject.id).to eq("https://doi.org/10.7910/dvn/nj7xso")
+    #   expect(subject.doi).to eq("10.7910/dvn/nj7xso")
+    #   expect(subject.types).to eq("bibtex"=>"misc", "citeproc"=>"dataset", "resourceTypeGeneral"=>"Dataset", "ris"=>"DATA", "schemaOrg"=>"Dataset")
+    #   expect(subject.titles).to eq([{"title"=>"Summary data ankylosing spondylitis GWAS"}])
+    #   expect(subject.container).to eq("identifier"=>"https://dataverse.harvard.edu", "identifierType"=>"URL", "title"=>"Harvard Dataverse", "type"=>"DataRepository")
+    #   expect(subject.creators).to eq([{"name" => "International Genetics Of Ankylosing Spondylitis Consortium (IGAS)", "nameIdentifiers"=>[], "affiliation" => []}])
+    # end
   end
 
   context "get schema_org metadata as string" do
@@ -154,7 +158,8 @@ describe Bolognese::Metadata, vcr: true do
       input = fixture_path + 'schema_org.json'
       subject = Bolognese::Metadata.new(input: input)
       expect(subject.valid?).to be true
-      expect(subject.identifiers).to eq([{"identifier"=>"https://doi.org/10.5438/4k3m-nyvg", "identifierType"=>"DOI"}])
+      expect(subject.language).to eq("en")
+      expect(subject.id).to eq("https://doi.org/10.5438/4k3m-nyvg")
       expect(subject.url).to eq("https://blog.datacite.org/eating-your-own-dog-food")
       expect(subject.types).to eq("bibtex"=>"article", "citeproc"=>"post-weblog", "resourceTypeGeneral"=>"Text", "ris"=>"GEN", "schemaOrg"=>"BlogPosting")
       expect(subject.creators).to eq([{"familyName"=>"Fenner", "givenName"=>"Martin", "name"=>"Fenner, Martin", "nameIdentifiers"=> [{"nameIdentifier"=>"https://orcid.org/0000-0003-1419-2405", "nameIdentifierScheme"=>"ORCID",
@@ -174,7 +179,8 @@ describe Bolognese::Metadata, vcr: true do
       subject = Bolognese::Metadata.new(input: input)
 
       expect(subject.valid?).to be true
-      expect(subject.identifiers).to eq([{"identifier"=>"https://doi.org/10.25491/d50j-3083", "identifierType"=>"DOI"}, {"identifier"=>"687610993", "identifierType"=>"md5"}])
+      expect(subject.id).to eq("https://doi.org/10.25491/d50j-3083")
+      expect(subject.identifiers).to eq([{"identifier"=>"687610993", "identifierType"=>"md5"}])
       expect(subject.url).to eq("https://ors.datacite.org/doi:/10.25491/d50j-3083")
       expect(subject.content_url).to eq(["https://storage.googleapis.com/gtex_analysis_v7/single_tissue_eqtl_data/GTEx_Analysis_v7_eQTL_expression_matrices.tar.gz"])
       expect(subject.types).to eq("bibtex"=>"misc", "citeproc"=>"dataset", "resourceType"=>"Gene expression matrices", "resourceTypeGeneral"=>"Dataset", "ris"=>"DATA", "schemaOrg"=>"Dataset")
@@ -194,8 +200,7 @@ describe Bolognese::Metadata, vcr: true do
       input = fixture_path + 'schema_org_topmed.json'
       subject = Bolognese::Metadata.new(input: input)
       expect(subject.valid?).to be true
-      expect(subject.identifiers).to eq([{"identifier"=>"https://doi.org/10.23725/8na3-9s47", "identifierType"=>"DOI"},
-        {"identifier"=>"3b33f6b9338fccab0901b7d317577ea3", "identifierType"=>"md5"},
+      expect(subject.identifiers).to eq([{"identifier"=>"3b33f6b9338fccab0901b7d317577ea3", "identifierType"=>"md5"},
         {"identifier"=>"ark:/99999/fk41CrU4eszeLUDe", "identifierType"=>"minid"},
         {"identifier"=>"dg.4503/c3d66dc9-58da-411c-83c4-dd656aa3c4b7", "identifierType"=>"dataguid"}])
       expect(subject.url).to eq("https://ors.datacite.org/doi:/10.23725/8na3-9s47")
@@ -247,7 +252,8 @@ describe Bolognese::Metadata, vcr: true do
       subject = Bolognese::Metadata.new(input: input)
 
       expect(subject.valid?).to be true
-      expect(subject.identifiers).to eq([{"identifier"=>"https://doi.org/10.1594/pangaea.842237", "identifierType"=>"DOI"}])
+      expect(subject.language).to eq("en")
+      expect(subject.id).to eq("https://doi.org/10.1594/pangaea.842237")
       expect(subject.types).to eq("bibtex"=>"misc", "citeproc"=>"dataset", "resourceTypeGeneral"=>"Dataset", "ris"=>"DATA", "schemaOrg"=>"Dataset")
       expect(subject.creators.length).to eq(2)
       expect(subject.creators.first).to eq("name"=>"Tara Oceans Consortium, Coordinators", "nameType"=>"Organizational", "nameIdentifiers"=>[], "affiliation" => [])
@@ -263,8 +269,8 @@ describe Bolognese::Metadata, vcr: true do
       input = JSON.parse(data).first.to_json
       subject = Bolognese::Metadata.new(input: input)
       expect(subject.valid?).to be true
-      expect(subject.identifiers).to eq([{"identifier"=>"https://doi.org/10.23725/7jg3-v803", "identifierType"=>"DOI"},
-        {"identifier"=>"ark:/99999/fk4E1n6n1YHKxPk", "identifierType"=>"minid"},
+      expect(subject.id).to eq("https://doi.org/10.23725/7jg3-v803")
+      expect(subject.identifiers).to eq([{"identifier"=>"ark:/99999/fk4E1n6n1YHKxPk", "identifierType"=>"minid"},
         {"identifier"=>"dg.4503/01b048d0-e128-4cb0-94e9-b2d2cab7563d",
          "identifierType"=>"dataguid"},
         {"identifier"=>"f9e72bdf25bf4b4f0e581d9218fec2eb", "identifierType"=>"md5"}])
@@ -285,7 +291,7 @@ describe Bolognese::Metadata, vcr: true do
       subject = Bolognese::Metadata.new(input: input)
 
       expect(subject.valid?).to be true
-      expect(subject.identifiers).to eq([{"identifier"=>"https://doi.org/10.23698/aida/drov", "identifierType"=>"DOI"}])
+      expect(subject.id).to eq("https://doi.org/10.23698/aida/drov")
       expect(subject.url).to eq("https://doi.aida.medtech4health.se/10.23698/aida/drov")
       expect(subject.types).to eq("bibtex"=>"misc", "citeproc"=>"dataset", "resourceTypeGeneral"=>"Dataset", "ris"=>"DATA", "schemaOrg"=>"Dataset")
       # expect(subject.creators).to eq([{"familyName"=>"Lindman", "givenName"=>"Karin", "name"=>"Lindman, Karin", "nameIdentifiers"=>[{"nameIdentifier"=> "https://orcid.org/0000-0003-1298-517X", "nameIdentifierScheme"=>"ORCID", "schemeUri"=>"https://orcid.org"}], "nameType"=>"Personal"}])
@@ -320,7 +326,7 @@ describe Bolognese::Metadata, vcr: true do
 
       expect(subject.valid?).to be true
       expect(subject.doi).to eq("10.5281/zenodo.1239")
-      expect(subject.identifiers).to eq([{"identifier"=>"https://doi.org/10.5281/zenodo.1239", "identifierType"=>"DOI"}])
+      expect(subject.id).to eq("https://doi.org/10.5281/zenodo.1239")
       expect(subject.types["schemaOrg"]).to eq("Dataset")
       expect(subject.types["resourceTypeGeneral"]).to eq("Dataset")
       expect(subject.creators).to eq([{"familyName"=>"Jahn", "givenName"=>"Najko", "name"=>"Jahn, Najko", "type"=>"Person"}])

data/spec/writers/bibtex_writer_spec.rb

@@ -112,7 +112,7 @@ describe Bolognese::Metadata, vcr: true do
       expect(bibtex[:doi]).to eq("10.5061/dryad.8515")
       expect(bibtex[:title]).to eq("Data from: A new malaria agent in African hominids.")
       expect(bibtex[:author]).to eq("Ollomo, Benjamin and Durand, Patrick and Prugnolle, Franck and Douzery, Emmanuel J. P. and Arnathau, Céline and Nkoghe, Dieudonné and Leroy, Eric and Renaud, François")
-      expect(bibtex[:publisher]).to eq("Dryad Digital Repository")
+      expect(bibtex[:publisher]).to eq("Dryad")
       expect(bibtex[:year]).to eq("2011")
       expect(bibtex[:copyright]).to eq("Creative Commons Zero v1.0 Universal")
     end
@@ -153,7 +153,7 @@ describe Bolognese::Metadata, vcr: true do
       expect(bibtex[:bibtex_type].to_s).to eq("misc")
       expect(bibtex[:bibtex_key]).to eq("https://doi.org/10.1594/pangaea.721193")
       expect(bibtex[:doi]).to eq("10.1594/pangaea.721193")
-      expect(bibtex[:keywords]).to eq("Animalia, Bottles or small containers/Aquaria ( 20 L), Calcification/Dissolution, Coast and continental shelf, Crassostrea gigas, Development, Growth/Morphology, Laboratory experiment, Mollusca, North Pacific, Pelagos, Single species, Temperate, Zooplankton, Experimental treatment, Carbonate system computation flag, Temperature, water, Salinity, pH, Alkalinity, total, Carbon, inorganic, dissolved, Carbon dioxide, Bicarbonate ion, Carbonate ion, Partial pressure of carbon dioxide (water) at sea surface temperature (wet air), Fugacity of carbon dioxide (water) at sea surface temperature (wet air), Aragonite saturation state, Calcite saturation state, Proportion, Crassostrea gigas, larvae length, Crassostrea gigas, larvae height, Crassostrea gigas, non mineralized, Crassostrea gigas, partially mineralized, Crassostrea gigas, fully mineralized, Calculated using seacarb after Nisumaa et al. (2010), Refractometer (Atago 100-S), pH meter (Mettler Toledo), pH meter (PHM290, Radiometer), Measured, European Project on Ocean Acidification (EPOCA), European network of excellence for Ocean Ecosystems Analysis (EUR-OCEANS), Ocean Acidification International Coordination Centre (OA-ICC)")
+      expect(bibtex[:keywords]).to start_with("Animalia, Bottles or small containers/Aquaria (<20 L), Calcification/Dissolution")
       expect(bibtex[:year]).to eq("2007")
       expect(bibtex[:copyright]).to eq("Creative Commons Attribution 3.0 Unported")
     end

data/spec/writers/citation_writer_spec.rb

@@ -12,19 +12,19 @@ describe Bolognese::Metadata, vcr: true do
       expect(subject.citation).to eq("Sankar, M., Nieminen, K., Ragni, L., Xenarios, I., &amp; Hardtke, C. S. (2014). Automated quantitative histology reveals vascular morphodynamics during Arabidopsis hypocotyl secondary growth. <i>ELife</i>, <i>3</i>. https://doi.org/10.7554/elife.01567")
     end
 
-    # it "Journal article vancouver style" do
-    #   input = "10.7554/eLife.01567"
-    #   subject = Bolognese::Metadata.new(input: input, from: "crossref", style: "vancouver", locale: "de-de")
-    #   expect(subject.style).to eq("vancouver")
-    #   expect(subject.locale).to eq("de-de")
-    #   expect(subject.citation).to eq("Sankar M, Nieminen K, Ragni L, Xenarios I, Hardtke CS. Automated quantitative histology reveals vascular morphodynamics during Arabidopsis hypocotyl secondary growth. eLife [Internet]. 11. Februar 2014;3. Verfügbar unter: https://elifesciences.org/articles/01567")
-    # end
+    it "Journal article vancouver style" do
+      input = "10.7554/eLife.01567"
+      subject = Bolognese::Metadata.new(input: input, from: "crossref", style: "vancouver", locale: "en-US")
+      expect(subject.style).to eq("vancouver")
+      expect(subject.locale).to eq("en-US")
+      expect(subject.citation).to eq("Sankar M, Nieminen K, Ragni L, Xenarios I, Hardtke CS. Automated quantitative histology reveals vascular morphodynamics during Arabidopsis hypocotyl secondary growth. eLife [Internet]. 2014Feb11;3. Available from: https://elifesciences.org/articles/01567")
+    end
 
     it "Dataset" do
       input = "https://doi.org/10.5061/DRYAD.8515"
       subject = Bolognese::Metadata.new(input: input, from: "datacite")
 
-      expect(subject.citation).to eq("Ollomo, B., Durand, P., Prugnolle, F., Douzery, E. J. P., Arnathau, C., Nkoghe, D., Leroy, E., &amp; Renaud, F. (2011). <i>Data from: A new malaria agent in African hominids.</i> (Version 1) [Data set]. Dryad Digital Repository. https://doi.org/10.5061/dryad.8515")
+      expect(subject.citation).to eq("Ollomo, B., Durand, P., Prugnolle, F., Douzery, E. J. P., Arnathau, C., Nkoghe, D., Leroy, E., &amp; Renaud, F. (2011). <i>Data from: A new malaria agent in African hominids.</i> (Version 1) [Data set]. Dryad. https://doi.org/10.5061/dryad.8515")
     end
 
     it "Missing author" do
@@ -40,5 +40,13 @@ describe Bolognese::Metadata, vcr: true do
       expect(subject.locale).to eq("en-US")
       expect(subject.citation).to eq("Lab For Exosphere And Near Space Environment Studies. (2019). <i>lenses-lab/LYAO_RT-2018JA026426: Original Release</i> (Version 1.0.0) [Computer software]. Zenodo. https://doi.org/10.5281/zenodo.2598836")
     end
+
+    it "interactive resource without dates" do
+      input = "https://doi.org/10.34747/g6yb-3412"
+      subject = Bolognese::Metadata.new(input: input, from: "datacite")
+      expect(subject.style).to eq("apa")
+      expect(subject.locale).to eq("en-US")
+      expect(subject.citation).to eq("Clark, D. (2019). <i>Exploring the \"Many analysts, one dataset\" project from COS</i>. Gigantum, Inc. https://doi.org/10.34747/g6yb-3412")
+    end
   end
 end

data/spec/writers/citeproc_writer_spec.rb

@@ -21,7 +21,7 @@ describe Bolognese::Metadata, vcr: true do
                                     {"family"=>"Nkoghe", "given"=>"Dieudonné"},
                                     {"family"=>"Leroy", "given"=>"Eric"},
                                     {"family"=>"Renaud", "given"=>"François"}])
-      expect(json["publisher"]).to eq("Dryad Digital Repository")
+      expect(json["publisher"]).to eq("Dryad")
       expect(json["issued"]).to eq("date-parts" => [[2011]])
       expect(json["submitted"]).to be_nil
       expect(json["copyright"]).to eq("Creative Commons Zero v1.0 Universal")
@@ -244,7 +244,7 @@ describe Bolognese::Metadata, vcr: true do
       expect(json["type"]).to eq("dataset")
       expect(json["id"]).to eq("https://doi.org/10.1594/pangaea.721193")
       expect(json["DOI"]).to eq("10.1594/pangaea.721193")
-      expect(json["categories"]).to include("Animalia", "Bottles or small containers/Aquaria ( 20 L)", "Calcification/Dissolution", "Coast and continental shelf", "Development", "Growth/Morphology", "Laboratory experiment", "Mollusca", "Pelagos", "Single species", "Temperate", "Zooplankton", "Experimental treatment", "Carbonate system computation flag", "Temperature, water", "Salinity", "pH", "Alkalinity, total", "Carbon, inorganic, dissolved", "Carbon dioxide", "Bicarbonate ion", "Carbonate ion", "Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)", "Fugacity of carbon dioxide (water) at sea surface temperature (wet air)", "Aragonite saturation state", "Calcite saturation state", "Proportion", "Crassostrea gigas, larvae length", "Crassostrea gigas, larvae height", "Crassostrea gigas, non mineralized", "Crassostrea gigas, partially mineralized", "Crassostrea gigas, fully mineralized", "Calculated using seacarb after Nisumaa et al. (2010)", "Refractometer (Atago 100-S)", "pH meter (Mettler Toledo)", "pH meter (PHM290, Radiometer)", "Measured", "European Project on Ocean Acidification (EPOCA)", "European network of excellence for Ocean Ecosystems Analysis (EUR-OCEANS)", "Ocean Acidification International Coordination Centre (OA-ICC)")
+      expect(json["categories"]).to include("Animalia", "Bottles or small containers/Aquaria (<20 L)", "Calcification/Dissolution", "Coast and continental shelf", "Development", "Growth/Morphology", "Laboratory experiment", "Mollusca", "Pelagos", "Single species", "Temperate", "Zooplankton", "Experimental treatment", "Carbonate system computation flag", "Temperature, water", "Salinity", "pH", "Alkalinity, total", "Carbon, inorganic, dissolved", "Carbon dioxide", "Bicarbonate ion", "Carbonate ion", "Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)", "Fugacity of carbon dioxide (water) at sea surface temperature (wet air)", "Aragonite saturation state", "Calcite saturation state", "Proportion", "Crassostrea gigas, larvae length", "Crassostrea gigas, larvae height", "Crassostrea gigas, non mineralized", "Crassostrea gigas, partially mineralized", "Crassostrea gigas, fully mineralized", "Calculated using seacarb after Nisumaa et al. (2010)", "Refractometer (Atago 100-S)", "pH meter (Mettler Toledo)", "pH meter (PHM290, Radiometer)", "Measured", "European Project on Ocean Acidification (EPOCA)", "European network of excellence for Ocean Ecosystems Analysis (EUR-OCEANS)", "Ocean Acidification International Coordination Centre (OA-ICC)")
       expect(json["copyright"]).to eq("Creative Commons Attribution 3.0 Unported")
     end
 
@@ -264,5 +264,14 @@ describe Bolognese::Metadata, vcr: true do
         {"literal"=>"The Genome Denmark Consortium"}])
       expect(json["container-title"]).to eq("GigaScience")
     end
+
+    it "interactive resource without dates" do
+      input = "https://doi.org/10.34747/g6yb-3412"
+      subject = Bolognese::Metadata.new(input: input, from: "datacite")
+      json = JSON.parse(subject.citeproc)
+      expect(json["type"]).to eq("article")
+      expect(json["DOI"]).to eq("10.34747/g6yb-3412")
+      expect(json["issued"]).to eq("date-parts"=>[[2019]])
+    end
   end
 end

data/spec/writers/codemeta_writer_spec.rb

@@ -27,7 +27,6 @@ describe Bolognese::Metadata, vcr: true do
       expect(json["@context"]).to eq("https://raw.githubusercontent.com/codemeta/codemeta/master/codemeta.jsonld")
       expect(json["@id"]).to eq("https://doi.org/10.5063/f1m61h5x")
       expect(json["@type"]).to eq("SoftwareSourceCode")
-      expect(json["identifier"]).to eq("@type"=>"PropertyValue", "propertyID"=>"DOI", "value"=>"https://doi.org/10.5063/f1m61h5x")
       expect(json["authors"]).to eq([{"name"=>"Jones, Matthew B.; Slaughter, Peter; Nahf, Rob; Boettiger, Carl ; Jones, Chris; Read, Jordan; Walker, Lauren; Hart, Edmund; Chamberlain, Scott", "nameIdentifiers" => [], "affiliation" => []}])
       expect(json["name"]).to eq("dataone: R interface to the DataONE network of data repositories")
       expect(json["datePublished"]).to eq("2016")

data/spec/writers/crosscite_writer_spec.rb

@@ -83,11 +83,11 @@ describe Bolognese::Metadata, vcr: true do
       input = "https://doi.org/10.5061/DRYAD.8515"
       subject = Bolognese::Metadata.new(input: input, from: "datacite")
       crosscite = JSON.parse(subject.crosscite)
-      expect(crosscite.fetch("url")).to eq("https://datadryad.org/resource/doi:10.5061/dryad.8515")
+      expect(crosscite.fetch("url")).to eq("http://datadryad.org/stash/dataset/doi:10.5061/dryad.8515")
       expect(crosscite.fetch("titles")).to eq([{"title"=>"Data from: A new malaria agent in African hominids."}])
       expect(crosscite.fetch("creators").length).to eq(8)
-      expect(crosscite.fetch("creators").first).to eq("familyName" => "Ollomo", "givenName" => "Benjamin", "name" => "Ollomo, Benjamin", "nameType" => "Personal", "nameIdentifiers" => [], "affiliation" => [])
-      expect(crosscite.fetch("dates")).to eq([{"date"=>"2011", "dateType"=>"Issued"}])
+      expect(crosscite.fetch("creators").first).to eq("familyName" => "Ollomo", "givenName" => "Benjamin", "name" => "Ollomo, Benjamin", "nameType" => "Personal", "nameIdentifiers" => [], "affiliation" => [{"affiliationIdentifier"=>"https://ror.org/01wyqb997", "affiliationIdentifierScheme"=>"ROR", "name"=>"Centre International de Recherches Médicales de Franceville"}])
+      expect(crosscite.fetch("dates")).to eq([{"date"=>"2011-02-01T17:22:41Z", "dateType"=>"Available"}, {"date"=>"2011", "dateType"=>"Issued"}])
       expect(crosscite.fetch("publication_year")).to eq("2011")
       expect(crosscite.fetch("provider_id")).to eq("dryad")
       expect(crosscite.fetch("client_id")).to eq("dryad.dryad")

data/spec/writers/datacite_writer_spec.rb

@@ -127,7 +127,8 @@ describe Bolognese::Metadata, vcr: true do
       input = "https://doi.org/10.5281/zenodo.28518"
       subject = Bolognese::Metadata.new(input: input, from: "datacite", regenerate: true)
       expect(subject.valid?).to be true
-      expect(subject.identifiers).to eq([{"identifier"=>"https://doi.org/10.5281/zenodo.28518", "identifierType"=>"DOI"}, {"identifier"=>"https://zenodo.org/record/28518", "identifierType"=>"URL"}])
+      expect(subject.id).to eq("https://doi.org/10.5281/zenodo.28518")
+      expect(subject.identifiers).to eq([{"identifier"=>"https://zenodo.org/record/28518", "identifierType"=>"URL"}])
       expect(subject.types).to eq("bibtex" => "misc",
         "citeproc" => "article",
         "resourceTypeGeneral" => "Software",
@@ -155,7 +156,7 @@ describe Bolognese::Metadata, vcr: true do
       input = "https://doi.org/10.23640/07243.5153971"
       subject = Bolognese::Metadata.new(input: input, from: "datacite")
       expect(subject.valid?).to be true
-      expect(subject.identifiers).to eq([{"identifier"=>"https://doi.org/10.23640/07243.5153971", "identifierType"=>"DOI"}])
+      expect(subject.id).to eq("https://doi.org/10.23640/07243.5153971")
       expect(subject.types).to eq("bibtex"=>"article", "citeproc"=>"article-journal", "resourceType"=>"Paper", "resourceTypeGeneral"=>"Text", "ris"=>"RPRT", "schemaOrg"=>"ScholarlyArticle")
       expect(subject.creators.length).to eq(20)
       expect(subject.creators.first).to eq("nameType"=>"Personal", "familyName" => "Paglione", "givenName" => "Laura", "nameIdentifiers" => [{"nameIdentifier"=>"https://orcid.org/0000-0003-3188-6273", "nameIdentifierScheme"=>"ORCID", "schemeUri"=>"https://orcid.org"}], "name" => "Paglione, Laura", "affiliation" => [])
@@ -181,7 +182,7 @@ describe Bolognese::Metadata, vcr: true do
       input = "https://doi.org/10.23640/07243.5153971"
       subject = Bolognese::Metadata.new(input: input, from: "datacite", doi: "10.5072/07243.5153971")
       expect(subject.valid?).to be true
-      expect(subject.identifiers).to eq([{"identifier"=>"https://doi.org/10.5072/07243.5153971", "identifierType"=>"DOI"}])
+      expect(subject.id).to eq("https://doi.org/10.5072/07243.5153971")
       expect(subject.types).to eq("bibtex"=>"article", "citeproc"=>"article-journal", "resourceType"=>"Paper", "resourceTypeGeneral"=>"Text", "ris"=>"RPRT", "schemaOrg"=>"ScholarlyArticle")
       expect(subject.creators.length).to eq(20)
       expect(subject.creators.first).to eq("nameType" => "Personal", "familyName" => "Paglione", "givenName" => "Laura", "name" => "Paglione, Laura", "nameIdentifiers" => [{"nameIdentifier"=>"https://orcid.org/0000-0003-3188-6273", "nameIdentifierScheme"=>"ORCID", "schemeUri"=>"https://orcid.org"}],"affiliation" => [])
@@ -207,24 +208,22 @@ describe Bolognese::Metadata, vcr: true do
       input = "https://doi.org/10.5061/DRYAD.8515"
       subject = Bolognese::Metadata.new(input: input, from: "datacite", regenerate: true)
       expect(subject.valid?).to be true
-      expect(subject.types).to eq("bibtex"=>"misc", "citeproc"=>"dataset", "resourceType"=>"DataPackage", "resourceTypeGeneral"=>"Dataset", "ris"=>"DATA", "schemaOrg"=>"Dataset")
+      expect(subject.types).to eq("bibtex"=>"misc", "citeproc"=>"dataset", "resourceType"=>"dataset", "resourceTypeGeneral"=>"Dataset", "ris"=>"DATA", "schemaOrg"=>"Dataset")
       expect(subject.creators.length).to eq(8)
-      expect(subject.creators.first).to eq("nameType" => "Personal", "name"=>"Ollomo, Benjamin", "givenName"=>"Benjamin", "familyName"=>"Ollomo", "nameIdentifiers"=>[], "affiliation" => [])
+      expect(subject.creators.first).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"}])
       expect(subject.titles).to eq([{"title"=>"Data from: A new malaria agent in African hominids."}])
-      expect(subject.identifiers).to eq([{"identifier"=>"https://doi.org/10.5061/dryad.8515", "identifierType"=>"DOI"},
-        {"identifier"=>
-         "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.",
-         "identifierType"=>"citation"}])
+      expect(subject.id).to eq("https://doi.org/10.5061/dryad.8515")
       expect(subject.rights_list).to eq([{"rights"=>"Creative Commons Zero v1.0 Universal",
         "rightsIdentifier"=>"cc0-1.0",
         "rightsIdentifierScheme"=>"SPDX",
         "rightsUri"=>"https://creativecommons.org/publicdomain/zero/1.0/legalcode",
         "schemeUri"=>"https://spdx.org/licenses/"}])
-      expect(subject.dates).to eq([{"date"=>"2011", "dateType"=>"Issued"}])
+      expect(subject.dates).to eq([{"date"=>"2011-02-01T17:22:41Z", "dateType"=>"Available"}, {"date"=>"2011", "dateType"=>"Issued"}])
       expect(subject.publication_year).to eq("2011")
-      expect(subject.related_identifiers.length).to eq(6)
-      expect(subject.related_identifiers.last).to eq("relatedIdentifier"=>"19478877", "relatedIdentifierType"=>"PMID", "relationType"=>"IsSupplementTo")
-      expect(subject.publisher).to eq("Dryad Digital Repository")
+      expect(subject.related_identifiers.length).to eq(1)
+      expect(subject.related_identifiers.last).to eq("relatedIdentifier" => "10.1371/journal.ppat.1000446",
+        "relatedIdentifierType" => "DOI","relationType"=>"IsSupplementTo")
+      expect(subject.publisher).to eq("Dryad")
       expect(subject.agency).to eq("DataCite")
       expect(subject.schema_version).to eq("http://datacite.org/schema/kernel-4")
 
@@ -241,7 +240,7 @@ describe Bolognese::Metadata, vcr: true do
       expect(subject.creators.length).to eq(6)
       expect(subject.creators.first).to eq("affiliation"=>[{"name"=>"UC Merced"}, {"name"=>"NSF"}], "familyName"=>"Bales", "givenName"=>"Roger", "name"=>"Bales, Roger", "nameType"=>"Personal", "nameIdentifiers"=>[])
       expect(subject.titles).to eq([{"title"=>"Southern Sierra Critical Zone Observatory (SSCZO), Providence Creek meteorological data, soil moisture and temperature, snow depth and air temperature"}])
-      expect(subject.identifiers).to eq([{"identifier"=>"https://doi.org/10.6071/z7wc73", "identifierType"=>"DOI"}])
+      expect(subject.id).to eq("https://doi.org/10.6071/z7wc73")
       expect(subject.rights_list).to eq([{"rights"=>"Creative Commons Attribution 4.0 International",
         "rightsIdentifier"=>"cc-by-4.0",
         "rightsIdentifierScheme"=>"SPDX",
@@ -272,7 +271,7 @@ describe Bolognese::Metadata, vcr: true do
       input = "https://doi.org/10.4124/05F6C379-DD68-4CDB-880D-33D3E9576D52/1"
       subject = Bolognese::Metadata.new(input: input, from: "datacite")
       expect(subject.valid?).to be false
-      expect(subject.identifiers).to eq([{"identifier"=>"https://doi.org/10.4124/05f6c379-dd68-4cdb-880d-33d3e9576d52/1", "identifierType"=>"DOI"}])
+      expect(subject.id).to eq("https://doi.org/10.4124/05f6c379-dd68-4cdb-880d-33d3e9576d52/1")
       expect(subject.doi).to eq("10.4124/05f6c379-dd68-4cdb-880d-33d3e9576d52/1")
       expect(subject.agency).to eq("DataCite")
       expect(subject.state).to eq("not_found")
@@ -383,6 +382,17 @@ describe Bolognese::Metadata, vcr: true do
       expect(subject.state).to eq("registered")
     end
 
+    it "change identifiers" do
+      input = "10.7554/eLife.01567"
+      subject = Bolognese::Metadata.new(input: input, from: "crossref")
+      expect(subject.valid?).to be true
+      expect(subject.identifiers).to eq( [{"identifier"=>"e01567", "identifierType"=>"Publisher ID"}])
+      subject.identifiers = [{ "identifierType" => "Publisher ID", "identifier" => "abc" }]
+      datacite = Maremma.from_xml(subject.datacite).fetch("resource", {})
+      expect(datacite.dig("identifier", "__content__")).to eq("10.7554/elife.01567")
+      expect(subject.identifiers).to eq([{"identifier"=>"abc", "identifierType"=>"Publisher ID"}])
+    end
+
     it "validates against schema" do
       input = "10.7554/eLife.01567"
       subject = Bolognese::Metadata.new(input: input, from: "crossref")

data/spec/writers/jats_writer_spec.rb

@@ -52,12 +52,12 @@ describe Bolognese::Metadata, vcr: true do
       subject = Bolognese::Metadata.new(input: input, from: "crossref")
       jats = Maremma.from_xml(subject.jats).fetch("element_citation", {})
       expect(jats.dig("publication_type")).to eq("chapter")
-      expect(jats.dig("chapter_title")).to eq("Chapter-02 Physical Examinations")
+      expect(jats.dig("chapter_title")).to eq("Physical Examinations")
       expect(jats.dig("source")).to eq("Jaypee Brothers Medical Publishers (P) Ltd.")
       expect(jats.dig("person_group", "name")).to eq("surname"=>"Saha", "given_names"=>"Ashis")
       expect(jats.dig("year")).to eq("iso_8601_date"=>"2015", "__content__"=>"2015")
       expect(jats.dig("fpage")).to eq("27")
-      expect(jats.dig("lpage")).to eq("145")
+      expect(jats.dig("lpage")).to eq("27")
       expect(jats.dig("pub_id")).to eq("pub_id_type"=>"doi", "__content__"=>"10.5005/jp/books/12414_3")
     end
 
@@ -138,7 +138,7 @@ describe Bolognese::Metadata, vcr: true do
       jats = Maremma.from_xml(subject.jats).fetch("element_citation", {})
       expect(jats.dig("publication_type")).to eq("data")
       expect(jats.dig("data_title")).to eq("Data from: A new malaria agent in African hominids.")
-      expect(jats.dig("source")).to eq("Dryad Digital Repository")
+      expect(jats.dig("source")).to eq("Dryad")
       expect(jats.dig("person_group", "name").length).to eq(8)
       expect(jats.dig("person_group", "name").first).to eq("surname"=>"Ollomo", "given_names"=>"Benjamin")
       expect(jats.dig("year")).to eq("iso_8601_date"=>"2011", "__content__"=>"2011")
@@ -158,6 +158,20 @@ describe Bolognese::Metadata, vcr: true do
       expect(jats.dig("day")).to eq("20")
       expect(jats.dig("pub_id")).to eq("pub_id_type"=>"doi", "__content__"=>"10.5438/4k3m-nyvg")
     end
+
+    it "interactive resource without dates" do
+      input = "https://doi.org/10.34747/g6yb-3412"
+      subject = Bolognese::Metadata.new(input: input, from: "datacite")
+      jats = Maremma.from_xml(subject.jats).fetch("element_citation", {})
+      expect(jats.dig("publication_type")).to be_nil
+      expect(jats.dig("source")).to eq("Exploring the \"Many analysts, one dataset\" project from COS")
+      expect(jats.dig("publisher_name")).to eq("Gigantum, Inc.")
+      expect(jats.dig("person_group", "name")).to eq("given_names"=>"Dav", "surname"=>"Clark")
+      expect(jats.dig("year")).to eq("__content__"=>"2019", "iso_8601_date"=>"2019")
+      expect(jats.dig("month")).to be_nil
+      expect(jats.dig("day")).to be_nil
+      expect(jats.dig("pub_id")).to eq("pub_id_type"=>"doi", "__content__"=>"10.34747/g6yb-3412")
+    end
   end
 
   context "change metadata as datacite xml" do