bolognese 1.9.7 → 1.9.11

data/spec/readers/datacite_reader_spec.rb

@@ -36,12 +36,11 @@ describe Bolognese::Metadata, vcr: true do
       expect(subject.publication_year).to eq("2011")
       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")
+        "relatedIdentifierType" => "DOI","relationType"=>"Cites")
       expect(subject.subjects).to eq([{"subject"=>"Plasmodium"},
         {"subject"=>"malaria"},
         {"subject"=>"taxonomy"},
         {"subject"=>"mitochondrial genome"},
-        {"subject"=>"phylogeny"},
         {"subject"=>"Parasites"}])
       expect(subject.publisher).to eq("Dryad")
       expect(subject.agency).to eq("datacite")
@@ -61,14 +60,22 @@ describe Bolognese::Metadata, vcr: true do
       expect(subject.creators).to eq([{"nameIdentifiers"=> [{"nameIdentifier"=>"https://orcid.org/0000-0003-1419-2405", "nameIdentifierScheme"=>"ORCID", "schemeUri"=>"https://orcid.org"}], "name"=>"Fenner, Martin", "givenName"=>"Martin", "familyName"=>"Fenner"}])
       expect(subject.titles).to eq([{"title"=>"Eating your own Dog Food"}])
       expect(subject.id).to eq("https://doi.org/10.5438/4k3m-nyvg")
-      expect(subject.identifiers).to eq([{"identifier"=>"MS-49-3632-5083", "identifierType"=>"Local accession number"}])
       expect(subject.descriptions.first["description"]).to start_with("Eating your own dog food")
       expect(subject.dates).to eq([{"date"=>"2016-12-20", "dateType"=>"Created"}, {"date"=>"2016-12-20", "dateType"=>"Issued"}, {"date"=>"2016-12-20", "dateType"=>"Updated"}])
       expect(subject.publication_year).to eq("2016")
       expect(subject.related_identifiers.length).to eq(3)
       expect(subject.related_identifiers.last).to eq("relatedIdentifier"=>"10.5438/0000-00ss", "relatedIdentifierType"=>"DOI", "relationType"=>"IsPartOf")
       expect(subject.publisher).to eq("DataCite")
-      expect(subject.subjects).to eq([{"subject"=>"datacite"}, {"subject"=>"doi"}, {"subject"=>"metadata"}])
+      expect(subject.subjects).to eq([{"subject"=>"datacite"},
+        {"subject"=>"doi"},
+        {"subject"=>"metadata"},
+        {"schemeUri"=>"http://www.oecd.org/science/inno",
+         "subject"=>"FOS: Computer and information sciences",
+         "subjectScheme"=>"Fields of Science and Technology (FOS)",
+         "valueUri"=>"http://www.oecd.org/science/inno/38235147.pdf"},
+        {"schemeUri"=>"http://www.oecd.org/science/inno/38235147.pdf",
+         "subject"=>"FOS: Computer and information sciences",
+         "subjectScheme"=>"Fields of Science and Technology (FOS)"}])
       expect(subject.agency).to eq("datacite")
       expect(subject.schema_version).to eq("http://datacite.org/schema/kernel-4")
     end
@@ -235,15 +242,25 @@ describe Bolognese::Metadata, vcr: true do
       expect(subject.publication_year).to eq("2016")
       expect(subject.related_identifiers.length).to eq(1)
       expect(subject.related_identifiers.last).to eq("relatedIdentifier"=>"10.6084/m9.figshare.4234751", "relatedIdentifierType"=>"DOI", "relationType"=>"IsIdenticalTo")
-      expect(subject.publisher).to eq("Figshare")
-      expect(subject.subjects).to eq([{"subject"=>"Bioinformatics"},
-       {"schemeUri"=>"http://www.oecd.org/science/inno/38235147.pdf",
-        "subject"=>"FOS: Computer and information sciences",
-        "subjectScheme"=>"Fields of Science and Technology (FOS)"},
-       {"subject"=>"Computational Biology"},
-       {"subject"=>"Systems Biology"}])
+      expect(subject.publisher).to eq("figshare")
+      expect(subject.subjects).to eq([
+        {"schemeUri"=>
+          "http://www.abs.gov.au/ausstats/abs@.nsf/0/6BB427AB9696C225CA2574180004463E",
+          "subject"=>"60102 Bioinformatics",
+          "subjectScheme"=>"FOR"},
+            {"schemeUri"=>"http://www.oecd.org/science/inno/38235147.pdf",
+             "subject"=>"FOS: Computer and information sciences",
+             "subjectScheme"=>"Fields of Science and Technology (FOS)"},
+            {"subject"=>"Computational Biology"},
+         {"schemeUri"=>
+          "http://www.abs.gov.au/ausstats/abs@.nsf/0/6BB427AB9696C225CA2574180004463E",
+          "subject"=>"60114 Systems Biology",
+          "subjectScheme"=>"FOR"},
+         {"schemeUri"=>"http://www.oecd.org/science/inno/38235147.pdf",
+          "subject"=>"FOS: Biological sciences",
+          "subjectScheme"=>"Fields of Science and Technology (FOS)"}])
       expect(subject.agency).to eq("datacite")
-      expect(subject.schema_version).to eq("http://datacite.org/schema/kernel-3")
+      expect(subject.schema_version).to eq("http://datacite.org/schema/kernel-4")
     end
 
     it "subject scheme FOR" do
@@ -299,11 +316,11 @@ describe Bolognese::Metadata, vcr: true do
       input = "10.6084/m9.figshare.1286826.v1"
       subject = Bolognese::Metadata.new(input: input)
       expect(subject.valid?).to be true
-      expect(subject.rights_list).to eq([{"rights"=>"Creative Commons Attribution 3.0 Unported",
-        +  "rightsIdentifier"=>"cc-by-3.0",
-        +  "rightsIdentifierScheme"=>"SPDX",
-        +  "rightsUri"=>"https://creativecommons.org/licenses/by/3.0/legalcode",
-        +  "schemeUri"=>"https://spdx.org/licenses/"}])
+      expect(subject.rights_list).to eq([{"rights"=>"Creative Commons Attribution 4.0 International",
+        "rightsIdentifier"=>"cc-by-4.0",
+        "rightsIdentifierScheme"=>"SPDX",
+        "rightsUri"=>"https://creativecommons.org/licenses/by/4.0/legalcode",
+        "schemeUri"=>"https://spdx.org/licenses/"}])
     end
 
     it "funding schema version 3" do
@@ -914,7 +931,7 @@ describe Bolognese::Metadata, vcr: true do
       expect(subject.id).to eq("https://doi.org/10.5067/terra+aqua/ceres/cldtyphist_l3.004")
       expect(subject.types["schemaOrg"]).to eq("Dataset")
       expect(subject.types["resourceTypeGeneral"]).to eq("Dataset")
-      expect(subject.creators).to eq([{"nameType"=>"Personal", "name"=>"Wong, Takmeng", "givenName"=>"Takmeng", "familyName"=>"Wong", "nameIdentifiers" => [], "affiliation" => []}])
+      expect(subject.creators).to eq([{"familyName"=>"Wong", "givenName"=>"Takmeng", "name"=>"Wong, Takmeng"}])
       expect(subject.titles).to eq([{"title"=>"CERES Level 3 Cloud Type Historgram Terra+Aqua HDF file - Edition4"}])
       expect(subject.publication_year).to eq("2016")
       expect(subject.publisher).to eq("NASA Langley Atmospheric Science Data Center DAAC")
@@ -935,7 +952,27 @@ describe Bolognese::Metadata, vcr: true do
       expect(subject.contributors.length).to eq(18)
       expect(subject.contributors.first).to eq("affiliation"=>[{"name"=>"Europäische Kommission, Brüssel"}], "contributorType"=>"Researcher", "familyName"=>"Reif", "givenName"=>"Karlheinz", "name"=>"Reif, Karlheinz", "nameType"=>"Personal", "nameIdentifiers" => [])
       expect(subject.titles).to eq([{"lang"=>"de", "title"=>"Flash Eurobarometer 54 (Madrid Summit)"}, {"lang"=>"en", "title"=>"Flash Eurobarometer 54 (Madrid Summit)"}, {"titleType"=>"Subtitle","lang"=>"de", "title"=>"The Common European Currency"}, {"titleType"=>"Subtitle", "lang"=>"en", "title"=>"The Common European Currency"}])
-      expect(subject.subjects).to eq([{"subjectScheme"=>"ZA", "lang"=>"en", "subject"=>"KAT12 International Institutions, Relations, Conditions"}])
+      expect(subject.subjects).to eq([{"lang"=>"en",
+        "subject"=>"KAT12 International Institutions, Relations, Conditions",
+        "subjectScheme"=>"ZA"},
+       {"lang"=>"de",
+        "subject"=>"Internationale Politik und Institutionen",
+        "subjectScheme"=>"CESSDA Topic Classification"},
+       {"lang"=>"de",
+        "subject"=>"Regierung, politische Systeme, Parteien und Verbände",
+        "subjectScheme"=>"CESSDA Topic Classification"},
+       {"lang"=>"de",
+        "subject"=>"Wirtschaftssysteme und wirtschaftliche Entwicklung",
+        "subjectScheme"=>"CESSDA Topic Classification"},
+       {"lang"=>"en",
+        "subject"=>"International politics and organisation",
+        "subjectScheme"=>"CESSDA Topic Classification"},
+       {"lang"=>"en",
+        "subject"=>"Government, political systems and organisation",
+        "subjectScheme"=>"CESSDA Topic Classification"},
+       {"lang"=>"en",
+        "subject"=>"Economic systems and development",
+        "subjectScheme"=>"CESSDA Topic Classification"}])
       expect(subject.dates).to eq([{"date"=>"1995-12", "dateType"=>"Collected"}, {"date"=>"1996", "dateType"=>"Issued"}])
       expect(subject.publication_year).to eq("1996")
       expect(subject.publisher).to eq("GESIS Data Archive")
@@ -1046,11 +1083,11 @@ describe Bolognese::Metadata, vcr: true do
       expect(subject.state).to eq("not_found")
     end
 
-    it "DOI in test system" do
-      input = "https://handle.test.datacite.org/10.22002/d1.694"
+    it "DOI in staging system" do
+      input = "https://handle.stage.datacite.org/10.22002/d1.694"
       subject = Bolognese::Metadata.new(input: input, sandbox: true)
       expect(subject.valid?).to be true
-      expect(subject.id).to eq("https://handle.test.datacite.org/10.22002/d1.694")
+      expect(subject.id).to eq("https://handle.stage.datacite.org/10.22002/d1.694")
       expect(subject.types["schemaOrg"]).to eq("Dataset")
       expect(subject.types["resourceTypeGeneral"]).to eq("Dataset")
       expect(subject.creators).to eq([{"affiliation"=>[{"name"=>"Caltech"}], "name"=>"Tester", "nameIdentifiers" => []}])
@@ -1063,11 +1100,11 @@ describe Bolognese::Metadata, vcr: true do
       expect(subject.state).to eq("findable")
     end
 
-    it "DOI in test system schema 3" do
+    it "DOI in staging system schema 3" do
       input = "10.21956/wellcomeopenres.25947.r17364"
       subject = Bolognese::Metadata.new(input: input, doi: input, sandbox: true)
       expect(subject.valid?).to be true
-      expect(subject.id).to eq("https://handle.test.datacite.org/10.21956/wellcomeopenres.25947.r17364")
+      expect(subject.id).to eq("https://handle.stage.datacite.org/10.21956/wellcomeopenres.25947.r17364")
       expect(subject.types["schemaOrg"]).to eq("ScholarlyArticle")
       expect(subject.types["resourceTypeGeneral"]).to eq("Text")
       expect(subject.creators).to eq([{"name"=>"Fran2 Levy", "nameIdentifiers" => [], "affiliation" => []}])
@@ -1080,11 +1117,11 @@ describe Bolognese::Metadata, vcr: true do
       expect(subject.state).to eq("findable")
     end
 
-    it "Referee report in test system" do
+    it "Referee report in staging system" do
       input = "10.21956/gatesopenres.530.r190"
       subject = Bolognese::Metadata.new(input: input, sandbox: true)
       expect(subject.valid?).to be true
-      expect(subject.id).to eq("https://handle.test.datacite.org/10.21956/gatesopenres.530.r190")
+      expect(subject.id).to eq("https://handle.stage.datacite.org/10.21956/gatesopenres.530.r190")
       expect(subject.types["schemaOrg"]).to eq("ScholarlyArticle")
       expect(subject.types["resourceTypeGeneral"]).to eq("Text")
       expect(subject.types["ris"]).to eq("RPRT")
@@ -1226,7 +1263,7 @@ describe Bolognese::Metadata, vcr: true do
       expect(subject.types["schemaOrg"]).to eq("Dataset")
       expect(subject.types["resourceTypeGeneral"]).to eq("Dataset")
       expect(subject.titles).to eq([{"title"=>"BPI Challenge 2012"}])
-      expect(subject.dates).to eq([{"date"=>"2011-10-01/2012-03-14", "dateInformation"=>"Temporal coverage of this dataset.", "dateType"=>"Other"}, {"date"=>"2012", "dateType"=>"Issued"}])
+      expect(subject.dates).to eq([{"date"=>"2012-04-23", "dateType"=>"Issued"}])
       expect(subject.publication_year).to eq("2012")
       expect(subject.state).to eq("findable")
     end

data/spec/readers/schema_org_reader_spec.rb

@@ -3,11 +3,8 @@
 require 'spec_helper'
 
 describe Bolognese::Metadata, vcr: true do
-  let(:input) { "https://blog.datacite.org/eating-your-own-dog-food/" }
   let(:fixture_path) { "spec/fixtures/" }
 
-  subject { Bolognese::Metadata.new(input: input) }
-
   context "get schema_org raw" do
     it "BlogPosting" do
       input = fixture_path + 'schema_org.json'
@@ -18,6 +15,8 @@ describe Bolognese::Metadata, vcr: true do
 
   context "get schema_org metadata" do
     it "BlogPosting" do
+      input = "https://blog.datacite.org/eating-your-own-dog-food/"
+      subject = Bolognese::Metadata.new(input: input, from: "schema_org")
       expect(subject.valid?).to be true
       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")
@@ -36,6 +35,7 @@ describe Bolognese::Metadata, vcr: true do
     end
 
     it "BlogPosting with new DOI" do
+      input = "https://blog.datacite.org/eating-your-own-dog-food/"
       subject = Bolognese::Metadata.new(input: input, doi: "10.5438/0000-00ss")
       expect(subject.valid?).to be true
       expect(subject.id).to eq("https://doi.org/10.5438/0000-00ss")
@@ -47,7 +47,7 @@ describe Bolognese::Metadata, vcr: true do
     it "BlogPosting with type as array" do
       input = fixture_path + 'schema_org_type_as_array.json'
       subject = Bolognese::Metadata.new(input: input)
-      #expect(subject.valid?).to be true
+      expect(subject.valid?).to be true
       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")
@@ -66,7 +66,6 @@ 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.id).to eq("https://doi.org/10.5281/zenodo.1196821")
@@ -97,7 +96,6 @@ describe Bolognese::Metadata, vcr: true do
     it "pangaea" do
       input = "https://doi.pangaea.de/10.1594/PANGAEA.836178"
       subject = Bolognese::Metadata.new(input: input, from: "schema_org")
-      
       expect(subject.valid?).to be true
       expect(subject.id).to eq("https://doi.org/10.1594/pangaea.836178")
       expect(subject.doi).to eq("10.1594/pangaea.836178")

data/spec/utils_spec.rb

@@ -64,6 +64,18 @@ describe Bolognese::Metadata, vcr: true do
       expect(response).to eq("0000-0002-1394-3097")
     end
 
+    it "validate_orcid sandbox" do
+      orcid = "http://sandbox.orcid.org/0000-0002-2590-225X"
+      response = subject.validate_orcid(orcid)
+      expect(response).to eq("0000-0002-2590-225X")
+    end
+
+    it "validate_orcid sandbox https" do
+      orcid = "https://sandbox.orcid.org/0000-0002-2590-225X"
+      response = subject.validate_orcid(orcid)
+      expect(response).to eq("0000-0002-2590-225X")
+    end
+
     it "validate_orcid wrong id" do
       orcid = "0000-0002-1394-309"
       response = subject.validate_orcid(orcid)
@@ -179,15 +191,15 @@ describe Bolognese::Metadata, vcr: true do
     end
 
     it "sandbox via url" do
-      url = "https://handle.test.datacite.org/10.20375/0000-0001-ddb8-7"
+      url = "https://handle.stage.datacite.org/10.20375/0000-0001-ddb8-7"
       response = subject.normalize_id(url)
-      expect(response).to eq("https://handle.test.datacite.org/10.20375/0000-0001-ddb8-7")
+      expect(response).to eq("https://handle.stage.datacite.org/10.20375/0000-0001-ddb8-7")
     end
 
     it "sandbox via options" do
       url = "10.20375/0000-0001-ddb8-7"
       response = subject.normalize_id(url, sandbox: true)
-      expect(response).to eq("https://handle.test.datacite.org/10.20375/0000-0001-ddb8-7")
+      expect(response).to eq("https://handle.stage.datacite.org/10.20375/0000-0001-ddb8-7")
     end
   end
 

data/spec/writers/bibtex_writer_spec.rb

@@ -145,17 +145,15 @@ describe Bolognese::Metadata, vcr: true do
 
     it "authors with affiliations" do
       input = "10.16910/jemr.9.1.2"
-      subject = Bolognese::Metadata.new(input: input, from: "datacite")
+      subject = Bolognese::Metadata.new(input: input, from: "crossref")
       bibtex = BibTeX.parse(subject.bibtex).to_a(quotes: '').first
-      expect(bibtex[:bibtex_type].to_s).to eq("misc")
+      expect(bibtex[:bibtex_type].to_s).to eq("article")
       expect(bibtex[:bibtex_key]).to eq("https://doi.org/10.16910/jemr.9.1.2")
       expect(bibtex[:doi]).to eq("10.16910/jemr.9.1.2")
       expect(bibtex[:title]).to eq("Eye tracking scanpath analysis techniques on web pages: A survey, evaluation and comparison")
-      expect(bibtex[:author]).to eq("{Eraslan, Sukru; University Of Manchester, UK, & Middle East Technical University, Northern Cyprus Campus,  Kalkanli, Guzelyurt, Turkey} and {Yesilada, Yeliz; Middle East Technical University, Northern Cyprus Campus, 99738 Kalkanli, Guzelyurt, Mersin 10, Turkey} and {Harper, Simon; School Of Computer Science, University Of Manchester, Manchester, United Kingdom}")
-      expect(bibtex[:publisher]).to eq("eyemovement.org")
-      expect(bibtex[:keywords]).to eq("eye tracking; eye movements; scanpaths; eye movement sequence; web pages; visual elements; web pages; scanpath analysis techniques; scanpath analysis; pattern detection; common scanpaths")
+      expect(bibtex[:author]).to eq("Eraslan, Sukru and Yesilada, Yeliz and Harper, Simon")
+      expect(bibtex[:publisher]).to eq("University of Bern")
       expect(bibtex[:year]).to eq("2015")
-      expect(bibtex[:copyright]).to eq("Creative Commons Attribution 4.0 International")
     end
 
     it "keywords subject scheme" do

data/spec/writers/citeproc_writer_spec.rb

@@ -75,8 +75,8 @@ describe Bolognese::Metadata, vcr: true do
       expect(json["id"]).to eq("https://doi.org/10.26301/qdpd-2250")
       expect(json["DOI"]).to eq("10.26301/qdpd-2250")
       expect(json["title"]).to eq("USS Pampanito Submarine")
-      expect(json["author"]).to eq([{"literal"=>"USS Pampanito"}])
-      expect(json["publisher"]).to eq("Open Heritage 3D")
+      expect(json["author"]).to eq([{"literal"=>"CyArk"}])
+      expect(json["publisher"]).to eq("Open Heritage")
       expect(json["issued"]).to eq("date-parts"=>[[2020]])
     end
 
@@ -257,7 +257,7 @@ 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)")
       expect(json["copyright"]).to eq("Creative Commons Attribution 3.0 Unported")
     end
 

data/spec/writers/csv_writer_spec.rb

@@ -67,7 +67,7 @@ describe Bolognese::Metadata, vcr: true do
       expect(csv[2]).to eq("2014-01-15")
       expect(csv[3]).to eq("findable")
       expect(csv[4]).to eq("Dataset")
-      expect(csv[5]).to be_nil
+      expect(csv[5]).to eq("Dataset")
       expect(csv[6]).to eq("Integrated Multi-Mission Ocean Altimeter Data for Climate Research Version 2")
       expect(csv[7]).to eq("{GSFC}")
       expect(csv[8]).to eq("NASA Physical Oceanography DAAC")

data/spec/writers/datacite_writer_spec.rb

@@ -222,7 +222,7 @@ describe Bolognese::Metadata, vcr: true do
       expect(subject.publication_year).to eq("2011")
       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")
+        "relatedIdentifierType" => "DOI","relationType"=>"Cites")
       expect(subject.publisher).to eq("Dryad")
       expect(subject.agency).to eq("datacite")
       expect(subject.schema_version).to eq("http://datacite.org/schema/kernel-4")

data/spec/writers/jats_writer_spec.rb

@@ -35,7 +35,7 @@ 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("journal")
-      expect(jats.dig("article_title")).to eq("Triose Phosphate Isomerase Deficiency Is Caused by Altered Dimerization–Not Catalytic Inactivity–of the Mutant Enzymes")
+      expect(jats.dig("article_title")).to eq("Triose Phosphate Isomerase Deficiency Is Caused by Altered Dimerization???Not Catalytic Inactivity???of the Mutant Enzymes")
       expect(jats.dig("source")).to eq("PLoS ONE")
       expect(jats.dig("person_group", 0, "name").length).to eq(5)
       expect(jats.dig("person_group", 0, "name").first).to eq("surname"=>"Ralser", "given_names"=>"Markus")

data/spec/writers/rdf_xml_writer_spec.rb

@@ -45,7 +45,7 @@ describe Bolognese::Metadata, vcr: true do
       rdf_xml = Maremma.from_xml(subject.rdf_xml).fetch("RDF", {})
       expect(rdf_xml.dig("ScholarlyArticle", "rdf:about")).to eq("https://doi.org/10.5438/4k3m-nyvg")
       expect(rdf_xml.dig("ScholarlyArticle", "name")).to eq("Eating your own Dog Food")
-      expect(rdf_xml.dig("ScholarlyArticle", "keywords")).to eq("datacite, doi, metadata")
+      expect(rdf_xml.dig("ScholarlyArticle", "keywords")).to eq("datacite, doi, metadata, FOS: Computer and information sciences, FOS: Computer and information sciences")
       expect(rdf_xml.dig("ScholarlyArticle", "datePublished", "__content__")).to eq("2016-12-20")
     end
     

data/spec/writers/ris_writer_spec.rb

@@ -96,10 +96,13 @@ describe Bolognese::Metadata, vcr: true do
       expect(ris[4]).to eq("UR  - https://blog.datacite.org/eating-your-own-dog-food/")
       expect(ris[5]).to eq("AB  - Eating your own dog food is a slang term to describe that an organization should itself use the products and services it provides. For DataCite this means that we should use DOIs with appropriate metadata and strategies for long-term preservation for...")
       expect(ris[6]).to eq("KW  - datacite")
-      expect(ris[9]).to eq("PY  - 2016")
-      expect(ris[10]).to eq("PB  - DataCite")
-      expect(ris[11]).to eq("SN  - 10.5438/0000-00ss")
-      expect(ris[12]).to eq("ER  - ")
+      expect(ris[9]).to eq("KW  - FOS: Computer and information sciences")
+      expect(ris[10]).to eq("KW  - FOS: Computer and information sciences")
+      expect(ris[11]).to eq("PY  - 2016")
+      expect(ris[12]).to eq("PB  - DataCite")
+      expect(ris[13]).to eq("LA  - en")
+      expect(ris[14]).to eq("SN  - 10.5438/0000-00ss")
+      expect(ris[15]).to eq("ER  - ")
     end
 
     it "BlogPosting Citeproc JSON" do
@@ -163,10 +166,9 @@ describe Bolognese::Metadata, vcr: true do
       expect(ris[10]).to eq("DO  - 10.5061/dryad.8515")
       expect(ris[11]).to eq("UR  - http://datadryad.org/stash/dataset/doi:10.5061/dryad.8515")
       expect(ris[13]).to eq("KW  - Plasmodium")
-      expect(ris[19]).to eq("PY  - 2011")
-      expect(ris[20]).to eq("PB  - Dryad")
-      expect(ris[21]).to eq("LA  - en")
-      expect(ris[22]).to eq("ER  - ")
+      expect(ris[19]).to eq("PB  - Dryad")
+      expect(ris[20]).to eq("LA  - en")
+      expect(ris[21]).to eq("ER  - ")
     end
 
     it "maremma" do

data/spec/writers/schema_org_writer_spec.rb

@@ -53,9 +53,9 @@ describe Bolognese::Metadata, vcr: true do
       json = JSON.parse(subject.schema_org)
       expect(json["@id"]).to eq("https://doi.org/10.5061/dryad.8515")
       expect(json["@type"]).to eq("Dataset")
-      expect(json["@reverse"]).to eq("isBasedOn"=>{"@id"=>"https://doi.org/10.1371/journal.ppat.1000446", "@type"=>"ScholarlyArticle"})
+      expect(json["citation"]).to eq("@id"=>"https://doi.org/10.1371/journal.ppat.1000446", "@type"=>"CreativeWork")
       expect(json["license"]).to eq("https://creativecommons.org/publicdomain/zero/1.0/legalcode")
-      expect(json["keywords"]).to eq("Plasmodium, malaria, taxonomy, mitochondrial genome, phylogeny, Parasites")
+      expect(json["keywords"]).to eq("Plasmodium, malaria, taxonomy, mitochondrial genome, Parasites")
     end
 
     it "Schema.org JSON IsSupplementTo" do
@@ -128,7 +128,7 @@ describe Bolognese::Metadata, vcr: true do
       expect(json["@id"]).to eq("https://doi.org/10.4232/1.2745")
       expect(json["@type"]).to eq("Dataset")
       expect(json["name"]).to eq("Flash Eurobarometer 54 (Madrid Summit)")
-      expect(json["keywords"]).to eq("KAT12 International Institutions, Relations, Conditions")
+      expect(json["keywords"]).to eq("KAT12 International Institutions, Relations, Conditions, Internationale Politik und Institutionen, Regierung, politische Systeme, Parteien und Verbände, Wirtschaftssysteme und wirtschaftliche Entwicklung, International politics and organisation, Government, political systems and organisation, Economic systems and development")
     end
 
     it "subject scheme multiple keywords" do
@@ -138,7 +138,7 @@ describe Bolognese::Metadata, vcr: true do
       expect(json["@id"]).to eq("https://doi.org/10.1594/pangaea.721193")
       expect(json["@type"]).to eq("Dataset")
       expect(json["name"]).to eq("Seawater carbonate chemistry and processes during experiments with Crassostrea gigas, 2007, supplement to: Kurihara, Haruko; Kato, Shoji; Ishimatsu, Atsushi (2007): Effects of increased seawater pCO2 on early development of the oyster Crassostrea gigas. Aquatic Biology, 1(1), 91-98")
-      expect(json["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, Experiment, 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["keywords"]).to include("Animalia, Bottles or small containers/Aquaria (<20 L)")
       expect(json["license"]).to eq("https://creativecommons.org/licenses/by/3.0/legalcode")
     end
 

data/spec/writers/turtle_writer_spec.rb

@@ -18,7 +18,7 @@ describe Bolognese::Metadata, vcr: true do
       expect(subject.valid?).to be true
       ttl = subject.turtle.split("\n")
       expect(ttl[0]).to eq("@prefix schema: <http://schema.org/> .")
-      expect(ttl[2]).to eq("<https://doi.org/10.1371/journal.ppat.1000446> a schema:ScholarlyArticle;")
+      expect(ttl[2]).to eq("<https://doi.org/10.5061/dryad.8515> a schema:Dataset;")
     end
 
     it "BlogPosting" do

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bolognese
 version: !ruby/object:Gem::Version
-  version: 1.9.7
+  version: 1.9.11
 platform: ruby
 authors:
 - Martin Fenner
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-05-26 00:00:00.000000000 Z
+date: 2021-08-17 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: maremma
@@ -16,7 +16,7 @@ dependencies:
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: '4.7'
+        version: 4.9.4
     - - "<"
       - !ruby/object:Gem::Version
         version: '5'
@@ -26,7 +26,7 @@ dependencies:
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: '4.7'
+        version: 4.9.4
     - - "<"
       - !ruby/object:Gem::Version
         version: '5'
@@ -831,7 +831,6 @@ files:
 - spec/fixtures/vcr_cassettes/Bolognese_CLI/convert_from_id/datacite/to_jats.yml
 - spec/fixtures/vcr_cassettes/Bolognese_CLI/convert_from_id/datacite/to_schema_org.yml
 - spec/fixtures/vcr_cassettes/Bolognese_CLI/convert_from_id/schema_org/default.yml
-- spec/fixtures/vcr_cassettes/Bolognese_CLI/convert_from_id/schema_org/to_bibtex.yml
 - spec/fixtures/vcr_cassettes/Bolognese_CLI/convert_from_id/schema_org/to_datacite.yml
 - spec/fixtures/vcr_cassettes/Bolognese_CLI/convert_from_id/schema_org/to_schema_org.yml
 - spec/fixtures/vcr_cassettes/Bolognese_CLI/find_from_format_by_id/crossref.yml
@@ -846,7 +845,6 @@ files:
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/authors_as_string/with_organization.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/change_datacite_metadata/change_state.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/change_datacite_metadata/change_title.yml
-- spec/fixtures/vcr_cassettes/Bolognese_Metadata/change_metadata_as_datacite_xml/change_alternate_identifiers.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/change_metadata_as_datacite_xml/change_description.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/change_metadata_as_datacite_xml/change_identifiers.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/change_metadata_as_datacite_xml/change_license.yml
@@ -878,10 +876,10 @@ files:
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_resolver/doi.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_resolver/doi_with_protocol.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_resolver/dx_doi_org_url.yml
-- spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_resolver/force_test_resolver.yml
+- spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_resolver/force_stage_resolver.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_resolver/https_url.yml
-- spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_resolver/test_resolver.yml
-- spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_resolver/test_resolver_http.yml
+- spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_resolver/stage_resolver.yml
+- spec/fixtures/vcr_cassettes/Bolognese_Metadata/doi_resolver/stage_resolver_http.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/find_from_format_by_ID/crossref.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/find_from_format_by_ID/crossref_doi_not_url.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/find_from_format_by_ID/datacite.yml
@@ -901,6 +899,7 @@ files:
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/find_from_format_from_file/schema_org.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/find_from_format_from_string/crosscite.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/fos/hsh_to_fos_for_match.yml
+- spec/fixtures/vcr_cassettes/Bolognese_Metadata/fos/hsh_to_fos_for_with_schemeUri_in_hash.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/fos/hsh_to_fos_match.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/fos/hsh_to_fos_no_match.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/fos/name_to_fos_for_match.yml
@@ -955,15 +954,15 @@ files:
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/yet_another_book_chapter.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_datacite_json_metadata/metadata_from_api.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_datacite_metadata/BlogPosting.yml
-- spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_datacite_metadata/DOI_in_test_system.yml
-- spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_datacite_metadata/DOI_in_test_system_schema_3.yml
+- spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_datacite_metadata/DOI_in_staging_system.yml
+- spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_datacite_metadata/DOI_in_staging_system_schema_3.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_datacite_metadata/DOI_in_with_related_id_system.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_datacite_metadata/DOI_not_found.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_datacite_metadata/Dataset.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_datacite_metadata/Funding.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_datacite_metadata/Funding_empty_awardTitle.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_datacite_metadata/Funding_schema_version_4.yml
-- spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_datacite_metadata/Referee_report_in_test_system.yml
+- spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_datacite_metadata/Referee_report_in_staging_system.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_datacite_metadata/Schema_org_type.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_datacite_metadata/author_only_full_name.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_datacite_metadata/author_with_scheme.yml
@@ -1105,6 +1104,17 @@ files:
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/to_schema_org/with_id.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/to_schema_org_identifiers/with_identifiers.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/validate_doi/doi.yml
+- spec/fixtures/vcr_cassettes/Bolognese_Metadata/validate_funder_doi/1_7_10.yml
+- spec/fixtures/vcr_cassettes/Bolognese_Metadata/validate_funder_doi/1_7_11.yml
+- spec/fixtures/vcr_cassettes/Bolognese_Metadata/validate_funder_doi/1_7_12.yml
+- spec/fixtures/vcr_cassettes/Bolognese_Metadata/validate_funder_doi/1_7_13.yml
+- spec/fixtures/vcr_cassettes/Bolognese_Metadata/validate_funder_doi/1_7_14.yml
+- spec/fixtures/vcr_cassettes/Bolognese_Metadata/validate_funder_doi/1_7_4.yml
+- spec/fixtures/vcr_cassettes/Bolognese_Metadata/validate_funder_doi/1_7_5.yml
+- spec/fixtures/vcr_cassettes/Bolognese_Metadata/validate_funder_doi/1_7_6.yml
+- spec/fixtures/vcr_cassettes/Bolognese_Metadata/validate_funder_doi/1_7_7.yml
+- spec/fixtures/vcr_cassettes/Bolognese_Metadata/validate_funder_doi/1_7_8.yml
+- spec/fixtures/vcr_cassettes/Bolognese_Metadata/validate_funder_doi/1_7_9.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/validate_funder_doi/funder_doi.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/validate_funder_doi/funder_doi_without_prefix.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/validate_funder_doi/non-funder_doi.yml