bolognese 0.10.19 → 0.10.20

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: d49364f6f1e055284d8b07478da47af2522a89983caf8c5d7fa96775df7a4c7d
+  metadata.gz: 31db4f5d8e8f78c81d0fda3744f2eb4340d281c5e2ddcdc3c261fe5a8481da63
+  data.tar.gz: f417e060447bc674b83e12e4bed8c0116d83d85a0618ec3d2ab9638933407b44
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+  metadata.gz: b25610719fa9fe5a1b211335656879ad6e70379b167c5a9dd6ee5830bb57c18d59c3a1b58261809474edeb630b4c2a9967ca87e42ebde7495cb241fe8f7c53c9
+  data.tar.gz: 1e00542610634fca09fce0e78c0c8593c71b8b5b87c8930d303d5e1b8bf9643b9b01d5906c02d196a7a04cecc184ddeb363a498618a28f3a91c44e3a04bfaf1a

data/Gemfile.lock

@@ -1,7 +1,7 @@
 PATH
   remote: .
   specs:
-    bolognese (0.10.19)
+    bolognese (0.10.20)
       activesupport (>= 4.2.5, < 6)
       benchmark_methods (~> 0.7)
       bibtex-ruby (~> 4.1)

data/lib/bolognese/author_utils.rb

@@ -11,7 +11,14 @@ module Bolognese
     }
 
     def get_one_author(author)
-      type = author.fetch("type", nil) && author.fetch("type").titleize
+      if author.fetch("type", nil).present?
+        type = author.fetch("type").titleize
+      elsif author.fetch("creatorName", nil).is_a?(Hash)
+        type = author.dig("creatorName", "nameType") == "Organizational" ? "Organization" : "Person"
+      else
+        type = nil
+      end
+
       name_identifiers = get_name_identifiers(author)
       id = author.fetch("id", nil).presence || name_identifiers.first
       identifier = name_identifiers.length > 1 ? name_identifiers.unwrap : nil

data/lib/bolognese/version.rb

@@ -1,3 +1,3 @@
 module Bolognese
-  VERSION = "0.10.19"
+  VERSION = "0.10.20"
 end

data/spec/author_utils_spec.rb

@@ -106,7 +106,7 @@ 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"))
-      expect(response).to eq("type"=>"Person", "name"=>"Dr. Störi, Kunstsalon")
+      expect(response).to eq("type"=>"Organization", "name"=>"Dr. Störi, Kunstsalon")
     end
 
     it "name with affiliation and country" do
@@ -133,6 +133,14 @@ describe Bolognese::Metadata, vcr: true do
       expect(response).to eq("type"=>"Person", "id"=>"https://orcid.org/0000-0003-4514-4211", "name"=>"Thomas Dubos", "givenName"=>"Thomas", "familyName"=>"Dubos", "identifier"=>["https://orcid.org/0000-0003-4514-4211", "http://isni.org/isni/0000-0003-5752-6882"])
     end
 
+    it "nameType organizational" do
+      input = fixture_path + 'gtex.xml'
+      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"))
+      expect(response).to eq("type"=>"Organization", "name"=>"The GTEx Consortium")
+    end
+
     it "only familyName and givenName" do
       input = "https://doi.pangaea.de/10.1594/PANGAEA.836178"
       subject = Bolognese::Metadata.new(input: input, from: "schema_org")

data/spec/fixtures/gtex.xml

@@ -0,0 +1,67 @@
+<?xml version="1.0" encoding="UTF-8"?>
+
+<resource xmlns="http://datacite.org/schema/kernel-4" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://datacite.org/schema/kernel-4 http://schema.datacite.org/meta/kernel-4/metadata.xsd">  
+  <identifier identifierType="DOI">10.25491/9HX8-KE93</identifier>  
+  <creators> 
+    <creator> 
+      <creatorName nameType="Organizational">The GTEx Consortium</creatorName> 
+    </creator> 
+  </creators>  
+  <titles> 
+    <title>DroNc-seq data</title> 
+  </titles>  
+  <publisher>GTEx</publisher>  
+  <publicationYear>2017</publicationYear>  
+  <subjects> 
+    <subject>gtex</subject>  
+    <subject>annotation</subject>  
+    <subject>phenotype</subject>  
+    <subject>gene regulation</subject>  
+    <subject>transcriptomics</subject> 
+  </subjects>  
+  <fundingReferences> 
+    <fundingReference> 
+      <funderName>Common Fund of the Office of the Director of the NIH</funderName>  
+      <funderIdentifier funderIdentifierType="Crossref Funder ID">http://doi.org/10.13039/100000052</funderIdentifier> 
+    </fundingReference>  
+    <fundingReference> 
+      <funderName>National Cancer Institute (NCI)</funderName>  
+      <funderIdentifier funderIdentifierType="Crossref Funder ID">http://doi.org/10.13039/100000054</funderIdentifier> 
+    </fundingReference>  
+    <fundingReference> 
+      <funderName>National Human Genome Research Institute (NHGRI)</funderName>  
+      <funderIdentifier funderIdentifierType="Crossref Funder ID">http://doi.org/10.13039/100000051</funderIdentifier> 
+    </fundingReference>  
+    <fundingReference> 
+      <funderName>National Heart, Lung, and Blood Institute (NHLBI)</funderName>  
+      <funderIdentifier funderIdentifierType="Crossref Funder ID">http://doi.org/10.13039/100000050</funderIdentifier> 
+    </fundingReference>  
+    <fundingReference> 
+      <funderName>National Institute on Drug Abuse (NIDA)</funderName>  
+      <funderIdentifier funderIdentifierType="Crossref Funder ID">http://doi.org/10.13039/100000026</funderIdentifier> 
+    </fundingReference>  
+    <fundingReference> 
+      <funderName>National Institute of Mental Health (NIMH)</funderName>  
+      <funderIdentifier funderIdentifierType="Crossref Funder ID">http://doi.org/10.13039/100000025</funderIdentifier> 
+    </fundingReference>  
+    <fundingReference> 
+      <funderName>National Institute of Neurological Disorders and Stroke (NINDS)</funderName>  
+      <funderIdentifier funderIdentifierType="Crossref Funder ID">http://doi.org/10.13039/100000065</funderIdentifier> 
+    </fundingReference> 
+  </fundingReferences>  
+  <resourceType resourceTypeGeneral="Dataset">DroNc-seq data</resourceType>  
+  <dates> 
+    <date dateType="Issued">2017</date> 
+  </dates>  
+  <relatedIdentifiers> 
+    <relatedIdentifier relationType="Documents" relatedIdentifierType="URL">http://identifiers.org/dbgap:phs000424.v7.p2</relatedIdentifier>  
+    <relatedIdentifier relationType="IsDocumentedBy" relatedIdentifierType="DOI">https://doi.org/10.1038/nature24277</relatedIdentifier>  
+    <relatedIdentifier relationType="IsSupplementTo" relatedIdentifierType="DOI">https://doi.org/10.1038/nmeth.4407</relatedIdentifier> 
+  </relatedIdentifiers>  
+  <sizes> 
+    <size>15.7M</size> 
+  </sizes>
+  <descriptions> 
+    <description descriptionType="SeriesInformation">GTEx</description> 
+  </descriptions> 
+</resource>

data/spec/readers/datacite_reader_spec.rb

@@ -308,7 +308,7 @@ describe Bolognese::Metadata, vcr: true do
       expect(subject.identifier).to eq("https://doi.org/10.4232/1.2745")
       expect(subject.type).to eq("Dataset")
       expect(subject.resource_type_general).to eq("Dataset")
-      expect(subject.author).to eq("name"=>"Europäische Kommission")
+      expect(subject.author).to eq("type"=>"Organization", "name"=>"Europäische Kommission")
       expect(subject.title).to eq([{"lang"=>"de", "text"=>"Flash Eurobarometer 54 (Madrid Summit)"}, {"lang"=>"en", "text"=>"Flash Eurobarometer 54 (Madrid Summit)"}, {"title_type"=>"Subtitle","lang"=>"de", "text"=>"The Common European Currency"}, {"title_type"=>"Subtitle", "lang"=>"en", "text"=>"The Common European Currency"}])
       expect(subject.keywords).to eq([{"subject_scheme"=>"ZA", "text"=>"KAT12 International Institutions, Relations, Conditions"}])
       expect(subject.date_published).to eq("1996")

data/spec/writers/bibtex_writer_spec.rb

@@ -135,5 +135,14 @@ describe Bolognese::Metadata, vcr: true do
       expect(bibtex[:keywords]).to eq("GetInfo, 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(bibtex[:year]).to eq("2007")
     end
+
+    it "author is organization" do
+      input = fixture_path + 'gtex.xml'
+      subject = Bolognese::Metadata.new(input: input, from: "datacite")
+      bibtex = BibTeX.parse(subject.bibtex).to_a(quotes: '').first
+      expect(bibtex[:bibtex_type].to_s).to eq("misc")
+      expect(bibtex[:bibtex_key]).to eq("https://doi.org/10.25491/9hx8-ke93")
+      expect(bibtex[:author]).to eq("{The GTEx Consortium}")
+    end
   end
 end

data/spec/writers/citeproc_writer_spec.rb

@@ -155,6 +155,14 @@ describe Bolognese::Metadata, vcr: true do
       expect(json["issued"]).to eq("date-parts" => [[2014]])
     end
 
+    it "author is organization" do
+      input = fixture_path + 'gtex.xml'
+      subject = Bolognese::Metadata.new(input: input, from: "datacite")
+      json = JSON.parse(subject.citeproc)
+      expect(json["id"]).to eq("https://doi.org/10.25491/9hx8-ke93")
+      expect(json["author"]).to eq([{"literal"=>"The GTEx Consortium"}])
+    end
+
     it "maremma" do
       input = "https://github.com/datacite/maremma"
       subject = Bolognese::Metadata.new(input: input, from: "codemeta")

data/spec/writers/schema_org_writer_spec.rb

@@ -121,6 +121,14 @@ describe Bolognese::Metadata, vcr: true do
       expect(json["keywords"]).to eq("GetInfo, 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)")
     end
 
+    it "author is organization" do
+      input = fixture_path + 'gtex.xml'
+      subject = Bolognese::Metadata.new(input: input, from: "datacite")
+      json = JSON.parse(subject.schema_org)
+      expect(json["@id"]).to eq("https://doi.org/10.25491/9hx8-ke93")
+      expect(json["author"]).to eq("@type"=>"Organization", "name"=>"The GTEx Consortium")
+    end
+
     it "series information" do
       input = "10.4229/23RDEUPVSEC2008-5CO.8.3"
       subject = Bolognese::Metadata.new(input: input, from: "datacite")

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bolognese
 version: !ruby/object:Gem::Version
-  version: 0.10.19
+  version: 0.10.20
 platform: ruby
 authors:
 - Martin Fenner
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-06-04 00:00:00.000000000 Z
+date: 2018-06-07 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: maremma
@@ -559,6 +559,7 @@ files:
 - spec/fixtures/datacite_software.json
 - spec/fixtures/datacite_software_missing_comma.json
 - spec/fixtures/datacite_software_overlapping_keys.json
+- spec/fixtures/gtex.xml
 - spec/fixtures/maremma/codemeta.json
 - spec/fixtures/pure.bib
 - spec/fixtures/pure.ris