bolognese 1.3.1 → 1.3.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: a06ebcc4b7742d4744a921cdb6aceb159b37fe5a762326972a5028b4552961a5
-  data.tar.gz: 87daf32a007fe59560b8f0a7ad6b73474d15d518e24fed559615c8068a29e78a
+  metadata.gz: c470f4a7231fe120bbcfe85bb804b7b092df761a7273883211afca1dec075b07
+  data.tar.gz: 502d58d7e1e81be65cc22ced4d67d0e01408678b6f1601f338631c95455e7c41
 SHA512:
-  metadata.gz: 80ad70e2675f7591794f8baa040f27b07cfa314a65e04d1921c07cdfad73ff9966f3f9bb88398600e8e9a40cec0eaf5bea56de37c9ae50301bebeb20f7749cda
-  data.tar.gz: 5b9f862c651e4fdab2e4cb0e2fdc384c5d3cb2754ee37390e70acd4a32e2e017096d47f57fd6035012b15238372519fa6546e59e3c356b10feaea85620d1ba42
+  metadata.gz: 5ee3911bffb285fb868f7eb7dcea74cfe8fde2f7e64bcf06409b190bb71067da272deffefd50bbf9d8c10c6ca17442afd930aac8330c7918bcde235f996a6e37
+  data.tar.gz: 25cd55aae3ebea0206f93a46b4af8b51fede6bde3fc03be3f1aa37ed79b5bf1d36d5024338b21ba5e16a11609210ea607b8211ff8cf46da4db05a351bf0bd3b1

data/Gemfile.lock

@@ -1,7 +1,7 @@
 PATH
   remote: .
   specs:
-    bolognese (1.3.1)
+    bolognese (1.3.2)
       activesupport (>= 4.2.5, < 6)
       benchmark_methods (~> 0.7)
       bibtex-ruby (~> 4.1)

data/lib/bolognese/author_utils.rb

@@ -136,19 +136,22 @@ module Bolognese
     def get_affiliations(affiliations)
       Array.wrap(affiliations).map do |a|
         if a.is_a?(String)
-          id = nil
           name = a.squish
+          affiliation_identifier = nil
           affiliation_identifier_scheme = nil
+          scheme_uri = nil
         else
-          id = a["affiliationIdentifier"]
-          id = !id.to_s.start_with?("https://") && a["schemeURI"].present? ? normalize_id(a["schemeURI"] + id) : normalize_id(id)
+          affiliation_identifier = a["affiliationIdentifier"]
+          affiliation_identifier = !affiliation_identifier.to_s.start_with?("https://") && a["schemeURI"].present? ? normalize_id(a["schemeURI"] + affiliation_identifier) : normalize_id(affiliation_identifier)
           name = a["__content__"].squish
           affiliation_identifier_scheme = a["affiliationIdentifierScheme"]
+          scheme_uri = a["SchemeURI"]
         end
 
-        { "id" => id,
-          "name" => name,
-          "affiliationIdentifierScheme" => affiliation_identifier_scheme }.compact
+        { "name" => name,
+          "affiliationIdentifier" => affiliation_identifier,
+          "affiliationIdentifierScheme" => affiliation_identifier_scheme,
+          "schemeUri" => scheme_uri }.compact
       end.presence
     end
   end

data/lib/bolognese/datacite_utils.rb

@@ -76,7 +76,7 @@ module Bolognese
         xml.nameIdentifier(ni["nameIdentifier"], 'nameIdentifierScheme' => ni["nameIdentifierScheme"], 'schemeURI' => ni["schemeUri"])
       end
       Array.wrap(person["affiliation"]).each do |affiliation|
-        attributes = { "affiliationIdentifierScheme" => affiliation["affiliationIdentifierScheme"], "schemeURI" => affiliation["schemeUri"] }.compact
+        attributes = { "affiliationIdentifier" => affiliation["affiliationIdentifier"], "affiliationIdentifierScheme" => affiliation["affiliationIdentifierScheme"], "schemeURI" => affiliation["schemeUri"] }.compact
         xml.affiliation(affiliation["name"], attributes) 
       end
     end

data/lib/bolognese/utils.rb

@@ -582,7 +582,7 @@ module Bolognese
             id = nil
           else
             name = a["name"]
-            id = a["id"]
+            id = a["affiliationIdentifier"]
           end
 
           { 
@@ -605,7 +605,7 @@ module Bolognese
             id = nil
           else
             name = a["name"]
-            id = a["id"]
+            id = a["affiliationIdentifier"]
           end
 
           { 

data/lib/bolognese/version.rb

@@ -1,3 +1,3 @@
 module Bolognese
-  VERSION = "1.3.1"
+  VERSION = "1.3.2"
 end

data/spec/readers/datacite_reader_spec.rb

@@ -91,18 +91,19 @@ describe Bolognese::Metadata, vcr: true do
       expect(subject.types["ris"]).to eq("COMP")
       expect(subject.types["citeproc"]).to eq("article")
       expect(subject.creators.length).to eq(3)
-      expect(subject.creators.first).to eq("nameType"=>"Personal", "affiliation" => [{"affiliationIdentifierScheme"=>"ROR", "id"=>"https://ror.org/04wxnsj81", "name"=>"DataCite"}],
+      expect(subject.creators.first).to eq("nameType"=>"Personal", "affiliation" => [{"affiliationIdentifier"=>"https://ror.org/04wxnsj81", "affiliationIdentifierScheme"=>"ROR", "name"=>"DataCite"}],
         "familyName" => "Miller",
         "givenName" => "Elizabeth",
         "name" => "Miller, Elizabeth",
         "nameIdentifiers" => [{"nameIdentifier"=>"https://orcid.org/0000-0001-5000-0007", "nameIdentifierScheme"=>"ORCID", "schemeUri"=>"https://orcid.org"}],)
-      expect(subject.creators.dig(1, "affiliation")).to eq([{"affiliationIdentifierScheme"=>"ROR",
-        "id"=>"https://ror.org/05gq02987",
+      expect(subject.creators.dig(1, "affiliation")).to eq([{"affiliationIdentifier"=>"https://ror.org/05gq02987",
+        "affiliationIdentifierScheme"=>"ROR",
         "name"=>"Brown University"},
-       {"affiliationIdentifierScheme"=>"GRID",
-          "id"=>"https://grid.ac/institutes/grid.268117.b",
-          "name"=>"Wesleyan University"}])
-      expect(subject.creators.dig(2, "affiliation")).to eq([{"affiliationIdentifierScheme"=>"ROR", "id"=>"https://ror.org/05gq02987", "name"=>"Brown University"}])
+       {"affiliationIdentifier"=>"https://grid.ac/institutes/grid.268117.b",
+        "affiliationIdentifierScheme"=>"GRID",
+        "name"=>"Wesleyan University"}])
+      expect(subject.creators.dig(2, "affiliation")).to eq([{"affiliationIdentifier"=>"https://ror.org/05gq02987",
+        "affiliationIdentifierScheme"=>"ROR", "name"=>"Brown University"}])
       expect(subject.titles).to eq([{"lang"=>"en-US", "title"=>"Full DataCite XML Example"}, {"lang"=>"en-US", "title"=>"Demonstration of DataCite Properties.", "titleType"=>"Subtitle"}])
       expect(subject.identifiers).to eq([{"identifier"=>"https://doi.org/10.5072/example-full",
            "identifierType"=>"DOI"},
@@ -112,8 +113,8 @@ describe Bolognese::Metadata, vcr: true do
       expect(subject.rights_list).to eq([{"lang"=>"en-US", "rightsUri"=>"http://creativecommons.org/publicdomain/zero/1.0"}])
       expect(subject.publication_year).to eq("2014")
       expect(subject.contributors).to eq([{"nameType"=>"Personal", "name"=>"Starr, Joan", "givenName"=>"Joan", "familyName"=>"Starr", "nameIdentifiers"=>[{"nameIdentifier"=>"https://orcid.org/0000-0002-7285-027X", "schemeUri"=>"https://orcid.org", "nameIdentifierScheme"=>"ORCID"}], "affiliation"=>
-        [{"affiliationIdentifierScheme"=>"ROR",
-          "id"=>"https://ror.org/03yrm5c26",
+        [{"affiliationIdentifier"=>"https://ror.org/03yrm5c26",
+          "affiliationIdentifierScheme"=>"ROR",
           "name"=>"California Digital Library"}], "contributorType"=>"ProjectLeader"}])
       expect(subject.subjects).to eq([{"lang"=>"en-US", "schemeUri"=>"http://dewey.info/", "subject"=>"000 computer science", "subjectScheme"=>"dewey"}])
       expect(subject.dates).to eq([{"date"=>"2017-09-13", "dateInformation"=>"Updated with 4.2 properties", "dateType"=>"Updated"}, {"date"=>"2014", "dateType"=>"Issued"}])

data/spec/writers/schema_org_writer_spec.rb

@@ -186,6 +186,30 @@ describe Bolognese::Metadata, vcr: true do
       expect(json["contentUrl"]).to include("s3://cgp-commons-public/topmed_open_access/197bc047-e917-55ed-852d-d563cdbc50e4/NWD165827.recab.cram", "gs://topmed-irc-share/public/NWD165827.recab.cram")
     end
 
+    it "affiliation identifier" do
+      input = fixture_path + 'datacite-example-affiliation.xml'
+      subject = Bolognese::Metadata.new(input: input)
+      json = JSON.parse(subject.schema_org)
+      expect(json["@id"]).to eq("https://doi.org/10.5072/example-full")
+      expect(json["@type"]).to eq("SoftwareSourceCode")
+      expect(json["name"]).to eq("Full DataCite XML Example")
+      expect(json["author"].length).to eq(3)
+      expect(json["author"].first).to eq("@id" => "https://orcid.org/0000-0001-5000-0007",
+        "@type" => "Person",
+        "affiliation" => {"@id"=>"https://ror.org/04wxnsj81", "@type"=>"Organization", "name"=>"DataCite"},
+        "familyName" => "Miller",
+        "givenName" => "Elizabeth",
+        "name" => "Elizabeth Miller")
+      expect(json["identifier"]).to eq(
+        [{"@type"=>"PropertyValue",
+          "propertyID"=>"DOI",
+          "value"=>"https://doi.org/10.5072/example-full"},
+         {"@type"=>"PropertyValue",
+          "propertyID"=>"URL",
+          "value"=>"https://schema.datacite.org/meta/kernel-4.2/example/datacite-example-full-v4.2.xml"}]
+      )
+    end
+
     it "geo_location_point" do
       input = fixture_path + 'datacite-example-geolocation-2.xml'
       doi = "10.6071/Z7WC73"

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bolognese
 version: !ruby/object:Gem::Version
-  version: 1.3.1
+  version: 1.3.2
 platform: ruby
 authors:
 - Martin Fenner