bolognese 0.6.5 → 0.6.6

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 52deb6793101a56d9a824b036aff219ba58327eb
-  data.tar.gz: 9f96c1a7a6920e9395f92969822bc44064fdf179
+  metadata.gz: 4cf9b774c122a31d80d29bac90783498458f5aff
+  data.tar.gz: 970db12ff440f5907609eaabbac07676b06fe1e6
 SHA512:
-  metadata.gz: 893420085b143cff1dd78cbbc5ed96f34cc0497a9a998249076ba2372957bc87c0b0d48873572b10cf628e9b01df8ec0adb6d2580440afcf8c3e8037be6f49bf
-  data.tar.gz: 32378cb92d547a7ecb33f4a69a8e794ca0649a82865552b35794e8f7bb6af14a047fc84a6512cf6dea6df2195664977784a67e263eed1c4fde55d6d6b8b61702
+  metadata.gz: 14b38895e972a549842ec6a1f7388f4f2bd5dff742860689d189a15702843ef3babb1b6b9ff181faabd626391f2e41abf8825aff596c67b8aa9bc422dcde547d
+  data.tar.gz: 639783c23011fc7567b9c8397bf214d0dcc89604660297cc77da29fd9a899f17bffd7bd8f142b50ee4c24804246b201f5278fc5bd4f9d2938262038d239f8b28

data/Gemfile.lock

@@ -1,7 +1,7 @@
 PATH
   remote: .
   specs:
-    bolognese (0.6.5)
+    bolognese (0.6.6)
       activesupport (~> 4.2, >= 4.2.5)
       bibtex-ruby (~> 4.1)
       builder (~> 3.2, >= 3.2.2)

data/lib/bolognese/author_utils.rb

@@ -7,7 +7,7 @@ module Bolognese
       orcid = get_name_identifier(author)
       author = author.fetch("creatorName", nil)
 
-      return { "Name" => "" } if author.to_s.strip.blank?
+      return { "name" => "" } if author.to_s.strip.blank?
 
       author = cleanup_author(author)
       names = Namae.parse(author)
@@ -15,7 +15,7 @@ module Bolognese
       if names.blank? || !is_personal_name?(author)
         { "@type" => "Agent",
           "@id" => orcid,
-          "Name" => author }.compact
+          "name" => author }.compact
       else
         name = names.first
 

data/lib/bolognese/crossref.rb

@@ -171,21 +171,23 @@ module Bolognese
 
     def people(contributor_role)
       person = bibliographic_metadata.dig("contributors", "person_name")
-      Array.wrap(person).select { |a| a["contributor_role"] == contributor_role }.map do |a|
+      a = Array.wrap(person).select { |a| a["contributor_role"] == contributor_role }.map do |a|
         { "@type" => "Person",
           "@id" => parse_attributes(a["ORCID"]),
           "givenName" => a["given_name"],
           "familyName" => a["surname"] }.compact
-      end.presence
+      end
+      array_unwrap(a)
     end
 
     def funder
       fundref = Array.wrap(program_metadata).find { |a| a["name"] == "fundref" } || {}
-      Array.wrap(fundref.fetch("assertion", [])).select { |a| a["name"] == "fundgroup" }.map do |f|
+      a = Array.wrap(fundref.fetch("assertion", [])).select { |a| a["name"] == "fundgroup" }.map do |f|
         { "@type" => "Organization",
           "@id" => normalize_id(f.dig("assertion", "assertion", "__content__")),
           "name" => f.dig("assertion", "__content__").strip }.compact
-      end.presence
+      end
+      array_unwrap(a)
     end
 
     def date_published

data/lib/bolognese/datacite.rb

@@ -109,13 +109,13 @@ module Bolognese
     def author
       authors = metadata.dig("creators", "creator")
       authors = [authors] if authors.is_a?(Hash)
-      get_authors(authors).presence
+      array_unwrap(get_authors(authors))
     end
 
     def editor
       editors = Array.wrap(metadata.dig("contributors", "contributor"))
                      .select { |r| r["contributorType"] == "Editor" }
-      get_authors(editors).presence
+      array_unwrap(get_authors(editors))
     end
 
     def funder
@@ -186,20 +186,33 @@ module Bolognese
     end
 
     def related_identifiers(relation_type)
-      Array(metadata.dig("relatedIdentifiers", "relatedIdentifier"))
+      a = Array.wrap(metadata.dig("relatedIdentifiers", "relatedIdentifier"))
         .select { |r| relation_type.split(" ").include?(r["relationType"]) && %w(DOI URL).include?(r["relatedIdentifierType"]) }
         .map do |work|
           { "@type" => "CreativeWork",
             "@id" => normalize_id(work["__content__"]) }
         end
+      array_unwrap(a)
+    end
+
+    def same_as
+      related_identifiers("IsIdenticalTo")
     end
 
     def is_part_of
-      related_identifiers("IsPartOf").first
+      related_identifiers("IsPartOf")
     end
 
     def has_part
-      related_identifiers("HasPart").presence
+      related_identifiers("HasPart")
+    end
+
+    def predecessor_of
+      related_identifiers("IsPreviousVersionOf")
+    end
+
+    def successor_of
+      related_identifiers("IsNewVersionOf")
     end
 
     def citation

data/lib/bolognese/metadata.rb

@@ -16,7 +16,7 @@ module Bolognese
       :additional_type, :alternate_name, :url, :version, :keywords, :editor,
       :page_start, :page_end, :date_modified, :language, :spatial_coverage,
       :content_size, :funder, :journal, :bibtex_type, :date_created, :has_part,
-      :publisher, :contributor, :schema_version
+      :publisher, :contributor, :schema_version, :same_as, :predecessor_of, :successor_of
 
     alias_method :datacite, :as_datacite
 
@@ -29,8 +29,8 @@ module Bolognese
     end
 
     def author_string
-      author.map { |a| [a["familyName"], a["givenName"]].join(", ") }
-            .join(" and ").presence
+      Array.wrap(author).map { |a| [a["familyName"], a["givenName"]].join(", ") }
+                        .join(" and ").presence
     end
 
     def publisher_string
@@ -59,8 +59,11 @@ module Bolognese
         "pageStart" => page_start,
         "pageEnd" => page_end,
         "spatialCoverage" => spatial_coverage,
+        "sameAs" => same_as,
         "isPartOf" => is_part_of,
         "hasPart" => has_part,
+        "predecessor_of" => predecessor_of,
+        "successor_of" => successor_of,
         "citation" => citation,
         "schemaVersion" => schema_version,
         "publisher" => publisher,

data/lib/bolognese/schema_org.rb

@@ -100,16 +100,20 @@ module Bolognese
       normalize_ids(metadata.fetch(relation_type, nil))
     end
 
+    def same_as
+      related_identifiers("isIdenticalTo")
+    end
+
     def is_part_of
-      related_identifiers("isPartOf").first
+      related_identifiers("isPartOf")
     end
 
     def has_part
-      related_identifiers("hasPart").presence
+      related_identifiers("hasPart")
     end
 
     def citation
-      related_identifiers("citation").presence
+      related_identifiers("citation")
     end
 
     def publisher

data/lib/bolognese/utils.rb

@@ -75,12 +75,20 @@ module Bolognese
         element.fetch(content, nil)
       elsif element.is_a?(Array)
         a = element.map { |e| e.fetch(content, nil) }.uniq
-        a.length == 1 ? a.first : a
+        array_unwrap(a)
       else
         nil
       end
     end
 
+    def array_unwrap(element)
+      case element.length
+      when 0 then nil
+      when 1 then element.first
+      else element
+      end
+    end
+
     def normalize_id(id)
       return nil unless id.present?
 
@@ -96,7 +104,8 @@ module Bolognese
     end
 
     def normalize_ids(list)
-      Array.wrap(list).map { |url| url.merge("@id" => normalize_id(url["@id"])) }
+      a = Array.wrap(list).map { |url| url.merge("@id" => normalize_id(url["@id"])) }
+      array_unwrap(a)
     end
   end
 end

data/lib/bolognese/version.rb

@@ -1,3 +1,3 @@
 module Bolognese
-  VERSION = "0.6.5"
+  VERSION = "0.6.6"
 end

data/spec/crossref_spec.rb

@@ -50,7 +50,7 @@ describe Bolognese::Crossref, vcr: true do
                                     {"@type"=>"Person", "givenName"=>"Michael", "familyName"=>"Breitenbach"},
                                     {"@type"=>"Person", "givenName"=>"Hans", "familyName"=>"Lehrach"},
                                     {"@type"=>"Person", "givenName"=>"Sylvia", "familyName"=>"Krobitsch"}])
-      expect(subject.editor).to eq([{"@type"=>"Person", "givenName"=>"Guilhem", "familyName"=>"Janbon"}])
+      expect(subject.editor).to eq("@type"=>"Person", "givenName"=>"Guilhem", "familyName"=>"Janbon")
       expect(subject.name).to eq("Triose Phosphate Isomerase Deficiency Is Caused by Altered Dimerization–Not Catalytic Inactivity–of the Mutant Enzymes")
       expect(subject.license).to eq("http://creativecommons.org/licenses/by/4.0/")
       expect(subject.date_published).to eq("2006-12-20")

data/spec/datacite_spec.rb

@@ -25,7 +25,7 @@ describe Bolognese::Datacite, vcr: true do
       expect(subject.date_published).to eq("2011")
       expect(subject.has_part).to eq([{"@type"=>"CreativeWork", "@id"=>"https://doi.org/10.5061/dryad.8515/1"},
                                       {"@type"=>"CreativeWork", "@id"=>"https://doi.org/10.5061/dryad.8515/2"}])
-      expect(subject.citation).to eq([{"@type"=>"CreativeWork", "@id"=>"https://doi.org/10.1371/journal.ppat.1000446"}])
+      expect(subject.citation).to eq("@type"=>"CreativeWork", "@id"=>"https://doi.org/10.1371/journal.ppat.1000446")
       expect(subject.publisher).to eq("@type"=>"Organization", "name"=>"Dryad Digital Repository")
       expect(subject.provider).to eq("@type"=>"Organization", "name"=>"DataCite")
       expect(subject.schema_version).to eq("http://datacite.org/schema/kernel-3")
@@ -38,7 +38,7 @@ describe Bolognese::Datacite, vcr: true do
       expect(subject.type).to eq("ScholarlyArticle")
       expect(subject.additional_type).to eq("BlogPosting")
       expect(subject.resource_type_general).to eq("Text")
-      expect(subject.author).to eq([{"@type"=>"Person", "@id"=>"http://orcid.org/0000-0003-1419-2405", "givenName"=>"Martin", "familyName"=>"Fenner"}])
+      expect(subject.author).to eq("@type"=>"Person", "@id"=>"http://orcid.org/0000-0003-1419-2405", "givenName"=>"Martin", "familyName"=>"Fenner")
       expect(subject.name).to eq("Eating your own Dog Food")
       expect(subject.alternate_name).to eq("MS-49-3632-5083")
       expect(subject.description).to start_with("Eating your own dog food")
@@ -59,7 +59,7 @@ describe Bolognese::Datacite, vcr: true do
       expect(subject.type).to eq("ScholarlyArticle")
       expect(subject.additional_type).to eq("ConferencePaper")
       expect(subject.resource_type_general).to eq("Text")
-      expect(subject.author).to eq([{"@type"=>"Person", "givenName"=>"Nathaniel", "familyName"=>"Johnston"}])
+      expect(subject.author).to eq("@type"=>"Person", "givenName"=>"Nathaniel", "familyName"=>"Johnston")
       expect(subject.name).to eq("The Minimum Size of Qubit Unextendible Product Bases")
       expect(subject.description).to start_with("We investigate the problem of constructing unextendible product bases in the qubit case")
       expect(subject.date_published).to eq("2013")
@@ -75,16 +75,36 @@ describe Bolognese::Datacite, vcr: true do
       expect(subject.type).to eq("SoftwareSourceCode")
       expect(subject.additional_type).to eq("Software")
       expect(subject.resource_type_general).to eq("Software")
-      expect(subject.author).to eq([{"@type"=>"Agent", "Name"=>"Kristian Garza"}])
+      expect(subject.author).to eq("@type"=>"Agent", "name"=>"Kristian Garza")
       expect(subject.name).to eq("Analysis Tools for Crossover Experiment of UI using Choice Architecture")
       expect(subject.description).to start_with("<p>&nbsp;</p>\n\n<p>This tools are used to analyse the data produced by the Crosssover Experiment")
       expect(subject.license).to eq(["info:eu-repo/semantics/openAccess", "https://creativecommons.org/licenses/by-nc-sa/4.0/"])
       expect(subject.date_published).to eq("2016-03-27")
+      expect(subject.citation).to eq("@type"=>"CreativeWork", "@id"=>"https://github.com/kjgarza/frame_experiment_analysis/tree/v1.0")
       expect(subject.publisher).to eq("@type"=>"Organization", "name"=>"Zenodo")
       expect(subject.provider).to eq("@type"=>"Organization", "name"=>"DataCite")
       expect(subject.schema_version).to eq("http://datacite.org/schema/kernel-3")
     end
 
+    it "is identical to" do
+      id = "10.6084/M9.FIGSHARE.4234751.V1"
+      subject = Bolognese::Datacite.new(id: id)
+      expect(subject.id).to eq("https://doi.org/10.6084/m9.figshare.4234751.v1")
+      expect(subject.type).to eq("Dataset")
+      expect(subject.additional_type).to eq("Dataset")
+      expect(subject.resource_type_general).to eq("Dataset")
+      expect(subject.author.count).to eq(11)
+      expect(subject.author.first).to eq("@type"=>"Agent", "@id"=>"http://orcid.org/0000-0002-2410-9671", "name"=>"Alexander Junge")
+      expect(subject.name).to eq("RAIN v1")
+      expect(subject.description).to start_with("<div><b>RAIN: RNA–protein Association and Interaction Networks")
+      expect(subject.license).to eq("https://creativecommons.org/licenses/by/4.0/")
+      expect(subject.date_published).to eq("2016")
+      expect(subject.same_as).to eq("@type"=>"CreativeWork", "@id"=>"https://doi.org/10.6084/m9.figshare.4234751")
+      expect(subject.publisher).to eq("@type"=>"Organization", "name"=>"Figshare")
+      expect(subject.provider).to eq("@type"=>"Organization", "name"=>"DataCite")
+      expect(subject.schema_version).to eq("http://datacite.org/schema/kernel-3")
+    end
+
     it "funding schema version 3" do
       id = "https://doi.org/10.5281/ZENODO.1239"
       subject = Bolognese::Datacite.new(id: id)
@@ -153,7 +173,7 @@ describe Bolognese::Datacite, vcr: true do
       expect(subject.date_published).to eq("2011")
       expect(subject.has_part).to eq([{"@type"=>"CreativeWork", "@id"=>"https://doi.org/10.5061/dryad.8515/1"},
                                       {"@type"=>"CreativeWork", "@id"=>"https://doi.org/10.5061/dryad.8515/2"}])
-      expect(subject.citation).to eq([{"@type"=>"CreativeWork", "@id"=>"https://doi.org/10.1371/journal.ppat.1000446"}])
+      expect(subject.citation).to eq("@type"=>"CreativeWork", "@id"=>"https://doi.org/10.1371/journal.ppat.1000446")
       expect(subject.provider).to eq("@type"=>"Organization", "name"=>"DataCite")
     end
 
@@ -187,7 +207,7 @@ describe Bolognese::Datacite, vcr: true do
       expect(subject.date_published).to eq("2011")
       expect(subject.has_part).to eq([{"@type"=>"CreativeWork", "@id"=>"https://doi.org/10.5061/dryad.8515/1"},
                                       {"@type"=>"CreativeWork", "@id"=>"https://doi.org/10.5061/dryad.8515/2"}])
-      expect(subject.citation).to eq([{"@type"=>"CreativeWork", "@id"=>"https://doi.org/10.1371/journal.ppat.1000446"}])
+      expect(subject.citation).to eq("@type"=>"CreativeWork", "@id"=>"https://doi.org/10.1371/journal.ppat.1000446")
       expect(subject.publisher).to eq("@type"=>"Organization", "name"=>"Dryad Digital Repository")
       expect(subject.provider).to eq("@type"=>"Organization", "name"=>"DataCite")
       expect(subject.schema_version).to eq("http://datacite.org/schema/kernel-4")

data/spec/fixtures/vcr_cassettes/Bolognese_Datacite/get_metadata/is_identical_to.yml

@@ -0,0 +1,176 @@
+---
+http_interactions:
+- request:
+    method: get
+    uri: https://doi.org/10.6084/m9.figshare.4234751.v1
+    body:
+      encoding: US-ASCII
+      string: ''
+    headers:
+      User-Agent:
+      - Maremma - https://github.com/datacite/maremma
+      Accept:
+      - application/vnd.datacite.datacite+xml
+  response:
+    status:
+      code: 303
+      message: ''
+    headers:
+      Server:
+      - Apache-Coyote/1.1
+      Vary:
+      - Accept
+      Location:
+      - http://data.datacite.org/10.6084%2Fm9.figshare.4234751.v1
+      Expires:
+      - Thu, 23 Feb 2017 08:31:06 GMT
+      Content-Type:
+      - text/html;charset=utf-8
+      Content-Length:
+      - '199'
+      Date:
+      - Thu, 23 Feb 2017 07:48:39 GMT
+    body:
+      encoding: UTF-8
+      string: |-
+        <html><head><title>Handle Redirect</title></head>
+        <body><a href="http://data.datacite.org/10.6084%2Fm9.figshare.4234751.v1">http://data.datacite.org/10.6084%2Fm9.figshare.4234751.v1</a></body></html>
+    http_version: 
+  recorded_at: Thu, 23 Feb 2017 07:48:39 GMT
+- request:
+    method: get
+    uri: http://data.datacite.org/10.6084%2Fm9.figshare.4234751.v1
+    body:
+      encoding: US-ASCII
+      string: ''
+    headers:
+      User-Agent:
+      - Maremma - https://github.com/datacite/maremma
+      Accept:
+      - application/vnd.datacite.datacite+xml
+  response:
+    status:
+      code: 301
+      message: ''
+    headers:
+      Server:
+      - openresty/1.11.2.2
+      Date:
+      - Thu, 23 Feb 2017 07:48:39 GMT
+      Content-Type:
+      - text/html
+      Content-Length:
+      - '191'
+      Connection:
+      - keep-alive
+      Location:
+      - https://data.datacite.org/10.6084%2Fm9.figshare.4234751.v1
+    body:
+      encoding: UTF-8
+      string: "<html>\r\n<head><title>301 Moved Permanently</title></head>\r\n<body
+        bgcolor=\"white\">\r\n<center><h1>301 Moved Permanently</h1></center>\r\n<hr><center>openresty/1.11.2.2</center>\r\n</body>\r\n</html>\r\n"
+    http_version: 
+  recorded_at: Thu, 23 Feb 2017 07:48:39 GMT
+- request:
+    method: get
+    uri: https://data.datacite.org/10.6084%2Fm9.figshare.4234751.v1
+    body:
+      encoding: US-ASCII
+      string: ''
+    headers:
+      User-Agent:
+      - Maremma - https://github.com/datacite/maremma
+      Accept:
+      - application/vnd.datacite.datacite+xml
+  response:
+    status:
+      code: 200
+      message: ''
+    headers:
+      Server:
+      - openresty/1.11.2.2
+      Date:
+      - Thu, 23 Feb 2017 07:48:40 GMT
+      Content-Type:
+      - application/vnd.datacite.datacite+xml
+      Content-Length:
+      - '2704'
+      Connection:
+      - keep-alive
+      Cache-Control:
+      - no-transform, max-age=3600
+      Last-Modified:
+      - Wed, 16 Nov 2016 10:49:12 GMT
+      Vary:
+      - Accept
+      Access-Control-Allow-Origin:
+      - "*"
+      Access-Control-Allow-Methods:
+      - GET, POST, OPTIONS
+    body:
+      encoding: ASCII-8BIT
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+    http_version: 
+  recorded_at: Thu, 23 Feb 2017 07:48:40 GMT
+recorded_with: VCR 3.0.3

data/spec/utils_spec.rb

@@ -75,7 +75,7 @@ describe Bolognese::Crossref, vcr: true do
     it "url" do
       ids = [{"@type"=>"CreativeWork", "@id"=>"https://blog.datacite.org/eating-your-own-dog-food/"}]
       response = subject.normalize_ids(ids)
-      expect(response).to eq([{"@type"=>"CreativeWork", "@id"=>"https://blog.datacite.org/eating-your-own-dog-food"}])
+      expect(response).to eq("@type"=>"CreativeWork", "@id"=>"https://blog.datacite.org/eating-your-own-dog-food")
     end
   end
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bolognese
 version: !ruby/object:Gem::Version
-  version: 0.6.5
+  version: 0.6.6
 platform: ruby
 authors:
 - Martin Fenner
@@ -420,6 +420,7 @@ files:
 - spec/fixtures/vcr_cassettes/Bolognese_Datacite/get_metadata/Funding_schema_version_3.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Datacite/get_metadata/Funding_schema_version_4.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Datacite/get_metadata/Schema_org_JSON.yml
+- spec/fixtures/vcr_cassettes/Bolognese_Datacite/get_metadata/is_identical_to.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Datacite/get_metadata/multiple_licenses.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Datacite/get_metadata_as_bibtex/BlogPosting.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Datacite/get_metadata_as_bibtex/Dataset.yml