bolognese 0.8 → 0.8.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: d9c8e7a4955f749653d35917dae9f3a459c0f2da
-  data.tar.gz: b646899d5e3c5502320e754d25fc9cbfdafffc51
+  metadata.gz: 44ef0d823038f4256509d1215ce8fae2ca6d62f4
+  data.tar.gz: a4a9ad1a9530c9e4e96566c6e1c349205d2dd7e0
 SHA512:
-  metadata.gz: 892e8ccf9ad4354b93dca5b42d7fc099707007d2187dcaab5ad066ebf5357dc6ade3664e181408e05be3cfc07b8a77f86f1abe57f1348fd6a5d9fcfe5b293b06
-  data.tar.gz: 064b883d4eefefb064f4dc24fb5397a2c530f2dd1a52cc15319a52487820053d67b6a68dd94ae8a1dbd35dcb21d623e3a42e9539552172c0be536945edd4daf5
+  metadata.gz: 347c241f0201e837225394d7bec559fa0675696edd725df6a635f5ddf4b6975fe5194fa2fc25c7ba97069272e4440e1660ea0d2a2eb0dbf312a4d3370a49d970
+  data.tar.gz: a7906e3128cc090e14017716a3534c444ff18a9f209083f9e1d64a833f27fb7d01720fe07a2895c87af65bb1656b94716fe6e55dbd596f5056d5c8027653aed4

data/Gemfile.lock

@@ -1,7 +1,7 @@
 PATH
   remote: .
   specs:
-    bolognese (0.8)
+    bolognese (0.8.1)
       activesupport (~> 4.2, >= 4.2.5)
       bibtex-ruby (~> 4.1)
       builder (~> 3.2, >= 3.2.2)
@@ -123,4 +123,4 @@ DEPENDENCIES
   webmock (~> 1.22, >= 1.22.3)
 
 BUNDLED WITH
-   1.12.5
+   1.14.5

data/lib/bolognese/bibtex.rb

@@ -39,7 +39,7 @@ module Bolognese
     end
 
     def valid?
-      true
+      bibtex.present?
     end
 
     def type

data/lib/bolognese/codemeta.rb

@@ -21,7 +21,7 @@ module Bolognese
     end
 
     def valid?
-      true
+      codemeta.present?
     end
 
     def doi

data/lib/bolognese/crossref.rb

@@ -83,7 +83,7 @@ module Bolognese
     end
 
     def valid?
-      true
+      crossref.present?
     end
 
     def doi

data/lib/bolognese/datacite.rb

@@ -31,11 +31,13 @@ module Bolognese
     end
 
     def valid?
-      errors.blank?
+      datacite.present? && errors.blank?
     end
 
     def errors
       schema.validate(Nokogiri::XML(raw)).map { |error| error.to_s }.unwrap
+    rescue Nokogiri::XML::SyntaxError => e
+      e.message
     end
 
     def schema_version
@@ -227,8 +229,36 @@ module Bolognese
       related_identifier(relation_type: "IsNewVersionOf")
     end
 
+    def is_variant_form_of
+      related_identifier(relation_type: "IsVariantFormOf")
+    end
+
+    def is_original_form_of
+      related_identifier(relation_type: "IsOriginalFormOf")
+    end
+
     def references
-      related_identifier(relation_type: "Cites IsCitedBy Supplements IsSupplementTo References IsReferencedBy").presence
+      related_identifier(relation_type: "References Cites").presence
+    end
+
+    def is_referenced_by
+      related_identifier(relation_type: "IsCitedBy IsReferencedBy").presence
+    end
+
+    def is_supplement_to
+      related_identifier(relation_type: "IsSupplementTo")
+    end
+
+    def is_supplemented_by
+      get_related_identifier(relation_type: "isSupplementedBy")
+    end
+
+    def reviews
+      related_identifier(relation_type: "Reviews").presence
+    end
+
+    def is_reviewed_by
+      related_identifier(relation_type: "IsReviewedBy").presence
     end
 
     def publisher

data/lib/bolognese/datacite_json.rb

@@ -12,7 +12,7 @@ module Bolognese
     end
 
     def valid?
-      true
+      datacite_json.present?
     end
 
     def datacite

data/lib/bolognese/metadata.rb

@@ -41,7 +41,7 @@ module Bolognese
       :is_referenced_by, :references, :is_documented_by, :documents,
       :is_compiled_by, :compiles, :is_variant_form_of, :is_original_form_of,
       :is_reviewed_by, :reviews, :is_derived_from, :is_source_of, :format,
-      :related_identifier
+      :related_identifier, :reverse
 
     def publication_year
       date_published && date_published[0..3]
@@ -55,6 +55,11 @@ module Bolognese
       [page_start, page_end].compact.join("-").presence
     end
 
+    def reverse
+      { "citation" => Array.wrap(is_referenced_by).map { |r| { "@id" => r["id"] }}.unwrap,
+        "isBasedOn" => Array.wrap(is_supplement_to).map { |r| { "@id" => r["id"] }}.unwrap }.compact
+    end
+
     def schema_org
       hsh = {
         "@context" => id.present? ? "http://schema.org" : nil,
@@ -66,7 +71,7 @@ module Bolognese
         "alternateName" => alternate_name,
         "author" => to_schema_org(author),
         "editor" => editor,
-        "description" => description.present? ? description["text"] : nil,
+        "description" => Array.wrap(description).map { |d| d["text"] }.unwrap,
         "license" => license.present? ? license["id"] : nil,
         "version" => version,
         "keywords" => keywords,
@@ -84,6 +89,7 @@ module Bolognese
         "predecessor_of" => is_previous_version_of,
         "successor_of" => is_new_version_of,
         "citation" => references,
+        "@reverse" => reverse,
         "schemaVersion" => schema_version,
         "publisher" => { "@type" => "Organization", "name" => publisher },
         "funder" => funder,
@@ -151,7 +157,7 @@ module Bolognese
 
     def bibtex
       bib = {
-        bibtex_type: bibtex_type.to_sym,
+        bibtex_type: bibtex_type.present? ? bibtex_type.to_sym : "misc",
         bibtex_key: id,
         doi: doi,
         url: url,

data/lib/bolognese/schema_org.rb

@@ -31,7 +31,7 @@ module Bolognese
     end
 
     def valid?
-      true
+      schema_org.present?
     end
 
     def doi
@@ -114,13 +114,18 @@ module Bolognese
       Array.wrap(has_part) +
       Array.wrap(is_previous_version_of) +
       Array.wrap(is_new_version_of) +
-      Array.wrap(references)
+      Array.wrap(references) +
+      Array.wrap(is_supplemented_by)
     end
 
     def get_related_identifier(relation_type: nil)
       normalize_ids(metadata.fetch(relation_type, nil), SO_TO_DC_RELATION_TYPES[relation_type])
     end
 
+    def get_reverse_related_identifier(relation_type: nil)
+      normalize_ids(metadata.dig("@reverse", relation_type), SO_TO_DC_RELATION_TYPES[relation_type])
+    end
+
     def is_identical_to
       get_related_identifier(relation_type: "sameAs")
     end
@@ -145,6 +150,18 @@ module Bolognese
       get_related_identifier(relation_type: "citation")
     end
 
+    def is_referenced_by
+      get_reverse_related_identifier(relation_type: "citation")
+    end
+
+    def is_supplement_to
+      get_reverse_related_identifier(relation_type: "isBasedOn")
+    end
+
+    def is_supplemented_by
+      get_related_identifier(relation_type: "isBasedOn")
+    end
+
     def publisher
       metadata.dig("publisher", "name")
     end

data/lib/bolognese/version.rb

@@ -1,3 +1,3 @@
 module Bolognese
-  VERSION = "0.8"
+  VERSION = "0.8.1"
 end

data/spec/bibtex_spec.rb

@@ -7,6 +7,7 @@ describe Bolognese::Bibtex, vcr: true do
 
   context "get metadata" do
     it "Crossref DOI" do
+      expect(subject.valid?).to be true
       expect(subject.id).to eq("https://doi.org/10.7554/elife.01567")
       expect(subject.type).to eq("ScholarlyArticle")
       expect(subject.url).to eq("http://elifesciences.org/lookup/doi/10.7554/eLife.01567")

data/spec/codemeta_spec.rb

@@ -8,6 +8,7 @@ describe Bolognese::Codemeta, vcr: true do
 
   context "get metadata" do
     it "maremma" do
+      expect(subject.valid?).to be true
       expect(subject.id).to eq("https://doi.org/10.5438/qeg0-3gm3")
       expect(subject.url).to eq("https://github.com/datacite/maremma")
       expect(subject.type).to eq("SoftwareSourceCode")
@@ -76,6 +77,7 @@ describe Bolognese::Codemeta, vcr: true do
     it "maremma" do
       string = IO.read(fixture_path + 'maremma/codemeta.json')
       subject = Bolognese::Codemeta.new(string: string)
+      expect(subject.valid?).to be true
       expect(subject.id).to eq("https://doi.org/10.5438/qeg0-3gm3")
       expect(subject.url).to eq("https://github.com/datacite/maremma")
       expect(subject.type).to eq("SoftwareSourceCode")

data/spec/datacite_json_spec.rb

@@ -7,6 +7,7 @@ describe Bolognese::DataciteJson, vcr: true do
 
   context "get metadata as string" do
     it "BlogPosting" do
+      expect(subject.valid?).to be true
       expect(subject.id).to eq("https://doi.org/10.5438/4k3m-nyvg")
       expect(subject.type).to eq("ScholarlyArticle")
       expect(subject.additional_type).to eq("BlogPosting")
@@ -25,6 +26,7 @@ describe Bolognese::DataciteJson, vcr: true do
     it "SoftwareSourceCode" do
       string = IO.read(fixture_path + "datacite_software.json")
       subject = Bolognese::DataciteJson.new(string: string)
+      expect(subject.valid?).to be true
       json = JSON.parse(subject.codemeta)
       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")
@@ -52,6 +54,7 @@ describe Bolognese::DataciteJson, vcr: true do
     it "BlogPosting" do
       id = "https://doi.org/10.5438/4K3M-NYVG"
       subject = Bolognese::Datacite.new(id: id)
+      expect(subject.valid?).to be true
       bibtex = BibTeX.parse(subject.bibtex).to_a(quotes: '').first
       expect(bibtex[:bibtex_type].to_s).to eq("article")
       expect(bibtex[:bibtex_key]).to eq("https://doi.org/10.5438/4k3m-nyvg")

data/spec/datacite_spec.rb

@@ -19,7 +19,7 @@ describe Bolognese::Datacite, vcr: true do
       expect(subject.license).to eq("url"=>"http://creativecommons.org/publicdomain/zero/1.0/")
       expect(subject.date_published).to eq("2011")
       expect(subject.has_part).to eq([{"id"=>"https://doi.org/10.5061/dryad.8515/1", "relationType"=>"HasPart"}, {"id"=>"https://doi.org/10.5061/dryad.8515/2", "relationType"=>"HasPart"}])
-      expect(subject.references).to eq("id"=>"https://doi.org/10.1371/journal.ppat.1000446", "relationType"=>"IsReferencedBy")
+      expect(subject.is_referenced_by).to eq("id"=>"https://doi.org/10.1371/journal.ppat.1000446", "relationType"=>"IsReferencedBy")
       expect(subject.publisher).to eq("Dryad Digital Repository")
       expect(subject.provider).to eq("DataCite")
       expect(subject.schema_version).to eq("http://datacite.org/schema/kernel-3")
@@ -76,7 +76,7 @@ describe Bolognese::Datacite, vcr: true do
       expect(subject.description["text"]).to start_with("This tools are used to analyse the data produced by the Crosssover Experiment")
       expect(subject.license).to eq([{"url"=>"info:eu-repo/semantics/openAccess", "name"=>"Open Access"}, {"url"=>"https://creativecommons.org/licenses/by-nc-sa/4.0/", "name"=>"Creative Commons Attribution-NonCommercial-ShareAlike"}])
       expect(subject.date_published).to eq("2016-03-27")
-      expect(subject.references).to eq("id"=>"https://github.com/kjgarza/frame_experiment_analysis/tree/v1.0", "relationType"=>"IsSupplementTo")
+      expect(subject.is_supplement_to).to eq("id"=>"https://github.com/kjgarza/frame_experiment_analysis/tree/v1.0", "relationType"=>"IsSupplementTo")
       expect(subject.publisher).to eq("Zenodo")
       expect(subject.provider).to eq("DataCite")
       expect(subject.schema_version).to eq("http://datacite.org/schema/kernel-3")
@@ -146,9 +146,18 @@ describe Bolognese::Datacite, vcr: true do
                                                                           "funderName" => "European Commission")
     end
 
-    it "Schema.org JSON" do
+    it "Schema.org JSON isReferencedBy" do
       json = JSON.parse(subject.schema_org)
       expect(json["@id"]).to eq("https://doi.org/10.5061/dryad.8515")
+      expect(json["@reverse"]).to eq("citation"=>{"@id"=>"https://doi.org/10.1371/journal.ppat.1000446"})
+    end
+
+    it "Schema.org JSON IsSupplementTo" do
+      id = "https://doi.org/10.5517/CC8H01S"
+      subject = Bolognese::Datacite.new(id: id)
+      json = JSON.parse(subject.schema_org)
+      expect(json["@id"]).to eq("https://doi.org/10.5517/cc8h01s")
+      expect(json["@reverse"]).to eq("isBasedOn"=>{"@id"=>"https://doi.org/10.1107/s1600536804021154"})
     end
   end
 
@@ -196,7 +205,7 @@ describe Bolognese::Datacite, vcr: true do
       expect(subject.date_published).to eq("2011")
       expect(subject.has_part).to eq([{"id"=>"https://doi.org/10.5061/dryad.8515/1", "relationType"=>"HasPart"},
                                       {"id"=>"https://doi.org/10.5061/dryad.8515/2", "relationType"=>"HasPart"}])
-      expect(subject.references).to eq("id"=>"https://doi.org/10.1371/journal.ppat.1000446", "relationType"=>"IsReferencedBy")
+      expect(subject.is_referenced_by).to eq("id"=>"https://doi.org/10.1371/journal.ppat.1000446", "relationType"=>"IsReferencedBy")
       expect(subject.publisher).to eq("Dryad Digital Repository")
       expect(subject.provider).to eq("DataCite")
       expect(subject.schema_version).to eq("http://datacite.org/schema/kernel-3")

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

@@ -0,0 +1,171 @@
+---
+http_interactions:
+- request:
+    method: get
+    uri: https://doi.org/10.5517/cc8h01s
+    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/10.5517%2Fcc8h01s
+      Expires:
+      - Wed, 01 Mar 2017 22:34:28 GMT
+      Content-Type:
+      - text/html;charset=utf-8
+      Content-Length:
+      - '169'
+      Date:
+      - Wed, 01 Mar 2017 22:24:34 GMT
+    body:
+      encoding: UTF-8
+      string: |-
+        <html><head><title>Handle Redirect</title></head>
+        <body><a href="http://data.datacite.org/10.5517%2Fcc8h01s">http://data.datacite.org/10.5517%2Fcc8h01s</a></body></html>
+    http_version: 
+  recorded_at: Wed, 01 Mar 2017 22:24:35 GMT
+- request:
+    method: get
+    uri: http://data.datacite.org/10.5517%2Fcc8h01s
+    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:
+      - Wed, 01 Mar 2017 22:24:35 GMT
+      Content-Type:
+      - text/html
+      Content-Length:
+      - '191'
+      Connection:
+      - keep-alive
+      Location:
+      - https://data.datacite.org/10.5517%2Fcc8h01s
+    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: Wed, 01 Mar 2017 22:24:35 GMT
+- request:
+    method: get
+    uri: https://data.datacite.org/10.5517%2Fcc8h01s
+    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:
+      - Wed, 01 Mar 2017 22:24:35 GMT
+      Content-Type:
+      - application/vnd.datacite.datacite+xml
+      Content-Length:
+      - '2496'
+      Connection:
+      - keep-alive
+      Cache-Control:
+      - no-transform, max-age=3600
+      Last-Modified:
+      - Sun, 01 May 2016 13:41:38 GMT
+      Vary:
+      - Accept
+      Access-Control-Allow-Origin:
+      - "*"
+      Access-Control-Allow-Methods:
+      - GET, POST, OPTIONS
+    body:
+      encoding: ASCII-8BIT
+      string: !binary |-
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data/spec/fixtures/vcr_cassettes/Bolognese_Datacite/get_metadata/Schema_org_JSON_isReferencedBy.yml

@@ -0,0 +1,173 @@
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+- request:
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metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bolognese
 version: !ruby/object:Gem::Version
-  version: '0.8'
+  version: 0.8.1
 platform: ruby
 authors:
 - Martin Fenner
@@ -529,6 +529,8 @@ 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/Schema_org_JSON_IsSupplementTo.yml
+- spec/fixtures/vcr_cassettes/Bolognese_Datacite/get_metadata/Schema_org_JSON_isReferencedBy.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