commonmeta-ruby 3.5.1 → 3.5.3

checksums.yaml

@@ -1,7 +1,7 @@
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data/Gemfile.lock

@@ -1,7 +1,7 @@
 PATH
   remote: .
   specs:
-    commonmeta-ruby (3.5.1)
+    commonmeta-ruby (3.5.3)
       activesupport (>= 4.2.5, < 8.0)
       addressable (~> 2.8.1, < 2.8.2)
       base32-url (>= 0.7.0, < 1)
@@ -73,7 +73,7 @@ GEM
     feedparser (2.2.0)
       logutils (>= 0.6.1)
       textutils (>= 1.0.0)
-    ffi (1.15.5)
+    ffi (1.16.2)
     ffi-compiler (1.0.1)
       ffi (>= 1.0.0)
       rake
@@ -179,7 +179,7 @@ GEM
     rspec-xsd (0.1.0)
       nokogiri (~> 1.6)
       rspec (~> 3)
-    rubocop (1.56.3)
+    rubocop (1.56.4)
       base64 (~> 0.1.1)
       json (~> 2.3)
       language_server-protocol (>= 3.17.0)
@@ -202,7 +202,7 @@ GEM
       rubocop-ast (>= 0.4.0)
     rubocop-rake (0.6.0)
       rubocop (~> 1.0)
-    rubocop-rspec (2.24.0)
+    rubocop-rspec (2.24.1)
       rubocop (~> 1.33)
       rubocop-capybara (~> 2.17)
       rubocop-factory_bot (~> 2.22)

data/lib/commonmeta/metadata_utils.rb

@@ -22,6 +22,7 @@ require_relative 'writers/bibtex_writer'
 require_relative 'writers/citation_writer'
 require_relative 'writers/cff_writer'
 require_relative 'writers/codemeta_writer'
+require_relative 'writers/commonmeta_writer'
 require_relative 'writers/crossref_xml_writer'
 require_relative 'writers/csl_writer'
 require_relative 'writers/csv_writer'
@@ -56,6 +57,7 @@ module Commonmeta
     include Commonmeta::Writers::CitationWriter
     include Commonmeta::Writers::CffWriter
     include Commonmeta::Writers::CodemetaWriter
+    include Commonmeta::Writers::CommonmetaWriter
     include Commonmeta::Writers::CrossrefXmlWriter
     include Commonmeta::Writers::CslWriter
     include Commonmeta::Writers::CsvWriter

data/lib/commonmeta/readers/json_feed_reader.rb

@@ -129,8 +129,19 @@ module Commonmeta
       end
 
       def get_funding_references(meta)
-        # check that relationships resolve and have type "HasAward"
-        Array.wrap(meta["relationships"]).reduce([]) do |sum, relationship|
+        # check that relationships resolve and have type "HasAward" or funding is provided by blog metadata
+        if funding = meta.dig("blog", "funding")
+          fundref = { 
+            "funderIdentifier" => funding["funder_id"],
+            "funderIdentifierType" => "Crossref Funder ID",
+            "funderName" => funding["funder_name"], 
+            "awardNumber" => funding["award_number"]
+          }
+
+        else
+          fundref = nil
+        end
+        Array.wrap(fundref) + Array.wrap(meta["relationships"]).reduce([]) do |sum, relationship|
           begin
             # funder is European Commission
             if validate_prefix(relationship["url"]) == "10.3030" || URI.parse(relationship["url"]).host == "cordis.europa.eu"

data/lib/commonmeta/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module Commonmeta
-  VERSION = '3.5.1'
+  VERSION = '3.5.3'
 end

data/lib/commonmeta/writers/commonmeta_writer.rb

@@ -0,0 +1,11 @@
+# frozen_string_literal: true
+
+module Commonmeta
+  module Writers
+    module CommonmetaWriter
+      def commonmeta
+        JSON.pretty_generate meta
+      end
+    end
+  end
+end

data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_commonmeta/with_data_citation.yml

@@ -0,0 +1,247 @@
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+        Sciences Publications, Ltd.","value":"10.7554"}],"id":4374,"tokens":["elife","sciences","publications","ltd"],"counts-type":{"all":{"peer-review":33948,"journal-article":15366,"journal":1,"component":143802,"posted-content":1554},"backfile":{"peer-review":18437,"journal-article":9849},"current":{"peer-review":15511,"journal-article":5517,"posted-content":1554}},"coverage-type":{"all":{"peer-review":{"last-status-check-time":1696117222074,"affiliations":0.894721338517733,"abstracts":0.0,"orcids":0.7960410038882998,"licenses":1.0,"references":0.0,"funders":0.0,"similarity-checking":0.0,"award-numbers":0.0,"ror-ids":0.2387180393543066,"update-policies":0.0,"resource-links":0.0,"descriptions":0.0},"journal-article":{"last-status-check-time":1696117222074,"affiliations":0.9795001952362358,"abstracts":0.9806716126513081,"orcids":0.8825328647663673,"licenses":0.9999349212547182,"references":0.9737732656514382,"funders":0.8906677079265912,"similarity-checking":0.0,"award-numbers":0.8456982949368737,"ror-ids":0.2031758427697514,"update-policies":0.4905635819341403,"resource-links":0.9998698425094364,"descriptions":0.0},"journal":{"last-status-check-time":1696117222074,"affiliations":0.0,"abstracts":0.0,"orcids":0.0,"licenses":0.0,"references":0.0,"funders":0.0,"similarity-checking":0.0,"award-numbers":0.0,"ror-ids":0.0,"update-policies":0.0,"resource-links":0.0,"descriptions":0.0},"component":{"last-status-check-time":1696117222074,"affiliations":0.0,"abstracts":0.0,"orcids":0.0,"licenses":4.867804342081473E-4,"references":0.0,"funders":0.0,"similarity-checking":0.0,"award-numbers":0.0,"ror-ids":0.0,"update-policies":0.0,"resource-links":0.0,"descriptions":0.0},"posted-content":{"last-status-check-time":1696117222074,"affiliations":0.9967824967824968,"abstracts":1.0,"orcids":0.8442728442728443,"licenses":1.0,"references":0.0,"funders":0.0,"similarity-checking":0.0,"award-numbers":0.0,"ror-ids":0.0,"update-policies":0.0,"resource-links":0.0,"descriptions":0.0}},"backfile":{"peer-review":{"last-status-check-time":1696117222074,"affiliations":0.9971253457720887,"abstracts":0.0,"orcids":0.8638064761078267,"licenses":1.0,"references":0.0,"funders":0.0,"similarity-checking":0.0,"award-numbers":0.0,"ror-ids":0.003579758095134783,"update-policies":0.0,"resource-links":0.0,"descriptions":0.0},"journal-article":{"last-status-check-time":1696117222074,"affiliations":0.9761397096151894,"abstracts":0.9778657731749416,"orcids":0.8169357295156869,"licenses":0.9998984668494263,"references":0.9742105797542898,"funders":0.8765356889024266,"similarity-checking":0.0,"award-numbers":0.8231292517006803,"ror-ids":0.0,"update-policies":0.2051984973093715,"resource-links":0.9997969336988527,"descriptions":0.0}},"current":{"peer-review":{"last-status-check-time":1696117222074,"affiliations":0.7729998065888724,"abstracts":0.0,"orcids":0.7154922313197086,"licenses":1.0,"references":0.0,"funders":0.0,"similarity-checking":0.0,"award-numbers":0.0,"ror-ids":0.5182128811810973,"update-policies":0.0,"resource-links":0.0,"descriptions":0.0},"journal-article":{"last-status-check-time":1696117222074,"affiliations":0.9854993655972449,"abstracts":0.9856806235272793,"orcids":0.9996374841399311,"licenses":1.0,"references":0.9729925684248686,"funders":0.9158963204640203,"similarity-checking":0.0,"award-numbers":0.8859887620083379,"ror-ids":0.5658872575675186,"update-policies":1.0,"resource-links":1.0,"descriptions":0.0},"posted-content":{"last-status-check-time":1696117222074,"affiliations":0.9967824967824968,"abstracts":1.0,"orcids":0.8442728442728443,"licenses":1.0,"references":0.0,"funders":0.0,"similarity-checking":0.0,"award-numbers":0.0,"ror-ids":0.0,"update-policies":0.0,"resource-links":0.0,"descriptions":0.0}}},"flags":{"deposits-abstracts-current":true,"deposits-orcids-current":true,"deposits":true,"deposits-affiliations-backfile":true,"deposits-update-policies-backfile":true,"deposits-similarity-checking-backfile":false,"deposits-award-numbers-current":true,"deposits-resource-links-current":true,"deposits-ror-ids-current":true,"deposits-articles":true,"deposits-affiliations-current":true,"deposits-funders-current":true,"deposits-references-backfile":true,"deposits-ror-ids-backfile":true,"deposits-abstracts-backfile":true,"deposits-licenses-backfile":true,"deposits-award-numbers-backfile":true,"deposits-descriptions-current":false,"deposits-references-current":true,"deposits-resource-links-backfile":true,"deposits-descriptions-backfile":false,"deposits-orcids-backfile":true,"deposits-funders-backfile":true,"deposits-update-policies-current":true,"deposits-similarity-checking-current":false,"deposits-licenses-current":true},"location":"Cambridge,
+        United Kingdom","names":["eLife Sciences Publications, Ltd","eLife Sciences
+        Publications, Ltd."]}}'
+  recorded_at: Sun, 01 Oct 2023 12:13:44 GMT
+- request:
+    method: get
+    uri: https://doi.org/ra/10.7554
+    body:
+      encoding: ASCII-8BIT
+      string: ''
+    headers:
+      Connection:
+      - close
+      Host:
+      - doi.org
+      User-Agent:
+      - http.rb/5.1.1
+  response:
+    status:
+      code: 200
+      message: OK
+    headers:
+      Date:
+      - Sun, 01 Oct 2023 12:13:44 GMT
+      Content-Type:
+      - application/json;charset=UTF-8
+      Transfer-Encoding:
+      - chunked
+      Connection:
+      - close
+      Permissions-Policy:
+      - interest-cohort=(),browsing-topics=()
+      Cf-Cache-Status:
+      - DYNAMIC
+      Report-To:
+      - '{"endpoints":[{"url":"https:\/\/a.nel.cloudflare.com\/report\/v3?s=nOuUPCRwnnnKgtJDByQRCMt9TJmjGB94XmwG3TO3W%2Bzw68ztcEj4g5dVxW6m3PLWhlDjR6c9PvMvScqG1znqwbAoO0TybJBz%2FTt6SYC3bn6iBeBQ5Vg6%2Fqs5OYbcAc0h7y1CMxY%3D"}],"group":"cf-nel","max_age":604800}'
+      Nel:
+      - '{"success_fraction":0,"report_to":"cf-nel","max_age":604800}'
+      Strict-Transport-Security:
+      - max-age=31536000; includeSubDomains; preload
+      Server:
+      - cloudflare
+      Cf-Ray:
+      - 80f49f12dfb85c3a-AMS
+      Alt-Svc:
+      - h3=":443"; ma=86400
+    body:
+      encoding: UTF-8
+      string: |-
+        [
+          {
+            "DOI": "10.7554",
+            "RA": "Crossref"
+          }
+        ]
+  recorded_at: Sun, 01 Oct 2023 12:13:44 GMT
+recorded_with: VCR 6.2.0

data/spec/readers/json_feed_reader_spec.rb

@@ -95,7 +95,7 @@ describe Commonmeta::Metadata, vcr: true do
       expect(subject.date).to eq("published" => "2013-06-25", "updated" => "2023-09-07")
       expect(subject.descriptions.first["description"]).to start_with("This paper in markdown format was written by Ethan White et al.")
       expect(subject.publisher).to eq("name" => "Front Matter")
-      expect(subject.related_identifiers).to eq([{"id"=>"https://doi.org/10.4033/iee.2013.6b.6.f", "type"=>"IsPreprintOf"}])
+      expect(subject.related_identifiers).to eq([{ "id" => "https://doi.org/10.4033/iee.2013.6b.6.f", "type" => "IsPreprintOf" }])
       expect(subject.subjects).to eq([{ "subject" => "Computer and information sciences" },
                                       { "schemeUri" => "http://www.oecd.org/science/inno/38235147.pdf",
                                         "subject" => "FOS: Computer and information sciences",
@@ -120,7 +120,7 @@ describe Commonmeta::Metadata, vcr: true do
       expect(subject.date).to eq("published" => "2019-07-01", "updated" => "2023-09-07")
       expect(subject.descriptions.first["description"]).to start_with("The connections between scholarly resources generated by persistent identifiers (PIDs)")
       expect(subject.publisher).to eq("name" => "Front Matter")
-      expect(subject.funding_references).to eq([{ "awardNumber" => "777523", "funderIdentifier"=>"http://doi.org/10.13039/501100000780", "funderName" => "European Commission" }])
+      expect(subject.funding_references).to eq([{ "awardNumber" => "777523", "funderIdentifier" => "http://doi.org/10.13039/501100000780", "funderName" => "European Commission" }])
       expect(subject.related_identifiers).to eq([{ "id" => "https://doi.org/10.5438/bv9z-dc66", "type" => "IsIdenticalTo" }])
       expect(subject.subjects).to eq([{ "subject" => "Computer and information sciences" },
                                       { "schemeUri" => "http://www.oecd.org/science/inno/38235147.pdf",
@@ -140,7 +140,7 @@ describe Commonmeta::Metadata, vcr: true do
       expect(subject.type).to eq("Article")
       expect(subject.contributors.length).to eq(1)
       expect(subject.contributors.first).to eq("familyName" => "Sathe", "givenName" => "Tejas S.",
-                                           "id" => "https://orcid.org/0000-0003-0449-4469", "type" => "Person", "contributorRoles" => ["Author"])
+                                               "id" => "https://orcid.org/0000-0003-0449-4469", "type" => "Person", "contributorRoles" => ["Author"])
       expect(subject.titles).to eq([{ "title" => "The Residency Visual Abstract" }])
       expect(subject.license).to eq("id" => "CC-BY-4.0",
                                     "url" => "https://creativecommons.org/licenses/by/4.0/legalcode")
@@ -165,7 +165,7 @@ describe Commonmeta::Metadata, vcr: true do
       expect(subject.type).to eq("Article")
       expect(subject.contributors.length).to eq(1)
       expect(subject.contributors.first).to eq("familyName" => "Sathe", "givenName" => "Tejas S.", "type" => "Person", "contributorRoles" => ["Author"],
-                                           "id" => "https://orcid.org/0000-0003-0449-4469")
+                                               "id" => "https://orcid.org/0000-0003-0449-4469")
       expect(subject.titles).to eq([{ "title" => "How to Build an Academic Powerhouse: Let's Study Who's Doing it" }])
       expect(subject.license).to eq("id" => "CC-BY-4.0",
                                     "url" => "https://creativecommons.org/licenses/by/4.0/legalcode")
@@ -238,10 +238,10 @@ describe Commonmeta::Metadata, vcr: true do
       expect(subject.type).to eq("Article")
       expect(subject.contributors.length).to eq(1)
       expect(subject.contributors.first).to eq("contributorRoles" => ["Author"],
-        "type" => "Person",
-        "familyName" => "Stocker",
-        "givenName" => "Markus",
-        "id" => "https://orcid.org/0000-0001-5492-3212")
+           "type" => "Person",
+           "familyName" => "Stocker",
+           "givenName" => "Markus",
+           "id" => "https://orcid.org/0000-0001-5492-3212")
       expect(subject.titles).to eq([{ "title" => "ORCID Integration Series: PANGAEA" }])
       expect(subject.license).to eq("id" => "CC-BY-4.0",
                                     "url" => "https://creativecommons.org/licenses/by/4.0/legalcode")
@@ -253,6 +253,7 @@ describe Commonmeta::Metadata, vcr: true do
                                         "subject" => "FOS: Computer and information sciences",
                                         "subjectScheme" => "Fields of Science and Technology (FOS)" }])
       expect(subject.language).to eq("en")
+      expect(subject.funding_references).to eq([{ "awardNumber" => "654039", "funderIdentifier" => "https://doi.org/10.13039/501100007601", "funderIdentifierType"=>"Crossref Funder ID", "funderName" => "European Union’s Horizon 2020 research and innovation programme" }])
       expect(subject.container).to eq("identifier" => "https://project-thor.eu", "identifierType" => "URL", "title" => "Project THOR", "type" => "Periodical")
     end
 
@@ -364,7 +365,7 @@ describe Commonmeta::Metadata, vcr: true do
       expect(subject.type).to eq("Article")
       expect(subject.contributors.length).to eq(1)
       expect(subject.contributors.first).to eq("familyName" => "Karcher", "givenName" => "Sebastian",
-                                           "id" => "https://orcid.org/0000-0001-8249-7388", "type" => "Person", "contributorRoles" => ["Author"])
+                                               "id" => "https://orcid.org/0000-0001-8249-7388", "type" => "Person", "contributorRoles" => ["Author"])
       expect(subject.titles).to eq([{ "title" => "Seeking Public Comment on CSL 1.0.2 Release" }])
       expect(subject.license).to eq("id" => "CC-BY-4.0",
                                     "url" => "https://creativecommons.org/licenses/by/4.0/legalcode")

data/spec/writers/commonmeta_writer_spec.rb

@@ -0,0 +1,43 @@
+# frozen_string_literal: true
+
+require "spec_helper"
+
+describe Commonmeta::Metadata, vcr: true do
+  context "write metadata as commonmeta" do
+    it "with data citation" do
+      input = "10.7554/eLife.01567"
+      subject = described_class.new(input: input, from: "crossref")
+      json = JSON.parse(subject.commonmeta)
+      expect(json["id"]).to eq("https://doi.org/10.7554/elife.01567")
+      expect(json["type"]).to eq("JournalArticle")
+      expect(json["url"]).to eq("https://elifesciences.org/articles/01567")
+      expect(json["titles"]).to eq([{ "title" => "Automated quantitative histology reveals vascular morphodynamics during Arabidopsis hypocotyl secondary growth" }])
+      expect(json["contributors"].length).to eq(5)
+      expect(json["contributors"].first).to eq("affiliation" => [{ "name" => "Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland" }],
+                                               "contributorRoles" => ["Author"],
+                                               "familyName" => "Sankar",
+                                               "givenName" => "Martial",
+                                               "type" => "Person")
+      expect(json["container"]).to eq("identifier" => "2050-084X",
+                                      "identifierType" => "ISSN",
+                                      "title" => "eLife",
+                                      "type" => "Journal",
+                                      "volume" => "3")
+      expect(json["publisher"]).to eq("id" => "https://api.crossref.org/members/4374", "name" => "eLife Sciences Publications, Ltd")
+      expect(json["references"].length).to eq(27)
+      expect(json["references"].first).to eq("key" => "bib1",
+                                             "doi" => "https://doi.org/10.1038/nature02100",
+                                             "contributor" => "Bonke",
+                                             "title" => "APL regulates vascular tissue identity in Arabidopsis",
+                                             "publicationYear" => "2003",
+                                             "volume" => "426",
+                                             "firstPage" => "181",
+                                             "containerTitle" => "Nature")
+      expect(json["date"]).to eq("published"=>"2014-02-11", "updated"=>"2022-03-26")
+      expect(json["descriptions"].first["description"]).to start_with("Among various advantages,")
+      expect(json["license"]).to eq("id"=>"CC-BY-3.0", "url"=>"https://creativecommons.org/licenses/by/3.0/legalcode")
+      expect(json["provider"]).to eq("Crossref")
+      expect(json["files"].first).to eq("mimeType"=>"application/pdf", "url"=>"https://cdn.elifesciences.org/articles/01567/elife-01567-v1.pdf")
+    end
+  end
+end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: commonmeta-ruby
 version: !ruby/object:Gem::Version
-  version: 3.5.1
+  version: 3.5.3
 platform: ruby
 authors:
 - Martin Fenner
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2023-09-21 00:00:00.000000000 Z
+date: 2023-10-01 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: activesupport
@@ -644,6 +644,7 @@ files:
 - lib/commonmeta/writers/cff_writer.rb
 - lib/commonmeta/writers/citation_writer.rb
 - lib/commonmeta/writers/codemeta_writer.rb
+- lib/commonmeta/writers/commonmeta_writer.rb
 - lib/commonmeta/writers/crossref_xml_writer.rb
 - lib/commonmeta/writers/csl_writer.rb
 - lib/commonmeta/writers/csv_writer.rb
@@ -928,6 +929,7 @@ files:
 - spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_citation/software_w/version.yml
 - spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_codemeta/SoftwareSourceCode_DataCite.yml
 - spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_codemeta/SoftwareSourceCode_DataCite_check_codemeta_v2.yml
+- spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_commonmeta/with_data_citation.yml
 - spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/another_schema_org_from_front-matter.yml
 - spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/book_oup.yml
 - spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/journal_article.yml
@@ -1026,6 +1028,7 @@ files:
 - spec/writers/cff_writer_spec.rb
 - spec/writers/citation_writer_spec.rb
 - spec/writers/codemeta_writer_spec.rb
+- spec/writers/commonmeta_writer_spec.rb
 - spec/writers/crossref_xml_writer_spec.rb
 - spec/writers/csl_writer_spec.rb
 - spec/writers/csv_writer_spec.rb