commonmeta-ruby 3.4.3 → 3.4.4
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- checksums.yaml +4 -4
- data/Gemfile.lock +1 -1
- data/lib/commonmeta/crossref_utils.rb +21 -18
- data/lib/commonmeta/readers/json_feed_reader.rb +34 -5
- data/lib/commonmeta/version.rb +1 -1
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/ghost_post_with_related_identifiers_and_funding.yml +580 -0
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/json_feed_item_from_rogue_scholar_with_relations_and_funding.yml +580 -0
- data/spec/readers/json_feed_reader_spec.rb +26 -1
- data/spec/writers/crossref_xml_writer_spec.rb +36 -0
- metadata +4 -2
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the Growth of the PID Graph","summary":"The connections between scholarly
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resources generated by persistent identifiers (PIDs) and associated metadata
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form a graph: the PID Graph [Fenner & Aryani (2019)]. We developed this PID
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use cases and technical requirements.","content_html":" <p><img src=\"https://blog.front-matter.io/content/images/2022/08/download-19-.jpeg\"
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/></p><p>The connections between scholarly resources generated by persistent
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identifiers (PIDs) and associated metadata form a graph: the PID Graph [Fenner
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& Aryani (<a href=\"https://blog.datacite.org/tracking-the-growth-of-the-pid-graph/#ref-https://doi.org/10.5438/jwvf-8a66\">2019</a>)].
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We developed this PID Graph concept in the EC-funded <a href=\"https://www.project-freya.eu/en\">FREYA
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project</a>, and have identified important use cases and technical requirements.
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In May, DataCite introduced a GraphQL API to standardize and simplify how
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users can contribute to and consume the PID Graph [Fenner (<a href=\"https://blog.datacite.org/tracking-the-growth-of-the-pid-graph/#ref-https://doi.org/10.5438/qab1-n315\">2019b</a>)].
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Today we are announcing another important milestone: we added the required
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functionality to the DataCite GraphQL API that allows us to keep track of
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the growth of the PID Graph in terms of nodes (resources) and edges (connections).
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As before, we are using a Jupyter notebook to analyze and visualize the data.</p>\n<p>The
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graph visualizes the main resources currently available via the DataCite GraphQL
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API, and their connections. The required data are fetched via a single GraphQL
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API call:</p>\n<pre><code>{\n publications {\n totalCount\n publicationConnectionCount\n datasetConnectionCount\n softwareConnectionCount\n researcherConnectionCount\n funderConnectionCount\n }\n datasets
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{\n totalCount\n datasetConnectionCount\n softwareConnectionCount\n researcherConnectionCount\n funderConnectionCount\n }\n softwares
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{\n totalCount\n softwareConnectionCount\n researcherConnectionCount\n funderConnectionCount\n }\n researchers
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{\n totalCount\n }\n funders {\n totalCount\n }\n}</code></pre>\n<p>The
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numbers reflect what is currently available via the DataCite GraphQL API,
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not the total number of publications, datasets, etc. with persistent identifiers
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and linking metadata. This includes all publications, datasets and software
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with DataCite DOIs, all funders in the <a href=\"https://support.crossref.org/hc/en-us/articles/214360886-The-Open-Funder-Registry\">Crossref
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Open Funder Registry</a>, publications with Crossref DOIs linked to at least
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one DataCite DOI, and all researchers with an ORCID identifier linked to at
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least one DataCite DOI. A lot of work remains to be done to include the other
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resources with persistent identifiers made available by FREYA partners, including
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Crossref, ORCID and EMBL-EBI, as well as their connections. With this new
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API functionality we can now track the growth of the PID Graph with the key
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performance indicators (KPIs) number of <strong>nodes</strong> and number
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of <strong>connections</strong>.</p>\n<p>A few interesting observations can
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be made from the visualization: not surprisingly, given that datasets currently
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make up the largest number of resources in the PID Graph, by far the largest
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number of connections (9.4 million) is between datasets and other datasets.
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of them (8.5 million) don''t describe versioning or granularity (HasPart/IsPartOf
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relations), but use the relation type <strong>references</strong> between
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two <a href=\"https://www.gbif.org/en/\">GBIF</a> DOIs. This reflects the
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main <a href=\"https://www.gbif.org/en/document/81771/gbif-overview-powerpoint-slides\">use
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case for DOIs at GBIF</a>, tracking occurrences of species.</p>\n<p>The graph
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shows 1.5 million connections between publications and datasets, representing
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the data citations made available via the <a href=\"https://www.eventdata.crossref.org/guide/app-scholix/\">Crossref/DataCite
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Event Data Scholix API endpoint</a>. Twenty-five percent of datasets with
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DataCite DOIs have been referenced in the scholarly literature, according
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to this graph. We also see the number of software citations using DataCite
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DOIs for software found in the scholarly literature, and we can use this API
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call to keep track of them. Similarly, we can track the number of datasets,
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publications, and software linked to researchers (via their ORCID ID), and
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funding (via the Crossref Funder ID), but keep in mind that connections to
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researchers and funding via Crossref are still missing.</p>\n<p>The Jupyter
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notebook used to generate the visualization shown here is available via GitHub,
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where we store all PID Graph notebooks in a <a href=\"https://github.com/datacite/notebooks\">central
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repository</a>. Starting with this notebook [Fenner (<a href=\"https://blog.datacite.org/tracking-the-growth-of-the-pid-graph/#ref-https://doi.org/10.14454/3bpw-w381\">2019a</a>)]
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we are also issuing DOIs for the notebooks, which we generate using a <a href=\"https://codemeta.github.io/\">codemeta</a>
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file hosted in the same folder as the notebook. This should make these notebooks
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easier to discover, and they also become part of the PID Graph.</p>\n<p>Going
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forward we want to refine the GraphQL API to provide the numbers of <strong>nodes</strong>
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and <strong>connections</strong> as they change over time, making it easier
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to track progress. And of course, we will be adding more resource types and
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information from other FREYA partners. Keep an eye on this blog for further
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updates!</p>\n<h2>Acknowledgments</h2>\n<p>This blog post was <a href=\"https://doi.org/10.5438/bv9z-dc66\">originally
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published</a> on the DataCite Blog. This work was funded by the European Union’s
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Horizon 2020 research and innovation programme under <a href=\"https://doi.org/10.3030/777523\">grant
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agreement No. 777523</a>.</p>\n<h2>References</h2>\n<p>Fenner M. Jupyter Notebook
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FREYA PID Graph Key Performance Indicators (KPIs). Published online June 30,
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2019. doi:<a href=\"https://doi.org/10.14454/3BPW-W381\">10.14454/3BPW-W381</a></p>\n<p>Fenner
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M. The DataCite GraphQL API is now open for (pre-release) business. Published
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online May 15, 2019. doi:<a href=\"https://doi.org/10.53731/r79sa71-97aq74v-ag4vc\">10.53731/r79sa71-97aq74v-ag4vc</a></p>\n<p>Fenner
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M, Aryani A. Introducing the PID Graph. Published online 2019. doi:<a href=\"https://doi.org/10.5438/JWVF-8A66\">10.5438/JWVF-8A66</a></p>
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","published_at":1561939200,"updated_at":1694087432,"indexed_at":1694097846,"authors":[{"url":"https://orcid.org/0000-0003-1419-2405","name":"Martin
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- close
|
|
537
|
+
Host:
|
|
538
|
+
- doi.org
|
|
539
|
+
User-Agent:
|
|
540
|
+
- http.rb/5.1.1
|
|
541
|
+
response:
|
|
542
|
+
status:
|
|
543
|
+
code: 302
|
|
544
|
+
message: Found
|
|
545
|
+
headers:
|
|
546
|
+
Date:
|
|
547
|
+
- Thu, 07 Sep 2023 17:36:01 GMT
|
|
548
|
+
Content-Type:
|
|
549
|
+
- text/html;charset=utf-8
|
|
550
|
+
Content-Length:
|
|
551
|
+
- '211'
|
|
552
|
+
Connection:
|
|
553
|
+
- close
|
|
554
|
+
Location:
|
|
555
|
+
- https://datacite.org/blog/tracking-the-growth-of-the-pid-graph/
|
|
556
|
+
Vary:
|
|
557
|
+
- Accept
|
|
558
|
+
Expires:
|
|
559
|
+
- Thu, 07 Sep 2023 18:20:43 GMT
|
|
560
|
+
Permissions-Policy:
|
|
561
|
+
- interest-cohort=(),browsing-topics=()
|
|
562
|
+
Cf-Cache-Status:
|
|
563
|
+
- DYNAMIC
|
|
564
|
+
Report-To:
|
|
565
|
+
- '{"endpoints":[{"url":"https:\/\/a.nel.cloudflare.com\/report\/v3?s=k0kAB%2FD%2FpNiog%2Fn6sdV6VQ6b3a4z24FrTtoi0cKEQ3I4EiSg9s55jSykSMil1Hu1ie%2BqBTyCT%2F4EgGKcbef1uI3TvRPipYxdBOdS9NCCxtbYSt4wgqvMNJxkby%2FSV8OXGDKbEJc%3D"}],"group":"cf-nel","max_age":604800}'
|
|
566
|
+
Nel:
|
|
567
|
+
- '{"success_fraction":0,"report_to":"cf-nel","max_age":604800}'
|
|
568
|
+
Strict-Transport-Security:
|
|
569
|
+
- max-age=31536000; includeSubDomains; preload
|
|
570
|
+
Server:
|
|
571
|
+
- cloudflare
|
|
572
|
+
Cf-Ray:
|
|
573
|
+
- 8030b6271f24b8e4-AMS
|
|
574
|
+
Alt-Svc:
|
|
575
|
+
- h3=":443"; ma=86400
|
|
576
|
+
body:
|
|
577
|
+
encoding: UTF-8
|
|
578
|
+
string: ''
|
|
579
|
+
recorded_at: Thu, 07 Sep 2023 17:36:01 GMT
|
|
580
|
+
recorded_with: VCR 6.2.0
|
|
@@ -79,6 +79,31 @@ describe Commonmeta::Metadata, vcr: true do
|
|
|
79
79
|
expect(subject.container).to eq("identifier" => "https://blog.front-matter.io", "identifierType" => "URL", "title" => "Front Matter", "type" => "Periodical")
|
|
80
80
|
end
|
|
81
81
|
|
|
82
|
+
it "ghost post with related_identifiers and funding" do
|
|
83
|
+
input = "https://rogue-scholar.org/api/posts/e58dc9c8-b870-4db2-8896-238b3246c551"
|
|
84
|
+
subject = described_class.new(input: input)
|
|
85
|
+
expect(subject.valid?).to be true
|
|
86
|
+
expect(subject.id).to eq("https://doi.org/10.53731/r79s4nh-97aq74v-ag4t1")
|
|
87
|
+
expect(subject.url).to eq("https://blog.front-matter.io/posts/tracking-the-growth-of-the-pid-graph")
|
|
88
|
+
expect(subject.alternate_identifiers).to eq([{ "alternateIdentifier" => "e58dc9c8-b870-4db2-8896-238b3246c551", "alternateIdentifierType" => "UUID" }])
|
|
89
|
+
expect(subject.type).to eq("Article")
|
|
90
|
+
expect(subject.creators.length).to eq(1)
|
|
91
|
+
expect(subject.creators.first).to eq("id" => "https://orcid.org/0000-0003-1419-2405", "familyName" => "Fenner", "givenName" => "Martin", "type" => "Person")
|
|
92
|
+
expect(subject.titles).to eq([{ "title" => "Tracking the Growth of the PID Graph" }])
|
|
93
|
+
expect(subject.license).to eq("id" => "CC-BY-4.0",
|
|
94
|
+
"url" => "https://creativecommons.org/licenses/by/4.0/legalcode")
|
|
95
|
+
expect(subject.date).to eq("published" => "2019-07-01", "updated" => "2023-09-07")
|
|
96
|
+
expect(subject.descriptions.first["description"]).to start_with("The connections between scholarly resources generated by persistent identifiers (PIDs)")
|
|
97
|
+
expect(subject.publisher).to eq("name" => "Front Matter")
|
|
98
|
+
expect(subject.funding_references).to eq([{ "awardNumber" => "777523", "funderIdentifier"=>"http://doi.org/10.13039/501100000780", "funderName" => "European Commission" }])
|
|
99
|
+
expect(subject.related_identifiers).to eq([{ "id" => "https://doi.org/10.5438/bv9z-dc66", "type" => "IsIdenticalTo" }])
|
|
100
|
+
expect(subject.subjects).to eq([{ "subject" => "Computer and information sciences" },
|
|
101
|
+
{ "schemeUri" => "http://www.oecd.org/science/inno/38235147.pdf",
|
|
102
|
+
"subject" => "FOS: Computer and information sciences",
|
|
103
|
+
"subjectScheme" => "Fields of Science and Technology (FOS)" }])
|
|
104
|
+
expect(subject.language).to eq("en")
|
|
105
|
+
expect(subject.container).to eq("identifier" => "https://blog.front-matter.io", "identifierType" => "URL", "title" => "Front Matter", "type" => "Periodical")
|
|
106
|
+
end
|
|
82
107
|
it "ghost post without doi" do
|
|
83
108
|
input = "https://rogue-scholar.org/api/posts/c3095752-2af0-40a4-a229-3ceb7424bce2"
|
|
84
109
|
subject = described_class.new(input: input)
|
|
@@ -285,7 +310,7 @@ describe Commonmeta::Metadata, vcr: true do
|
|
|
285
310
|
expect(subject.type).to eq("Article")
|
|
286
311
|
expect(subject.creators.length).to eq(1)
|
|
287
312
|
expect(subject.creators.first).to eq("familyName" => "Karcher", "givenName" => "Sebastian",
|
|
288
|
-
|
|
313
|
+
"id" => "https://orcid.org/0000-0001-8249-7388", "type" => "Person")
|
|
289
314
|
expect(subject.titles).to eq([{ "title" => "Seeking Public Comment on CSL 1.0.2 Release" }])
|
|
290
315
|
expect(subject.license).to eq("id" => "CC-BY-4.0",
|
|
291
316
|
"url" => "https://creativecommons.org/licenses/by/4.0/legalcode")
|
|
@@ -323,6 +323,42 @@ describe Commonmeta::Metadata, vcr: true do
|
|
|
323
323
|
expect(crossref_xml.dig("group_title")).to eq("Computer and information sciences")
|
|
324
324
|
end
|
|
325
325
|
|
|
326
|
+
it "json_feed_item from rogue scholar with relations and funding" do
|
|
327
|
+
input = "https://rogue-scholar.org/api/posts/e58dc9c8-b870-4db2-8896-238b3246c551"
|
|
328
|
+
subject = described_class.new(input: input, doi: "10.53731/r79s4nh-97aq74v-ag4t1")
|
|
329
|
+
|
|
330
|
+
expect(subject.valid?).to be true
|
|
331
|
+
expect(subject.id).to eq("https://doi.org/10.53731/r79s4nh-97aq74v-ag4t1")
|
|
332
|
+
expect(subject.url).to eq("https://blog.front-matter.io/posts/tracking-the-growth-of-the-pid-graph")
|
|
333
|
+
expect(subject.alternate_identifiers).to eq([{ "alternateIdentifier" => "e58dc9c8-b870-4db2-8896-238b3246c551", "alternateIdentifierType" => "UUID" }])
|
|
334
|
+
expect(subject.type).to eq("Article")
|
|
335
|
+
expect(subject.creators.length).to eq(1)
|
|
336
|
+
expect(subject.creators.first).to eq("id" => "https://orcid.org/0000-0003-1419-2405", "familyName" => "Fenner", "givenName" => "Martin", "type" => "Person")
|
|
337
|
+
expect(subject.titles).to eq([{ "title" => "Tracking the Growth of the PID Graph" }])
|
|
338
|
+
expect(subject.license).to eq("id" => "CC-BY-4.0",
|
|
339
|
+
"url" => "https://creativecommons.org/licenses/by/4.0/legalcode")
|
|
340
|
+
expect(subject.date).to eq("published" => "2019-07-01", "updated" => "2023-09-07")
|
|
341
|
+
expect(subject.descriptions.first["description"]).to start_with("The connections between scholarly resources generated by persistent identifiers (PIDs)")
|
|
342
|
+
expect(subject.publisher).to eq("name" => "Front Matter")
|
|
343
|
+
expect(subject.funding_references).to eq([{ "awardNumber" => "777523", "funderIdentifier"=>"http://doi.org/10.13039/501100000780", "funderName" => "European Commission" }])
|
|
344
|
+
expect(subject.related_identifiers).to eq([{ "id" => "https://doi.org/10.5438/bv9z-dc66", "type" => "IsIdenticalTo" }])
|
|
345
|
+
expect(subject.subjects).to eq([{ "subject" => "Computer and information sciences" },
|
|
346
|
+
{ "schemeUri" => "http://www.oecd.org/science/inno/38235147.pdf",
|
|
347
|
+
"subject" => "FOS: Computer and information sciences",
|
|
348
|
+
"subjectScheme" => "Fields of Science and Technology (FOS)" }])
|
|
349
|
+
expect(subject.language).to eq("en")
|
|
350
|
+
expect(subject.container).to eq("identifier" => "https://blog.front-matter.io", "identifierType" => "URL", "title" => "Front Matter", "type" => "Periodical")
|
|
351
|
+
# puts subject.crossref_xml
|
|
352
|
+
crossref_xml = Hash.from_xml(subject.crossref_xml).dig("doi_batch", "body", "posted_content")
|
|
353
|
+
expect(Array.wrap(crossref_xml.dig("contributors", "person_name")).length).to eq(1)
|
|
354
|
+
expect(Array.wrap(crossref_xml.dig("contributors",
|
|
355
|
+
"person_name")).first).to eq({"ORCID"=>"https://orcid.org/0000-0003-1419-2405", "contributor_role"=>"author", "given_name"=>"Martin", "sequence"=>"first", "surname"=>"Fenner"})
|
|
356
|
+
expect(crossref_xml.dig("titles",
|
|
357
|
+
"title")).to eq("Tracking the Growth of the PID Graph")
|
|
358
|
+
expect(crossref_xml.dig("item_number")).to eq("__content__" => "e58dc9c8b8704db28896238b3246c551", "item_number_type" => "uuid")
|
|
359
|
+
expect(crossref_xml.dig("group_title")).to eq("Computer and information sciences")
|
|
360
|
+
end
|
|
361
|
+
|
|
326
362
|
it "json_feed_item from rogue scholar with anonymous author" do
|
|
327
363
|
input = "https://rogue-scholar.org/api/posts/a163e340-5b3c-4736-9ab0-8c54fdff6a3c"
|
|
328
364
|
subject = described_class.new(input: input, doi: "10.59350/9ry27-7cz42")
|